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Somatic variation is a major type of genetic variation contributing to human diseases including cancer. Of the vast quantities of somatic variants identified, the functional impact of many somatic variants, in particular the missense variants, remains unclear. Lack of the functional information prevents the translation of rich variation data into clinical applications. We previously developed a method named Ramachandran Plot–Molecular Dynamics Simulations (RP-MDS), aiming to predict the function of germline missense variants based on their effects on protein structure stability, and successfully applied to predict the deleteriousness of unclassified germline missense variants in multiple cancer genes. We hypothesized that regardless of their different genetic origins, somatic missense variants and germline missense variants could have similar effects on the stability of their affected protein structure. As such, the RP-MDS method designed for germline missense variants should also be applicable to predict the function of somatic missense variants. In the current study, we tested our hypothesis by using the somatic missense variants in TP53 as a model. Of the 397 somatic missense variants analyzed, RP-MDS predicted that 195 (49.1%) variants were deleterious as they significantly disturbed p53 structure. The results were largely validated by using a p53–p21 promoter–green fluorescent protein (GFP) reporter gene assay. Our study demonstrated that deleterious somatic missense variants can be identified by referring to their effects on protein structural stability. [ABSTRACT FROM AUTHOR]

The Human Epididymis Protein 4 (HE4) biomarker has been extensively investigated for its potential in diagnosing ovarian cancer (OC). For the application of diagnostic techniques and drug delivery, it is crucial to understand the protein tertiary structure. However, the Protein Data Bank (PDB) does not currently contain the three-dimensional (3D) structure of HE4. Therefore, an in silico analysis was conducted to model the HE4 protein using AlphaFold, I-TASSER, and Robetta servers, with the sequence retrieved from UniProt (ID: Q14508). These three servers employed deep learning algorithms, threading templates, and de novo methods, respectively. Subsequently, Molecular Dynamics (MD) simulation using the GROMACS software package improved each 3D structure model, resulting in optimised and refined structures: RF1, RF2, and RF3. PROCHECK and ERRAT programmes were employed to assess the structure quality. The Ramachandran plots from PROCHECK indicated that 100% of residues were within the allowed regions for all servers except for I-TASSER. For the refined structures, RF1 and RF3, all residues were concentrated within the allowed regions. According to the ERRAT programme, the RF1 model exhibited the highest overall quality factor of 97.701, followed by RF3 and AlphaFold models with scores of 94.643 and 93.750, respectively. After these validations, RF1 emerged as the most accurately predicted 3D structure of HE4 and has one tunnel identified by CAVER 3.0 tool that facilitates the transportation of small particles to the active site, supported by FTsite and PrankWeb binding site predictions. This model holds potential for various computational studies, including the development of OC diagnostic kits. It will enhance our comprehension of the interactions between the protein and other biomolecules. [ABSTRACT FROM AUTHOR]

Tannery effluent waste comprises various potentially toxic metals, including chromium (Cr) with varying acute or chronic toxicity. Cr(VI) is known to be a category‐A carcinogen. Reduction of toxic Cr(VI) to Cr(III), which has lesser bioavailability, is one of the mechanisms used by many microbes to withstand Cr(VI) toxicity in the contaminated effluents. Oxidoreductase (OXRs) reduces toxic Cr(VI) to Cr(III); hence a thorough understanding of the OXRs is important for developing a suitable strategy to minimize Cr(VI) toxicity. Therefore, the OXR‐encoding genes were sequenced using metagenomic DNA shotgun sequencing from the tannery effluent‐contaminated soil. Six OXR‐encoding genes were expressed in Escherichia coli, and OXR activity was confirmed by in situ quantitative assays. The six proteins were subjected to phylogenetic and evolutionary analysis. Further, detailed structural analysis of the two OXRs, namely, OXR3 and OXR8 with lowest and highest activity respectively, were investigated in silico for structural characteristics. The results revealed that both the proteins were soluble FMN‐linked oxidoreductases. Eight conserved active site residues (Pro24, Thr26, Ala59, Tyr139, His178, Tyr180, His219, Tyr221, Arg269, and Lys360) in the enzyme OXR3 were predicted. Similarly, nine conserved active site residues (Pro20, Thr22, Ala55, Glu97, His191, Tyr193, Arg241, Cys334, and Arg335) were predicted in OXR8. The tertiary structure of OXR8 was an aldolase TIM barrel structure, like Thermus scotoductus chromate reductase. Docking with FMN revealed the involvement of all the nine predicted active site residues in FMN binding with Pro20, Thr22, and Cys334 as the most important ones. [ABSTRACT FROM AUTHOR]

Background: The Zika virus, a mosquito-borne virus, was discovered in Uganda and quickly spread to Asia and the Pacific. Zika is mainly transmitted by the bite of an infected Aedes species mosquito (Aedes aegypti and Aedes albopictus). These mosquitos bite both during the day and at night. Methods: Numerous tools (SMART, Pfam, InterProScan and Scan Prosite, BepiPred-2.0 server, I-TASSER, PROCHECK, phyre 2, protparam, and GPS 6.0) were used to elaborate the content in this publication. Results: The results show that HABD (187 amino acids) is a DEAH-Box RNA helicase. We also used the Ramachandran plot to validate the epitope peptides and structure modeling. We also discovered the amino acid composition and various residues/parentages in the HABD protein phosphorylation site prediction and PK-specific phosphorylation sites (p-sites). Conclusion: The helicase ATP binding domain (HABD), HABD protein ATP binding sites, and epitope binding peptides are discussed in this work. There are five atoms in total: nitrogen, sulfur, hydrogen, carbon, and oxygen. Hydrogen atoms (1476) provide the most to the composition. We created a graph representing the protein's predicted phosphorylation sites (p-sites). Aside from the standard statistics, GPS 6.0 may identify PK-specific p-sites hierarchically. GPS 6.0 could be a valuable service for further phosphorylation study. [ABSTRACT FROM AUTHOR]

Pathogenic variation in DNA mismatch repair (MMR) gene MLH1 is associated with Lynch syndrome (LS), an autosomal dominant hereditary cancer. Of the 3798 MLH1 germline variants collected in the ClinVar database, 38.7% (1469) were missense variants, of which 81.6% (1199) were classified as Variants of Uncertain Significance (VUS) due to the lack of functional evidence. Further determination of the impact of VUS on MLH1 function is important for the VUS carriers to take preventive action. We recently developed a protein structure-based method named "Deep Learning-Ramachandran Plot-Molecular Dynamics Simulation (DL-RP-MDS)" to evaluate the deleteriousness of MLH1 missense VUS. The method extracts protein structural information by using the Ramachandran plot-molecular dynamics simulation (RP-MDS) method, then combines the variation data with an unsupervised learning model composed of auto-encoder and neural network classifier to identify the variants causing significant change in protein structure. In this report, we applied the method to classify 447 MLH1 missense VUS. We predicted 126/447 (28.2%) MLH1 missense VUS were deleterious. Our study demonstrates that DL-RP-MDS is able to classify the missense VUS based solely on their impact on protein structure. [ABSTRACT FROM AUTHOR]

Abstract With the world turning its attention towards sustainable protein sources, mung bean, in recent times has garnered significant research acclaim. As an emerging functional food that is rich in protein, little is known about its characteristics during processing. Hence, in this study, an molecular dynamic (MD) simulation approach was performed on 2CV6, the crystal structure of 8Sα globulin. GROMACS software was used to vary input thermal and pressure parameters (i.e., 300, 373, and 398 K at 3, 5, and 7 Kbar). Visual MD interface was used to picture the changes occurring in the protein's secondary structure as an effect of applied stress. The radius of gyration values decreased significantly with increasing pressure while high‐pressure high‐temperature treatment improved packing effects. STRIDE analysis showed that peripheral 2° structures such as α‐helices and β‐sheets underwent conformational changes to form turns and coils, indicating increased randomness. Despite subjecting the protein molecule to high temperature, the pressure applied counteracted the unwinding process, resulting in overall compaction.

Wnt signaling is a critical pathway involved in cell proliferation, differentiation and cellular homeostasis. To address treatment need of diseases associated with the dysregulated Wnt signaling like cancer, Alzheimer’s disease, Osteoporosis, Myocardial infarction etc.; small molecules that target the very first and unique component of the Wnt pathway, Porcupine enzyme, have been proven to be effective. Till date, none of the Porcupine inhibitor has reached to market. To design the novel Porcupine inhibitors, there was a need of crystal structure of Porcupine but in 2019, it was not resolved and deposited in the protein data bank. So, with an aim to predict its 3D structure, homology modeling study was performed using two distinct platforms; I-TASSER and Molsoft ICMPro so that we could use the best validated model for the designing of NCEs. Both the generated homology models were compared through Ramachandran plot, Protein health tool of Molsoft ICM and other tools available on metaserver, SAVES v6.0. Molsoft model was found better with 84.6 % residues in most favored region and only 0.3 % residues in disallowed region in Ramachandran plot in comparison to 75.9 % and 1.7 % residues respectively in I-TASSER model. The ICM model was further refined for 50 ns under MD simulation where it got stabilized after 36 ns. Quantification of protein was done by Radius of Gyration (ROG) where model showed larger ROG value of 23.25°A which indicated closely packed structure. Binding site in the predicted structure of Porcupine was identified using ICM binding pocket identifier and used for molecular docking of known Porcupine inhibitors like IWP-2, IWP-3, IWP-L6, and LKG974. Key binding site residues; Arg124, Phe257, Leu261, Val302, Trp305, Asn306, Ser310, Leu313, His341, Phen345, Ala349, Val350 etc. involved in the interaction were identified after MD simulation which can be useful in designing of novel porcupine inhibitors in future.

Protein structure, both at the global and local level, dictates function. Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. Here, we show that a Ramachandran-type plot focusing on the two dihedral angles separated by the peptide bond, and entirely contained within an amino acid pair, defines a local structural unit. We further demonstrate the usefulness of this cross-peptide-bond Ramachandran plot by showing that it captures β-turn conformations in coil regions, that traditional Ramachandran plot outliers fall into occupied regions of our plot, and that thermophilic proteins prefer specific amino acid pair conformations. Further, we demonstrate experimentally that the effect of a point mutation on backbone conformation and protein stability depends on the amino acid pair context, i.e., the identity of the adjacent amino acid, in a manner predictable by our method. [ABSTRACT FROM AUTHOR]

Helicobacter pylori (H. pylori) is a Gram-negative, slow-growing bacterium, microaerophilic, and a unique gastric pathogen that causes chronic inflammation in the gastric mucosa with the possibility of developing gastric cancer; one-third of its proteins are still uncharacterized. In this study, computational analysis was performed on the structural, functional, and epitopic characteristics of a hypothetical protein (HP) from H. pylori named HPF63-1454. The model prediction and primary, secondary, and three-dimensional structures of the chosen HP were built. The newly created model appeared to have high quality once refinement and structure validation had been completed. The anticipated tertiary structure was assessed using the Swiss Model assessment. The best materials were chosen using structural analyses and considering data from the Z scores, Swiss Interactive Workplace, and Ramachandran plot statistics. This investigation aimed to determine the importance of the H. pylori protein HPF63-1454. Therefore, this research increased our understanding of pathophysiology and allowed us to target the protein complex specifically. H. pylori infections are now treated with readily available antibiotics and acid-suppressing medications, but this species has established itself as a hardy pest. Long-term and taxing antibiotic therapy for H. pylori infection is increasingly beginning to fail, necessitating novel and creative therapeutic modalities. [ABSTRACT FROM AUTHOR]

With the world turning its attention towards sustainable protein sources, mung bean, in recent times has garnered significant research acclaim. As an emerging functional food that is rich in protein, little is known about its characteristics during processing. Hence, in this study, an molecular dynamic (MD) simulation approach was performed on 2CV6, the crystal structure of 8Sα globulin. GROMACS software was used to vary input thermal and pressure parameters (i.e., 300, 373, and 398 K at 3, 5, and 7 Kbar). Visual MD interface was used to picture the changes occurring in the protein's secondary structure as an effect of applied stress. The radius of gyration values decreased significantly with increasing pressure while highpressure high‐temperature treatment improved packing effects. STRIDE analysis showed that peripheral 2° structures such as α‐helices and β‐sheets underwent conformational changes to form turns and coils, indicating increased randomness. Despite subjecting the protein molecule to high temperature, the pressure applied counteracted the unwinding process, resulting in overall compaction. [ABSTRACT FROM AUTHOR]

Ramachandran plots report the distribution of the (ϕ, ψ) torsion angles of the protein backbone and are one of the best quality metrics of experimental structure models. Typically, validation software reports the number of residues belonging to "outlier," "allowed," and "favored" regions. While "zero unexplained outliers" can be considered the current "gold standard," this can be misleading if deviations from expected distributions are not considered. We revisited the Ramachandran Z score (Rama-Z), a quality metric introduced more than two decades ago but underutilized. We describe a reimplementation of the Rama-Z score in the Computational Crystallography Toolbox along with an algorithm to estimate its uncertainty for individual models; final implementations are available in Phenix and PDB-REDO. We discuss the interpretation of the Rama-Z score and advocate including it in the validation reports provided by the Protein Data Bank. We also advocate reporting it alongside the outlier/allowed/favored counts in structural publications.

The acetylation modification process of histone has an essential role in the epigenetic regulation of gene expression. This process is controlled by the balance between histone deacetylases (HDAC) and histone acetyltransferases (HAT). HDACs are thought to be vital for cell function. Particularly, higher HDAC expression is frequent in various cancers, resulting in the dysregulation of several target genes involved in cell proliferation, differentiation, and survival. In this study, the inhibitory feasibility of several HDAC inhibitors was investigated, including vorinostat (SAHA), N-hydroxy-3-phenylprop-2-enamide (CPD1), N-hydroxy-3-(pyridine-4-yl)prop-2-enamide (CPD2), N-hydroxy-3-(pyridine-2-yl)prop-2-enamide (CPD3), 4-(diphenylamino)-N-(5-(hydroxyamino)-5-oxopentyl)benzamide (CPD4), 2-(6-(((6-fluoronaphthalen-2-yl)methyl)amino)-3-azabicyclo[3.1.0]hex-3-yl)-N-hydroxypirimidine-5-carboxamide (CPD5), and N-(3-aminopropyl)-N-hydroxy-2-((naphthalene-1-yloxy)methyl)oct-2-enediamide (CPD6). By examining the stability of the enzyme, positional stability of the individual amino acids, and binding energies of HDLP-inhibitor complexes, the inhibitory feasibility was assessed. The complexes of the HDLP enzyme with SAHA, CPD4, CPD5, and CPD6 had higher stability than the other studied complexes, according to the results of trajectory analysis and the Ramachandran plot. Based on the calculated MM-PBSA binding free energies, the stability of the HDLP enzyme followed this order CPD4 > CPD5 > SAHA > CPD6 > CPD2 > CPD3 > CPD1. The drugability values followed the same trend as the previous ones. Based on the obtained in silico results, CPD4, CPD5, and CPD6 were discovered to be possible lead compounds as reference inhibitors of SAHA.

Pathogenic variation in DNA mismatch repair (MMR) gene MLH1 is associated with Lynch syndrome (LS), an autosomal dominant hereditary cancer. Of the 3798 MLH1 germline variants collected in the ClinVar database, 38.7% (1469) were missense variants, of which 81.6% (1199) were classified as Variants of Uncertain Significance (VUS) due to the lack of functional evidence. Further determination of the impact of VUS on MLH1 function is important for the VUS carriers to take preventive action. We recently developed a protein structure-based method named “Deep Learning-Ramachandran Plot-Molecular Dynamics Simulation (DL-RP-MDS)” to evaluate the deleteriousness of MLH1 missense VUS. The method extracts protein structural information by using the Ramachandran plot-molecular dynamics simulation (RP-MDS) method, then combines the variation data with an unsupervised learning model composed of auto-encoder and neural network classifier to identify the variants causing significant change in protein structure. In this report, we applied the method to classify 447 MLH1 missense VUS. We predicted 126/447 (28.2%) MLH1 missense VUS were deleterious. Our study demonstrates that DL-RP-MDS is able to classify the missense VUS based solely on their impact on protein structure.

phlD is a novel kind of polyketide synthase involved in the biosynthesis of non-volatile metabolite phloroglucinol by iteratively condensing and cyclizing three molecules of malonyl-CoA as substrate. Phloroglucinol or 2,4-diacetylphloroglucinol (DAPG) is an ecologically important rhizospheric antibiotic produced by pseudomonads; it exhibits broad spectrum anti-bacterial and anti-fungal properties, leading to disease suppression in the rhizosphere. Additionally, DAPG triggers systemic resistance in plants, stimulates root exudation, as well as induces phyto-enhancing activities in other rhizobacteria. Here, we report the cloning and analysis of the phlD gene from soil-borne gram-negative bacteria—Pseudomonas. The full-length phlD gene (from 1078 nucleotides) was successfully cloned and the structural details of the PHLD protein were analyzed in-depth via a three-dimensional topology and a refined three-dimensional model for the PHLD protein was predicted. Additionally, the stereochemical properties of the PHLD protein were analyzed by the Ramachandran plot, based on which, 94.3% of residues fell in the favored region and 5.7% in the allowed region. The generated model was validated by secondary structure prediction using PDBsum. The present study aimed to clone and characterize the DAPG-producing phlD gene to be deployed in the development of broad-spectrum biopesticides for the biocontrol of rhizospheric pathogens. [ABSTRACT FROM AUTHOR]

NrfA is the molecular marker for dissimilatory nitrate reduction to ammonium (DNRA) activity, catalysing cytochrome c nitrite reductase enzyme. However, the limited study has been made so far to understand the structural homology modeling of NrfA protein in DNRA bacteria. Therefore, three model DNRA bacteria (Escherechia coli, Wolinella succinogenes and Shewanella oneidensis) were chosen in this study for in-silico protein modeling of NrfA which roughly consists of similar length of amino acids and molecular weight and they belong to two contrasting taxonomic families (γ-proteobacteria with nrfABCDEFG and ε-proteobacteria with nrfHAIJ operon). Multiple bioinformatic tools were used to examine the primary, secondary, and tertiary structure of NrfA protein using three distinct homology modeling pipelines viz., Phyre2, Swiss model and Modeller. The results indicated that NrfA protein in E. coli, W. succinogenes and S. oneidensis was mostly periplasmic and hydrophilic. Four conserved Cys-X1-X2-Cys-His motifs, one Cys-X1-X2-Cys-Lys haem-binding motif and Ca ligand were also identified in NrfA protein irrespective of three model bacteria. Moreover, 11 identical conserved amino acids sequence was observed for the first time between serine and proline in NrfA protein. Secondary structure of NrfA revealed that α-helices were observed in 77.9%, 73.4%, and 77.4% in E. coli, W. succinogenes and S. oneidensis, respectively. Ramachandran plot showed that number of residue in favored region in E. coli, W. succinogenes and S. oneidensis was 97.03%, 97.01% and 97.25%, respectively. Our findings also revealed that among three pipelines, Modeller was considered the best in-silico tool for prediction of NrfA protein. Overall, significant findings of this study may aid in the identification of future unexplored DNRA bacteria containing cytochrome c nitrite reductase. The NrfA system, which is linked to respiratory nitrite ammonification, provides an analogous target for monitoring less studied N-retention processes, particularly in agricultural ecosystems. Furthermore, one of the challenging research tasks for the future is to determine how the NrfA protein responds to redox status in the microbial cells. [ABSTRACT FROM AUTHOR]

The definition of the structural basis of the conformational preferences of the genetically encoded amino acid residues is an important yet unresolved issue of structural biology. In order to gain insights into this intricate topic, we here determined and compared the amino acid propensity scales for different (φ, ψ) regions of the Ramachandran plot and for different secondary structure elements. These propensities were calculated using the Chou–Fasman approach on a database of non-redundant protein chains retrieved from the Protein Data Bank. Similarities between propensity scales were evaluated by linear regression analyses. One of the most striking and unexpected findings is that distant regions of the Ramachandran plot may exhibit significantly similar propensity scales. On the other hand, contiguous regions of the Ramachandran plot may present anticorrelated propensities. In order to provide an interpretative background to these results, we evaluated the role that the local variability of protein backbone geometry plays in this context. Our analysis indicates that (dis)similarities of propensity scales between different regions of the Ramachandran plot are coupled with (dis)similarities in the local geometry. The concept that similarities of the propensity scales are dictated by the similarity of the NCαC angle and not necessarily by the similarity of the (φ, ψ) conformation may have far-reaching implications in the field. [ABSTRACT FROM AUTHOR]

Streptococcus pneumoniae, generally known as pneumococcus, is a common bacterium associated with respiratory infection in humans, which in turn causes significant morbidity and mortality each year, particularly in children, the elderly. In current study we analysed membrane related proteins of Streptococcus pneumoniae to predict epitopes that can interact with MHC class-II proteins to produce immune response within the host against this harmful bacterium. We finalized VMLYYFLPNLSNRKI and IGYSFNVAAGSSIVL epitopes from membrane proteins of S. pneumoniae. These epitopes structure was found to be stable, also they were found to be capable in inducing IFNγ, IL10 and IL4. These epitopes can internalize in to subcellular organelles. Ramachandran plot for selected epitopes shows favourable regions were occupied by most of the residues. In docking analysis, it was found that HLA-DRB0101 receptor and VMLYYFLPNLSNRKI epitope show ACE (Atomic contact energy) value of − 132 while the same receptor of MHC class-II molecule docks with IGYSFNVAAGSSIVL epitope and shows ACE value of − 151. The docked complexes were found to be stable during MD simulations, as trajectory analysis shows RMSD values closer to 2.5 angstrom. Here, we identified VMLYYFLPNLSNRKI and IGYSFNVAAGSSIVL epitopes. These epitopes are antigenic, stable and can easily internalize in to subcellular compartments to elicit immune response. In future these epitopes could be added to adjuvants and linkers after synthesis for wet lab validations on test organism. [ABSTRACT FROM AUTHOR]

Single mutations that can substantially enhance stability are highly desirable for protein engineering. However, it is generally rare for this kind of mutant to emerge from directed evolution experiments. This study used computational approaches to identify hotspots in a diacylglycerol-specific lipase for mutagenesis with functional hotspot and sequence consensus strategies, followed by ∆∆G calculations for all possible mutations using the Rosetta ddg_monomer protocol. Single mutants with significant ∆∆G changes (≤−2.5 kcal/mol) were selected for expression and characterization. Three out of seven tested mutants showed a significantly enhanced thermostability, with Q282W and A292G in the catalytic pocket and D245G located on the opposite surface of the protein. Remarkably, A292G increased the T5015 (the temperature at which 50% of the enzyme activity was lost after a 15 min of incubation) by ~7 °C, concomitant with a twofold increase in enzymatic activity at the optimal reaction temperature. Structural analysis showed that both A292 and D245 adopted unfavored dihedral angles in the wild-type (WT) enzyme. Substitution of them by glycine might release a steric strain to increase the stability. In sum, substitution by glycine might be a promising strategy to improve protein thermostability. [ABSTRACT FROM AUTHOR]

Synthesis of C‐3 and C‐20 pregnenolone derivatives using Steglich and Heck reaction has been reported. The structures of compounds were established by 1H, 13C NMR, NOESY, FT‐IR, and ESI‐MS. The anticancer activity against lung cancer proficiency assessment was performed using the prediction of activity spectra for substances (PASS) technique and the results were compared with the FDA‐approved lung cancer drug dacomitinib. Molecular docking studies were carried out to investigate the inhibitory action of steroidal derivatives against the lung cancer cell protein (2ITO). The result of the docking exhibited a significant inhibitory action against the lung cancer protein (2ITO) and the binding energy (ΔG) values of 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11 against the protein 2ITO were found to be −10.1, −10.8, −9.2, −9.4, −10.1, −9.4, −11.0, −10.9, −9.7, and −9.5 Kcal/mol, respectively. In vitro lung cancer activity analyses of these compounds against lung cancer cell line (A549) showed that compounds 2 and 3 were more potent than other compounds. Results of in silico and in vitro analysis revealed that they showed good correlation. Drugs likeness and ADMET analysis of all derivatives have also been studied. [ABSTRACT FROM AUTHOR]

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom-the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide's conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone's internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the 'dead space' within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.

Helicobacter pylori (H. pylori) is a Gram-negative, slow-growing bacterium, microaerophilic, and a unique gastric pathogen that causes chronic inflammation in the gastric mucosa with the possibility of developing gastric cancer; one-third of its proteins are still uncharacterized. In this study, computational analysis was performed on the structural, functional, and epitopic characteristics of a hypothetical protein (HP) from H. pylori named HPF63-1454. The model prediction and primary, secondary, and three-dimensional structures of the chosen HP were built. The newly created model appeared to have high quality once refinement and structure validation had been completed. The anticipated tertiary structure was assessed using the Swiss Model assessment. The best materials were chosen using structural analyses and considering data from the Z scores, Swiss Interactive Workplace, and Ramachandran plot statistics. This investigation aimed to determine the importance of the H. pylori protein HPF63-1454. Therefore, this research increased our understanding of pathophysiology and allowed us to target the protein complex specifically. H. pylori infections are now treated with readily available antibiotics and acid-suppressing medications, but this species has established itself as a hardy pest. Long-term and taxing antibiotic therapy for H. pylori infection is increasingly beginning to fail, necessitating novel and creative therapeutic modalities.

Melioidosis is caused by the bacillus Burkholderia pseudomallei, this bacterium causes 165,000 new cases worldwide each year. Epitopes based vaccine a candidate of these bacterial species was identified by immunoinformatic study. Six epitopes VKAFRAAFAIPADVE, APVLIAVTAHTLTSK, GNPNFQAGDAARLIV, TLGAGINVDSTVGTS, LGAGINVDSTVGTSG, VKAFRAAFAIPADVE were linked to adjuvants, and linker molecules. Deep learning and artificial neural network tools were used to determine these epitopes, but structural prediction and validations shows multi-epitope vaccine was structurally and functionally sound. Molecular docking analysis shows interaction of multi-epitope vaccine and TLR-5 with ACE value of − 6.8 kcal/mol. Ramachandran plot shows greater than 97% amino acid residues are in allowed regions. The core objective of the current study is to craft multi-epitope vaccine against Burkholderia pseudomallei. This multi-epitope vaccine construct can be synthesised and validated by wet lab analysis in future studies, but in current study it shows good interaction patterns with TLR5 that will assist in its internalization. Here the validation of vaccine construct was conducted by simulation analysis that reveals stable interaction between ligand and receptor. Immunoinformatic studies not only save time but these methods were found to be economically beneficial. [ABSTRACT FROM AUTHOR]

Background: Mycobacterium tuberculosis has been ravaging humans by inflicting respiratory tuberculosis since centuries. Bacillus Calmette Guerine (BCG) is the only vaccine available for tuberculosis, and it is known to be poorly effective against adult tuberculosis. Proteins belonging to the ESAT-6 family and PE/PPE family show immune responses and are included in different vaccine trials. Herein, we study the functional and structural characterization of a 248 amino acid long putative protein novel hypothetical protein 1 (NHP1) present in the RD7 region of Mycobacterium tuberculosis (identified first by subtractive hybridization in the clinical isolate RGTB123) using bioinformatics tools. Results: Physicochemical properties were studied using Expasy ProtParam and SMS software. We predicted different B-cell and T-cell epitopes by using the immune epitope database (IEDB) and also tested antigenicity, immunogenicity, and allergenicity. Secondary structure of the protein predicted 30% alpha helices, 20% beta strands, and 48% random coils. Tertiary structure of the protein was predicted using the Robetta server using the Mycobacterium smegmatis protein as the putative protein with homology. Structural evaluations were done with Ramachandran plot analysis, ProSA-web, and VERIFY3D, and with GalaxyWEB server, a more stable structure was validated with good stereo chemical properties. Conclusion: The present study of a subtracted genomic locus using various bioinformatics tools indicated good immunological properties of the putative mycobacterial protein, NHP1. Evidence obtained from the analyses of NHP1 using structure prediction tools strongly point to the fact that NHP1 is an ancient protein having flavodoxin folding structure with ATP binding sites. Positive scores were obtained for antigenicity, immunogenicity, and virulence too, implying the possibility of NHP1 to be a potential vaccine candidate. Such computational studies might give clues for developing newer vaccines for tuberculosis, which is the need of the hour. [ABSTRACT FROM AUTHOR]

Cytochrome b (cyt b) is one of the cytochrome proteins involved in electron transport in the respiratory chain of mitochondria. Cyt b is the only gene among the cytochrome complex coded by mitochondrial DNA. It is the most widely used gene for phylogenetic assessment and inter species variation studies. Here, the amino acid sequence of cyt b in three snapping shrimps such as, Alpheus lobidens, A. randali, A. bellulus was analysed and the results showed higher similarity in A. lobidens and A. randali as reflected in the phylogenetic tree. This study describes the applications of bioinformatics tools to predict the physico-chemical characters of cyt b protein. This protein was composed of least percentage of Cys (0.8%) and highest percentage of Leu (13.8%). The maximum molecular weight (MW) was predicted as 42.62 KDa in A. randali. The theoretical pI value was ranged from 8.35 to 8.36 and confirmed that cyt b was alkali in nature. The instability index value was in the range of 42.29 to 46.94 which showed the protein was more stable. The secondary structure of this protein was primarily composed of α-helixes and random coil, revealing the stable structure. The comparative modelling was performed by Swiss model where the 3-D crystal structure of bovine cyt bc1 (6haw1.c) was used as template. Ramachandran plot analysis showed that most of the amino acids (>92%) falling on the favoured region. Seven conserved motifs were identified by MEME analysis. The modelled 3-D structure of this protein was validated by PROCHECK and QMEAN. The transmembrane protein topology and helix probability curve was predicted by TMHMM server. Protein-protein interactions was analysed by STRING tool and found the network of cyt b with related proteins. The results of this study may provide valuable insights into fundamental characteristics of cyt b in Alpheid shrimps.

Cytochrome b (cyt b) is one of the cytochrome proteins involved in electron transport in the respiratory chain of mitochondria. Cyt b is the only gene among the cytochrome complex coded by mitochondrial DNA. It is the most widely used gene for phylogenetic assessment and inter species variation studies. Here, the amino acid sequence of cyt b in three snapping shrimps such as, Alpheus lobidens, A. randali, A. bellulus was analysed and the results showed higher similarity in A. lobidens and A. randali as reflected in the phylogenetic tree. This study describes the applications of bioinformatics tools to predict the physico-chemical characters of cyt b protein. This protein was composed of least percentage of Cys (0.8%) and highest percentage of Leu (13.8%). The maximum molecular weight (MW) was predicted as 42.62 KDa in A. randali. The theoretical pI value was ranged from 8.35 to 8.36 and confirmed that cyt b was alkali in nature. The instability index value was in the range of 42.29 to 46.94 which showed the protein was more stable. The secondary structure of this protein was primarily composed of α-helixes and random coil, revealing the stable structure. The comparative modelling was performed by Swiss model where the 3-D crystal structure of bovine cyt bc1 (6haw1.c) was used as template. Ramachandran plot analysis showed that most of the amino acids (>92%) falling on the favoured region. Seven conserved motifs were identified by MEME analysis. The modelled 3-D structure of this protein was validated by PROCHECK and QMEAN. The transmembrane protein topology and helix probability curve was predicted by TMHMM server. Protein-protein interactions was analysed by STRING tool and found the network of cyt b with related proteins. The results of this study may provide valuable insights into fundamental characteristics of cyt b in Alpheid shrimps. [ABSTRACT FROM AUTHOR]

Abstract Background Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative fatal disease that can affect the neurons of brain and spinal cord. ALS genetics has identified various genes to be associated with disease pathology. Oxidative stress induced bunina and lewy bodies formation can be regulated through the action of SOD1 protein. Hence, in the present study we aim to analyse the structural and functional annotation of various reported SOD1 variants throughout and their putative correlation with the location of mutation and degree of ALS severity by inferring the structural and functional alterations in different SOD1 variants. Methods We have retrieved around 69 SNPs of SOD1 gene from Genecards. Structural annotation of SOD1 variants were performed using SWISS Model, I-Mutant 2.0, Dynamut, ConSurf. Similarly, the functional annotation of same variants were done using SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB. Ramachandran plot was also obtained for six synonymous SNPs to compare the amino acid distribution of wild-type SOD1 (WT SOD1) protein. Frequency analysis, Chi square analysis, ANOVA and multiple regression analysis were performed to compare the structural and functional components among various groups. Results and conclusion Results showed the mutations in conserved domain of SOD1 protein are more deleterious and significantly distort the tertiary structure of protein by altering Gibb’s free energy and entropy. Moreover, significant changes in SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB scores were also observed in mutations located in conserved domain of SOD1 protein. Multiple regression results were also suggesting the significant alterations in free energy and entropy for conserved domain mutations which were concordant with structural changes of SOD1 protein. Results of the study are suggesting the biological importance of location of mutation(s) which may derive the different disease phenotypes and must be dealt accordingly to provide precise therapy for ALS patients.

Background: Hyperemesis Gravidarum (HG) is a common pregnancy complication that occurs in 0.3–2% of pregnancies. Growth/Differentiation Factor (GDF) 15 serum levels are abnormally high in patients associated with HG. In silico analysis provides information about structure and function of GDF15. Aim and Objectives: The aim of this study was to enlist biochemical and functional properties of GDF15 protein and determine its three-dimensional structure, as GDF15 is known to be associated with risk of HG. Material and Methods: The PDB file of GDF15 [NP_004855] was created by RaptorX structure prediction server. The UCLA-DOE server was used to visual analysis of crystal structure of protein. The validation for structure models was performed by using PROCHECK. Model quality estimates were based on the QMEAN and ProSA. Results: The model showed good stereo-chemical property in terms of G-factor value -0.64, that indicates geometry of model corresponds to probability conformation with 95% residue in the favored region of Ramachandran plot, showing high accuracy of model prediction. The Zscore of -4.04 predicted by ProSA represents the good quality of the model. The energy plot shows the local model quality by plotting knowledge-based energies as a function of amino acid sequence position. Conclusion: The generated model could be supportive to understand the structure and functional characteristics of Homo sapiens growth/differentiation factor 15 [NP_004855]. As abnormal high serum levels of GDF15 were observe in patients associated with HG. Therefore, the structure model of GDF15 [NP_004855] is useful to understand its role in development of HG. In Silico docking study could be explain the molecular association of GDF15 [NP_004855] with HG and new drug designing, for that structure model is very useful.

The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural stability of their affected proteins, information from structural change caused by genetic variants can be used to identify the variants with deleterious effects. In order to measure the structural change for proteins with large size, we designed a method named RP-MDS composed of Ramachandran plot (RP) and Molecular Dynamics Simulation (MDS). Ramachandran plot captures the variant-caused secondary structural change, whereas MDS provides a quantitative measure for the variant-caused globular structural change. We tested the method using variants in TP53 DNA binding domain of 219 residues as the model. In total, RP-MDS identified 23 of 38 (60.5%) TP53 known Pathogenic variants and 17 of 42 (41%) TP53 VUS that caused significant changes of P53 structure. Our study demonstrates that RP-MDS method provides a powerful protein structure-based tool to screen deleterious genetic variants affecting large-size proteins.

phlD is a novel kind of polyketide synthase involved in the biosynthesis of non-volatile metabolite phloroglucinol by iteratively condensing and cyclizing three molecules of malonyl-CoA as substrate. Phloroglucinol or 2,4-diacetylphloroglucinol (DAPG) is an ecologically important rhizospheric antibiotic produced by pseudomonads; it exhibits broad spectrum anti-bacterial and anti-fungal properties, leading to disease suppression in the rhizosphere. Additionally, DAPG triggers systemic resistance in plants, stimulates root exudation, as well as induces phyto-enhancing activities in other rhizobacteria. Here, we report the cloning and analysis of the phlD gene from soil-borne gram-negative bacteria—Pseudomonas. The full-length phlD gene (from 1078 nucleotides) was successfully cloned and the structural details of the PHLD protein were analyzed in-depth via a three-dimensional topology and a refined three-dimensional model for the PHLD protein was predicted. Additionally, the stereochemical properties of the PHLD protein were analyzed by the Ramachandran plot, based on which, 94.3% of residues fell in the favored region and 5.7% in the allowed region. The generated model was validated by secondary structure prediction using PDBsum. The present study aimed to clone and characterize the DAPG-producing phlD gene to be deployed in the development of broad-spectrum biopesticides for the biocontrol of rhizospheric pathogens.

[Display omitted] Tectona grandis L.f. (Teak), a very important source of incomparable timber, withstands a wide range of tropical deciduous conditions. We achieved partial amplification of pectin methylesterase inhibitor 51 (PMEI) gene in teak by E. pilularis cinnamoyl Co-A reductase (CCR) gene specific primer. The amplified teak gene was of 750 bp, 79% identity and 97% query cover with PMEI of Sesamum indicum. The phylogenetic tree clustered the amplified gene with PMEI of database plant species, Erythranthe guttata and Sesamum indicum (87% bootstrap value). On conversion to amino acid sequence, the obtained protein comprised 237 amino acids. However, PMEI region spanned from 24 to 171 amino acids, 15.94 kDa molecular weight, 8.97 pI value and C 697 H 1117 N 199 O 211 S 9 molecular formula with four conserved cysteine residues as disulfide bridges. 25.9 % protein residues were hydrophilic, 42.7% hydrophobic and 31.2% neutral. Teak 3D PMEI protein structure corresponded well with Arabidopsis thaliana and Actinidia deliciosa PMEIs. The gene maintains integrity of pectin component of middle lamella of primary cell wall and confers tolerance against various kinds of stresses. Teak conferred with overexpression of PMEI may secure a wide adaptability as well as luxuriant timber productivity and quality in adverse/ fluctuating/ scarce climatic and environmental conditions of tropical forests. [ABSTRACT FROM AUTHOR]

The definition of the structural basis of the conformational preferences of the genetically encoded amino acid residues is an important yet unresolved issue of structural biology. In order to gain insights into this intricate topic, we here determined and compared the amino acid propensity scales for different (φ, ψ) regions of the Ramachandran plot and for different secondary structure elements. These propensities were calculated using the Chou–Fasman approach on a database of non-redundant protein chains retrieved from the Protein Data Bank. Similarities between propensity scales were evaluated by linear regression analyses. One of the most striking and unexpected findings is that distant regions of the Ramachandran plot may exhibit significantly similar propensity scales. On the other hand, contiguous regions of the Ramachandran plot may present anticorrelated propensities. In order to provide an interpretative background to these results, we evaluated the role that the local variability of protein backbone geometry plays in this context. Our analysis indicates that (dis)similarities of propensity scales between different regions of the Ramachandran plot are coupled with (dis)similarities in the local geometry. The concept that similarities of the propensity scales are dictated by the similarity of the NCαC angle and not necessarily by the similarity of the (φ, ψ) conformation may have far-reaching implications in the field.

Single mutations that can substantially enhance stability are highly desirable for protein engineering. However, it is generally rare for this kind of mutant to emerge from directed evolution experiments. This study used computational approaches to identify hotspots in a diacylglycerol-specific lipase for mutagenesis with functional hotspot and sequence consensus strategies, followed by ∆∆G calculations for all possible mutations using the Rosetta ddg_monomer protocol. Single mutants with significant ∆∆G changes (≤−2.5 kcal/mol) were selected for expression and characterization. Three out of seven tested mutants showed a significantly enhanced thermostability, with Q282W and A292G in the catalytic pocket and D245G located on the opposite surface of the protein. Remarkably, A292G increased the T5015 (the temperature at which 50% of the enzyme activity was lost after a 15 min of incubation) by ~7 °C, concomitant with a twofold increase in enzymatic activity at the optimal reaction temperature. Structural analysis showed that both A292 and D245 adopted unfavored dihedral angles in the wild-type (WT) enzyme. Substitution of them by glycine might release a steric strain to increase the stability. In sum, substitution by glycine might be a promising strategy to improve protein thermostability.

The CYP family enzymes are broadly used as biomarkers because of their pattern of expression. This study describes the application of in silico tools to predict the physico-chemical characters of CYP1A protein from the catfish, Clarias gariepinus. The nucleotide sequence analysis of C. gariepinus CYP1A gene showed higher similarity with C. batrachus and reflected in the phylogenetic tree. The comparative modelling results showed this CYP1A protein was highly similar with the 3-D crystal structure of human Cytochrome p450 1A1 (PDB: 1BE3). The prediction results depicted that most of the amino acids formed alpha helix. The predicted pI was 9.10, hydropathycity was -0.226, exposed and buried residues were 61.67, 38.33% respectively. Ramachandran plot analysis showed that most of the amino acids falling on the favoured region and exhibited right- handed alpha helices as the most stable secondary structure. Some amino acids were also found to form loops to interconnect different helices. The CYP1A protein was predicted to be localized in the mitochondrion of the eukaryotic cell.

Background: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative fatal disease that can affect the neurons of brain and spinal cord. ALS genetics has identified various genes to be associated with disease pathology. Oxidative stress induced bunina and lewy bodies formation can be regulated through the action of SOD1 protein. Hence, in the present study we aim to analyse the structural and functional annotation of various reported SOD1 variants throughout and their putative correlation with the location of mutation and degree of ALS severity by inferring the structural and functional alterations in different SOD1 variants.Methods: We have retrieved around 69 SNPs of SOD1 gene from Genecards. Structural annotation of SOD1 variants were performed using SWISS Model, I-Mutant 2.0, Dynamut, ConSurf. Similarly, the functional annotation of same variants were done using SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB. Ramachandran plot was also obtained for six synonymous SNPs to compare the amino acid distribution of wild-type SOD1 (WT SOD1) protein. Frequency analysis, Chi square analysis, ANOVA and multiple regression analysis were performed to compare the structural and functional components among various groups.Results and Conclusion: Results showed the mutations in conserved domain of SOD1 protein are more deleterious and significantly distort the tertiary structure of protein by altering Gibb's free energy and entropy. Moreover, significant changes in SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB scores were also observed in mutations located in conserved domain of SOD1 protein. Multiple regression results were also suggesting the significant alterations in free energy and entropy for conserved domain mutations which were concordant with structural changes of SOD1 protein. Results of the study are suggesting the biological importance of location of mutation(s) which may derive the different disease phenotypes and must be dealt accordingly to provide precise therapy for ALS patients. [ABSTRACT FROM AUTHOR]

Background: Hyperemesis Gravidarum (HG) is a common pregnancy complication that occurs in 0.3–2% of pregnancies. Growth/Differentiation Factor (GDF) 15 serum levels are abnormally high in patients associated with HG. In silico analysis provides information about structure and function of GDF15. Aim and Objectives: The aim of this study was to enlist biochemical and functional properties of GDF15 protein and determine its three-dimensional structure, as GDF15 is known to be associated with risk of HG. Material and Methods: The PDB file of GDF15 [NP_004855] was created by RaptorX structure prediction server. The UCLA-DOE server was used to visual analysis of crystal structure of protein. The validation for structure models was performed by using PROCHECK. Model quality estimates were based on the QMEAN and ProSA. Results: The model showed good stereo-chemical property in terms of G-factor value -0.64, that indicates geometry of model corresponds to probability conformation with 95% residue in the favored region of Ramachandran plot, showing high accuracy of model prediction. The Z-score of -4.04 predicted by ProSA represents the good quality of the model. The energy plot shows the local model quality by plotting knowledge-based energies as a function of amino acid sequence position. Conclusion: The generated model could be supportive to understand the structure and functional characteristics of Homo sapiens growth/differentiation factor 15 [NP_004855]. As abnormal high serum levels of GDF15 were observe in patients associated with HG. Therefore, the structure model of GDF15 [NP_004855] is useful to understand its role in development of HG. In Silico docking study could be explain the molecular association of GDF15 [NP_004855] with HG and new drug designing, for that structure model is very useful. [ABSTRACT FROM AUTHOR]

[Display omitted] • FT-IR theoretical data were determined from B3LYP/ LANL2DZ basis set. • HOMO-LUMO energies, NBO property of the title compound are predicted. • MEP, Hirshfeld, IRI and ED were estimated. • Fukui function, ADMET and PASS were discussed. • Molecular docking predictions for the title drug have an antiviral and antioxidant activity. As focuses on a set of pertinent compounds that incorporate a γ-substituted halophenol linkage with pentanamide (PA). The properties of these compounds were comprehensively assessed through various analytical techniques, including density functional theory (DFT) calculations, offering insights into their geometry and electronic energy gap characteristics. Charge delocalization and stability were explored via natural bond orbital (NBO) analysis. The chemical reactivity was further scrutinized by evaluating NBO, Molecular Electrostatic Potential (MEP), Hirshfeld surface analysis and Fukui functions. The compounds were found to exhibit stability attributed to a robust hydrogen bonding network, which was corroborated by Interaction Region Indicator (IRI) and Electron Density (ED) assessments. Additionally, pharmacological properties were predicted using the PASS (Prediction of Activity Spectra for Substances) server. Molecular docking studies suggested potential antiviral and antioxidant properties, particularly concerning carbonic anhydrase. The overall results imply that these compounds possess favorable drug-like characteristics and show promise for biological efficacy. The study also includes a 2D interaction profile image of the four most interacted proteins and a Ramachandran plot to elucidate the stereochemistry of a selected protein. Furthermore, the activities of 6FDM were investigated following a comprehensive literature survey, with detailed findings presented. [ABSTRACT FROM AUTHOR]

TP53 plays critical roles in maintaining genome stability. Deleterious genetic variants damage the function of TP53, causing genome instability and increased cancer risk. Of the large quantity of genetic variants identified in TP53, however, many remain functionally unclassified as variants of unknown significance (VUS) due to the lack of evidence. This is reflected by the presence of 749 (42%) VUS of the 1785 germline variants collected in the ClinVar database. In this study, we addressed the deleteriousness of TP53 missense VUS. Utilizing the protein structure-based Ramachandran Plot-Molecular Dynamics Simulation (RPMDS) method that we developed, we measured the effects of missense VUS on TP53 structural stability. Of the 340 missense VUS tested, we observed deleterious evidence for 193 VUS, as reflected by the TP53 structural changes caused by the VUS-substituted residues. We compared the results from RPMDS with those from other in silico methods and observed higher specificity of RPMDS in classification of TP53 missense VUS than these methods. Data from our current study address a long-standing challenge in classifying the missense VUS in TP53, one of the most important tumor suppressor genes.