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An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are realized through their 3D structures. Specific local structures, called structural motifs, are considered as related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function. [ABSTRACT FROM AUTHOR]

In this paper we report the synthesis of new azabicycloalkane scaffolds, which could be exploited to obtain cRGD-based bioconjugates that may find promising application for targeted drug delivery, theranostic, and general cancer-cell labeling. By exploiting a Hosomi-Sakurai intramolecular allylation reaction we efficiently converted a silylated aldehyde precursor into 7,5-fused lactam scaffolds endowed with an exocyclic double bond. The presence of the vinyl function should make it possible to conjugate bioactive compounds to selectively carry them to tumor sites. The optimized synthetic sequence allows the gram-scale preparation of the target scaffolds in a few steps and good 39% overall yield from readily accessible materials. The high reactivity of the exocyclic olefin moiety was ascertained by performing a Heck coupling reaction with 1-bromo-4-nitrobenzene, which gave the corresponding functionalized derivatives in good (80-91%) yields. [ABSTRACT FROM AUTHOR]

Physicochemcial properties of amino acids are important factors in determining protein structure and function. Most approaches make use of averaged properties over entire domains or even proteins to analyze their structure or function. This level of coarseness tends to hide the richness of the variability in the different properties across functional domains. This paper studies the conservation of physicochemical properties in a functionally similar family of proteins using a novel wavelet-based technique known as multiresolution analysis. Such an analysis can help uncover characteristics that can otherwise remain hidden. We have studied the protein kinase family of sequences and our findings are as follows: (a) a number of different properties are conserved over the functional catalytic domain irrespective of the sequence identities; (b) conservation of properties can be observed at different frequency levels and they agree well with the known structural/functional properties of the subdomains for the protein kinase family; (c) structural differences between the different kinase family members are reflected in the waveforms; and (d) functionally important mutations show distortions in the waveforms of conserved properties. The potential usefulness of the above findings in identifying functionally similar sequences in the twilight and midnight zones is demonstrated through a simple prediction model for the protein kinase family which achieved a recall of 93.7% and a precision of 96.75% in cross-validation tests. [ABSTRACT FROM AUTHOR]

This paper experimentally verifies the idea presented earlier that the contact of nonpolar clusters located on the surface of protein molecules with water destabilizes proteins. It is demonstrated that protein stabilization can be achieved by artificial hydrophilization of the surface area of protein globules by chemical modification. Two experimental systems are studied for the verification of the hydrophilization approach. 1. The surface tyrosine residues of trypsin are transformed to aminotyrosines using a two-step modification procedure: nitration by tetranitromethane followed by reduction with sodium dithionite. The modified enzyme is much more stable against irreversible thermoinactivation: the stabilizing effect increases with the number of aminotyrosine residues in trypsin and the modified enzyme can become even 100 times more stable than the native one. 2. α-Chymotrypsin is covalently modified by treatment with anhydrides or chloroanhydrides of aromatic carboxytic acids. As a result, different numbers of additional carboxylic groups (up to five depending on the structure of the modifying reagent) are introduced into each Lys residue modified. Acylation of all available amino groups of α-chymotrypsin by cyclic anhydrides of pyromellitic and mellitic acids results in a substantial hydrophilization of the protein as estimated by partitioning in an aqueous Ficoll-400/Dextran-70 biphasic system. These modified enzyme preparations are extremely stable against irreversible thermal inactivation at elevated temperatures (65-98 °C); their thermostability is practically equal to the stability of proteolytic enzymes from extremely thermophilic bacteria, the most stable proteinases known to date. [ABSTRACT FROM AUTHOR]

The influence of the second amino acid on the pH response of the genetically encoded pH indicators is studied. The second Trp has been substituted by Ala and Glu to reduce self-quenching. Compared with the previously reported Trp-Trp-Ala-Ser (WWAS), the two new tetrapeptides, Trp-Ala-Ala-Ser (WAAS) and Trp-Glu-Ala-Ser (WEAS), have higher fluorescence quantum yields, longer fluorescence lifetimes, and more sensitive pH responses. As novel genetically encoded pH indicators, the N-terminal Trp-Ala and Trp-Glu could be fused to proteins for monitoring the environmental pH values during the studies of functional proteins. [ABSTRACT FROM AUTHOR]

How cuticular proteins (CPs) interact with chitin and with each other in the cuticle remains unresolved. We employed LC-MS/MS to identify CPs from 5–6 day-old adults of Anopheles gambiae released after serial extraction with PBS, EDTA, 2-8M urea, and SDS as well as those that remained unextracted. Results were compared to published data on time of transcript abundance, localization of proteins within structures and within the cuticle, as well as properties of individual proteins, length, pI, percent histidine, tyrosine, glutamine, and number of AAP[A/V/L] repeats. Thirteen proteins were solubilized completely, all were CPRs, most belonging to the RR-1 group. Eleven CPs were identified in both soluble fractions and the final pellet, including 5 from other CP families. Forty-three were only detected from the final pellet. These included CPRs and members of the CPAP1, CPF, CPFL, CPLCA, CPLCG, CPLCP, and TWDL families, as well as several low complexity CPs, not assigned to families and named CPLX. For a given protein, many histidines or tyrosines or glutamines appear to be potential participants in cross-linking since we could not identify any peptide bearing these residues that was consistently absent. We failed to recover peptides from the amino-terminus of any CP. Whether this implicates that location in sclerotization or some modification that prevents detection is not known. Soluble CPRs had lower isoelectric points than those that remained in the final pellet; most members of other CP families had isoelectric points of 8 or higher. Obviously, techniques beyond analysis of differential solubility will be needed to learn how CPs interact with each other and with chitin. [ABSTRACT FROM AUTHOR]

The three main requirements for life as we know it are the presence of organic compounds, liquid water, and free energy. Several groups of organic compounds (e.g., amino acids, nucleobases, lipids) occur in all life forms on Earth and are used as diagnostic molecules, i.e., biomarkers, for the characterization of extant or extinct life. Due to their indispensability for life on Earth, these biomarkers are also prime targets in the search for life on Mars. Biomarkers degrade over time; in situ environmental conditions influence the preservation of those molecules. Nonetheless, upon shielding (e.g., by mineral surfaces), particular biomarkers can persist for billions of years, making them of vital importance in answering questions about the origins and limits of life on early Earth and Mars. The search for organic material and biosignatures on Mars is particularly challenging due to the hostile environment and its effect on organic compounds near the surface. In support of life detection on Mars, it is crucial to investigate analogue environments on Earth that resemble best past and present Mars conditions. Terrestrial extreme environments offer a rich source of information allowing us to determine how extreme conditions affect life and molecules associated with it. Extremophilic organisms have adapted to the most stunning conditions on Earth in environments with often unique geological and chemical features. One challenge in detecting biomarkers is to optimize extraction, since organic molecules can be low in abundance and can strongly adsorb to mineral surfaces. Methods and analytical tools in the field of life science are continuously improving. Amplification methods are very useful for the detection of low concentrations of genomic material but most other organic molecules are not prone to amplification methods. Therefore, a great deal depends on the extraction efficiency. The questions "what to look for", "where to look", and "how to look for it" require more of our attention to ensure the success of future life detection missions on Mars. [ABSTRACT FROM AUTHOR]

Recently, we demonstrated that yeast protein evolutionary rate at the level of individual amino acid residues scales linearly with degree of solvent accessibility. This residue-level structure-evolution relationship is sensitive to protein core size: surface residues from large-core proteins evolve much faster than those from small-core proteins, while buried residues are equally constrained independent of protein core size. In this work, we investigate the joint effects of protein core size and expression on the residue-level structure-evolution relationship. At the whole-protein level, protein expression is a much more dominant determinant of protein evolutionary rate than protein core size. In contrast, at the residue level, protein core size and expression both have major impacts on protein structure-evolution relationships. In addition, protein core size and expression influence residue-level structure-evolution relationships in qualitatively different ways. Protein core size preferentially affects the non-synonymous substitution rates of surface residues compared to buried residues, and has little influence on synonymous substitution rates. In comparison, protein expression uniformly affects all residues independent of degree of solvent accessibility, and affects both non-synonymous and synonymous substitution rates. Protein core size and expression exert largely independent effects on protein evolution at the residue level, and can combine to produce dramatic changes in the slope of the linear relationship between residue evolutionary rate and solvent accessibility. Our residue-level findings demonstrate that protein core size and expression are both important, yet qualitatively different, determinants of protein evolution. These results underscore the complementary nature of residue-level and whole-protein analysis of protein evolution. [ABSTRACT FROM AUTHOR]

Background: The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. Results: The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don't. While the nature of transitions of LCC's sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at higher interaction strength between amino acids, give extra stability to the tertiary structure of the thermophiles. All the subnetworks at different length scales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids. While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs and LRNs; we do not find the assortative mixing behaviour of any the subclusters in SRNs. The clustering coefficient of hydrophobic subclusters in long-range network is the highest among types of subnetworks. There exist highly cliquish hydrophobic nodes followed by charged nodes in LRNs and ARNs; on the other hand, we observe the highest dominance of charged residues cliques in short-range networks. Studies on the perimeter of the cliques also show higher occurrences of hydrophobic and charged residues' cliques. Conclusions: The simple framework of protein contact networks and their subnetworks based on London van der Waals force is able to capture several known properties of protein structure as well as can unravel several new features. The thermophiles do not only have the higher number of long-range interactions; they also have larger cluster of connected residues at higher interaction strengths among amino acids, than their mesophilic counterparts. It can reestablish the significant role of long-range hydrophobic clusters in protein folding and stabilization; at the same [ABSTRACT FROM AUTHOR]

Background: Similarity search in protein databases is one of the most essential issues in computational proteomics. With the growing number of experimentally resolved protein structures, the focus shifted from sequences to structures. The area of structure similarity forms a big challenge since even no standard definition of optimal structure similarity exists in the field. Results: We propose a protein structure similarity measure called SProt. SProt concentrates on high-quality modeling of local similarity in the process of feature extraction. SProt's features are based on spherical spatial neighborhood of amino acids where similarity can be well-defined. On top of the partial local similarities, global measure assessing similarity to a pair of protein structures is built. Finally, indexing is applied making the search process by an order of magnitude faster. Conclusions: The proposed method outperforms other methods in classification accuracy on SCOP superfamily and fold level, while it is at least comparable to the best existing solutions in terms of precision-recall or quality of alignment. [ABSTRACT FROM AUTHOR]

In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a ‘reaction graph’ abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular ‘tree’, and autonomous locomotion of a bipedal walker. [ABSTRACT FROM AUTHOR]

Magnesium chelatase is the first unique enzyme of the bacteriochlorophyll biosynthetic pathway. It consists of three subunits (BchI, BchD, and BchH). Amino acid sequence analysis of the Rhodobacter capsulatus BchH revealed a novel cysteine motif (393CX2CX3CX14C) that was found in only six other proteobacteria (CX2CX3CX11–14C). The cysteine motif is likely to coordinate an unprecedented [Fe–S] cluster. Purified BchH demonstrated absorbance in the 460 nm region. This absorbance was abolished in BchH proteins with alanine substitutions at positions Cys396 and Cys414. These modified proteins were also EPR silent. In contrast, wild type BchH protein in the reduced state showed EPR signals resembling those of a [4Fe–4S] cluster with rhombic symmetry and g values at 1.90, 1.93, and 2.09, superimposed with a [3Fe–4S] cluster centered at g = 2.02. The [3Fe–4S] signal was observed independently of the [4Fe–4S] signal under oxidizing conditions. Mg-chelatase activity assays showed that the cluster is not catalytic. We suggest that the [4Fe–4S] and [3Fe–4S] signals originate from a single coordination site on the monomeric BchH protein and that the [4Fe–4S] cluster is sensitive to oxidation. It is speculated that the cluster participates in the switching between aerobic and anaerobic life of the proteobacteria. [ABSTRACT FROM AUTHOR]

The stability of α-helices in proteins depends on both their compositions and environments. To see how these two factors match with each other, we selected three typical α-helices from real proteins each of them has different compositions of hydrophobic and hydrophilic amino acids. We simulated the dynamics of the three helices in vacuum and in water using molecular dynamics. The results show that the stabilities of the three α-helices are different in vacuum and in water, which are consistent with their locations in the proteins. We also found some interesting behaviors of these α-helices. [ABSTRACT FROM AUTHOR]

Biological motion is for a large part powered by motor proteins. These are tiny engines (about a millionth of an inch) that convert chemical energy into mechanical force and motion. Processive motor proteins are among the most sophisticated and well studied of the motor proteins. They consist of two identical 'feet' that literally step forward on a long polymer as the fuel is consumed. When a human or other large animal steps, the physics involves mass, gravity and inertia. But for the walking protein the physics is different. Inertial forces are negligible compared to the frictional forces and Brownian motion, i.e. the random movements of molecules at a microscopic level, becomes an issue. Much of the research of the last decades has been directed towards figuring out the amino acid sequence and three-dimensional structure of proteins, but less effort and progress has been made towards understanding the operation of proteins in action. With a simple but rigorous model it is shown how Brownian motion and the generation of real force actually team up to make the motor protein step. The model, moreover, accounts accurately for recently obtained data on moving motor proteins. [ABSTRACT FROM AUTHOR]

The human I1-imidazoline receptor candidate gene, iras, has previously been cloned and mapped to locus 3p21.1-9 (also known as Nischarin; accession #AC006208). By comparison to a database of expressed sequence tags (ESTs), three alternatively spliced transcripts have been deduced. A map of 21 exons was constructed for the medium-length transcript (IRAS-M) containing 5,232 base pairs (bp) and encoding 1,504 amino acids (aas). Introns 13B and 13C are inserted into the two alternative transcripts, forming IRAS-S and IRAS-L mRNA (short and long isoforms). Northern blots confirmed the existence of these mRNA isoforms. In most brain regions the order of mRNA abundance was IRAS-M > IRAS-L > IRAS-S mRNA. Although aas 1 through 510 are theoretically identical, truncated proteins could be derived from IRAS-S (2,678 bp transcript yields 515 aas) and IRAS-L (9,457 bp transcript yields 583 aas). Because exon-16 of the iras gene has been proposed to encode the functional domains of imidazoline and a-5 integrin binding, only IRAS-M is expected to possess I1 receptor properties. Subtype-selective cDNA expression constructs were therefore generated and used to transfect CHO cells. High-affinity I1 binding was endowed by IRAS-M and IRAS-L, but not by IRAS-S transfection. [ABSTRACT FROM AUTHOR]

The main source of marine organic carbon (OC) is autotrophic production, while heterotrophic degradation is its main sink. Increased anthropogenic CO2 release leads to ocean acidification and is expected to alter phytoplankton community composition, primary production rates and bacterial degradation processes in the coming decades with potential consequences for dissolved and particulate OC concentration and composition. Here we investigate effects of increased pCO2 on dissolved and particulate amino acids (AA) and carbohydrates (CHO), in arctic and sub-arctic planktonic communities in two large-scale mesocosm experiments. Dissolved AA concentrations responded to pCO2/pH changes during early bloom phases but did not show many changes after nutrient addition. A clear positive correlation in particulate AA was detected in post-bloom phases. Direct responses in CHO concentrations to changing pCO2/pH were lacking, suggesting that observed changes were rather indirect and dependent on the phytoplankton community composition. The relative composition of AA and CHO did not change as a direct consequence of pCO2 increase. Changes between bloom phases were associated with the prevailing nutrient status. Our results suggest that biomolecule composition will change under future ocean conditions but responses are highly complex, and seem to be dependent on many factors including bloom phase and sampling site. [ABSTRACT FROM AUTHOR]

Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small α protein domains have hidden sequence symmetries characteristic of their pseudo-symmetric tertiary structures. We also present a modified method of recurrent plot to reveal this kind of the hidden sequence symmetry. The results may enable us to understand part of the relations between protein sequences and their tertiary structures. [ABSTRACT FROM AUTHOR]