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As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label‐free and high‐throughput protein sequencing. In recent years, nanopore‐based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing. [ABSTRACT FROM AUTHOR]

The chemical modification of proteins is an effective technique for manipulating the properties and functions of proteins, and for creating protein‐based materials. The N‐terminus is a promising target for single‐site modification that provides modified proteins with uniform structures and properties. In this paper, a copper(II)‐mediated aldol reaction with 2‐pyridinecarboxaldehyde (2‐PC) derivatives is proposed as an operationally simple method to selectively modify the N‐terminus of peptides and proteins at room temperature and physiological pH. The copper(II) ion activates the N‐terminal amino acids by complexation with an imine of the N‐terminal amino acid and 2‐PCs, realizing the selective formation of the nucleophilic intermediate at the N‐terminus. This results in a stable carbon‐carbon bond between the 2‐PCs and the α‐carbon of various N‐terminal amino acids. The reaction is applied to four different proteins, including biopharmaceuticals such as filgrastim and trastuzumab. The modified trastuzumab retains the human epidermal growth factor receptor 2 recognition activity. [ABSTRACT FROM AUTHOR]

Cupin proteins share a double‐stranded β‐helix fold, form one of the largest protein superfamilies, and possess remarkable functional diversity. They usually exist in homooligomeric states. Goss and co‐workers recently reported that the cupin protein Pac13, which is a dehydratase that mediates the formation of the 3′‐deoxy nucleoside of pacidamycins, is an unusual small monomer. However, a careful analysis of the biophysical and structural data provided by the authors suggests that Pac13 is in fact a homodimer, similar to many other cupin proteins. [ABSTRACT FROM AUTHOR]

A method for the estimation of coordinates of atoms in proteins from coarse‐grained geometry by simple analytical formulas (ESCASA), for use in nuclear‐magnetic‐resonance (NMR) data‐assisted coarse‐grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side‐chain Hβ protons, given the Cα‐trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high‐resolution non‐homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR‐determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton–proton distances of the NMR‐determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all‐atom‐chain reconstruction algorithm and to the 0.12 Å standard deviation of the average‐structure proton–proton distance of NMR‐determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse‐grained molecular dynamics. [ABSTRACT FROM AUTHOR]

Consumers' preference to have a healthy eating pattern has led to an increasing demand for more nutrient‐dense and healthier plant‐based foods. Pulse proteins are exceptional quality ingredients with potential nutritional benefits, and might act as health‐promoting agents for addressing the new‐generation foods. However, the utilization of pulse protein in foods has been hampered by its relatively poor functionality and unpleasant flavor. Protein structure modification has been proved to be a useful means to improve the functionality and flavor profile of pulse protein. This paper begins with a brief introduction of hierarchical structure of pulse protein materials to better understand the structure characteristics. A comprehensive review is presented on the current techniques including chemical and enzymatic modifications and molecular breeding on pulse protein structure and functionality/flavor. The mechanism and the limitations and the toxicological concerns of these approaches are discussed. We conclude that understanding protein structure‒functionality relationship is extremely valuable in tailoring proteins for specific functional outcomes and expanding the availability of pulse proteins. Furthermore, selective protein modification is a valuable in‐depth toolkit for generating novel protein constructs with preferable functional attributes and flavor profiles. Innovative structure modification with special focus on the molecular basis for the exquisite protein designs is a pillar of pulse protein access to the desired functionality. [ABSTRACT FROM AUTHOR]

Summary: Advanced structures of food proteins are maintained by many forces such as hydrophobic activities, electrostatic interaction, and disulphide bond interaction, which can affect their functional characteristics to a certain extent. Therefore, many approaches have been utilised to improve functional characteristics of food proteins. pH‐shift process refers to the method that food proteins are treated under extreme alkaline or acid conditions followed by adjusting pH to isoelectric point or neutral pH. Many studies have showed that pH‐shift process can significantly affect the functional characteristics of food proteins, for example emulsifying activities, forming property, solubility and water/oil adsorption ability. pH‐shift process has been utilised to recover protein isolates from many sources including fish, fish by‐products, meat processing products. Many researches have indicated that the functional and physicochemical characteristics of recovered protein isolates are significantly influenced by pH‐shift process. In this paper, the latest studies regarding the functional and physicochemical characteristics of proteins treated or recovered through pH‐shift process, and potential applications of obtained protein isolates in the production of the hydrolysates or used as a delivery system were reviewed. [ABSTRACT FROM AUTHOR]

Proteopedia (proteopedia.org) is an open resource to explore the structure–function relationship of proteins and other biomolecules. This guide provides practical advice on how to incorporate Proteopedia into teaching the structure and function of proteins and other biomolecules. For 11 activities, we discuss desired outcomes, setting expectations, preparing students for the tasks, using resources within Proteopedia, and evaluating student work. We point out features of Proteopedia that make it especially suitable for teaching and give examples of how to avoid common pitfalls. [ABSTRACT FROM AUTHOR]

Structure‐determination methods are needed to resolve the atomic details that underlie protein function. X‐ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro‐electron diffraction and single‐particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular‐weight threshold required for single‐particle reconstruction. Cryo‐electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure‐determination methods. Here, a data‐processing scheme is presented that combines routines from X‐ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image‐processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade‐off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure. [ABSTRACT FROM AUTHOR]

PII proteins are ubiquitous signaling proteins that are involved in the regulation of the nitrogen/carbon balance in bacteria, archaea, and some plants and algae. Signal transduction via PII proteins is modulated by effector molecules and post‐translational modifications in the PII T‐loop. Whereas the binding of ADP, ATP and the concomitant binding of ATP and 2‐oxoglutarate (2OG) engender two distinct conformations of the T‐loop that either favor or disfavor the interaction with partner proteins, the structural consequences of post‐translational modifications such as phosphorylation, uridylylation and adenylylation are far less well understood. In the present study, crystal structures of the PII protein GlnK from Corynebacterium glutamicum have been determined, namely of adenylylated GlnK (adGlnK) and unmodified unadenylylated GlnK (unGlnK). AdGlnK has been proposed to act as an inducer of the transcription repressor AmtR, and the adenylylation of Tyr51 in GlnK has been proposed to be a prerequisite for this function. The structures of unGlnK and adGlnK allow the first atomic insights into the structural implications of the covalent attachment of an AMP moiety to the T‐loop. The overall GlnK fold remains unaltered upon adenylylation, and T‐loop adenylylation does not appear to interfere with the formation of the two major functionally important T‐loop conformations, namely the extended T‐loop in the canonical ADP‐bound state and the compacted T‐loop that is adopted upon the simultaneous binding of Mg‐ATP and 2OG. Thus, the PII‐typical conformational switching mechanism appears to be preserved in GlnK from C. glutamicum, while at the same time the functional repertoire becomes expanded through the accommodation of a peculiar post‐translational modification. [ABSTRACT FROM AUTHOR]

The exponential increase in protein structures deposited in the Protein Data Bank (PDB) has resulted in the elucidation of most, if not all, protein folds, thus making molecular replacement (MR) the most frequently used method for structure determination. A survey of the PDB shows that most of the structures determined by molecular replacement contain less than ten molecules in the asymmetric unit and that it is predominantly virus and ribosome structures that contain more than 20 molecules in the asymmetric unit. While the success of the MR method depends on several factors, such as the homology and the size of an input model, it is also a well known fact that this method can become significantly difficult in cases with a large number of molecules in the asymmetric unit, higher crystallographic symmetry and tight packing. In this paper, five representative structures containing 16-18 homomeric molecules in the asymmetric unit and the strategies that have been used to solve these structures are described. The difficulties faced and the lessons learned from these structure-determination efforts will be useful for selected and similar future situations with a large number of molecules in the asymmetric unit. [ABSTRACT FROM AUTHOR]

Prions are proteins that cause a group of invariably fatal neurodegenerative diseases, one of the most known being bovine spongiform encephalopathy. The three‐dimensional structure of PrPSc, the altered isoform of the prion protein, has not been fully elucidated yet, and studies on prion conversion mechanisms must rely on hypothetical β‐rich structures. Experimental and computational studies indicate that the use of low pH is capable to produce a gain of β‐structure content in the otherwise unstructured N‐terminal region. These in silico studies have used different PrP fragments from distinct organisms, and with different lengths and simulation protocols, making it difficult to identify the influence of the force fields on the formation of such structures. Here, we performed a systematic study of the influence of six well‐established force fields (GROMOS96 53a6, GROMOS96 43a1, AMBER99SB, AMBER99SB‐ILDN, CHARMM27, and OPLS‐AA/L) on the process of structural conversion of the Syrian hamster cellular prion protein simulated at acidic and neutral pH. From our analysis, we observe a strong dependence of the results with the different force fields employed. Additionally, only GROMOS96 53A6 and AMBER99SB force fields are capable to capture a high β‐sheet formation at acidic pH and adequately reproduce the neutral pH. In both cases, the β‐sheet elongation seems to be guided by the movement of the N‐terminal tail toward the N‐terminal of α‐helix HB under acidic condition. These results comprise the most wide‐ranging study to date correlating force fields to structural changes in the cellular prion protein. © 2018 Wiley Periodicals, Inc. Prions are proteins that cause a group of invariably fatal neurodegenerative diseases. The pathological isoform of the prion protein has not been fully elucidated yet, and studies on prion conversion mechanisms must rely on hypothetical β‐rich structures. The use of different force fields to investigate the structural conversion of Syrian hamster cellular prion protein simulated at acidic pH is crucial to understand which are the most relevant structural events on this biological process. [ABSTRACT FROM AUTHOR]

Protein amyloid aggregation has been widely observed to occur and plays important roles in both physiological processes and pathological diseases. Remarkably, amyloid aggregates assembled by native proteins gain a variety of different biological activities, which cannot be adopted by the unassembled protein alone. Thus, it is important to investigate the molecular basis of self-assembly of protein amyloid aggregates and how the aggregated protein structure determines its function. In the review, we firstly introduce our structural knowledge on how different amyloid proteins undergo conformational transition and assemble into amyloid aggregate, with the main focus on amyloid fibril, which is the major species of amyloid aggregate. Then, we elaborate how different structures of amyloid fibrils enable them to fulfill highly diverse functions in either physiological or pathological condition. Furthermore, we discuss the structural polymorph which is a very unique feature of amyloid fibril, and its implication in understanding the structure-function relationship of amyloid fibrils. Finally, we point out the importance of applying and integrating new approaches for deepening the structure-function study of amyloid fibrils and highlight the potential of designing amyloid fibril-based functional bio-nanomaterials for application. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate the effect of pH‐shifting on the textural and microstructural properties of mung bean starch (MBS)‐flaxseed protein (FP) composite gels. Results showed that different pH‐shifting treatments caused changes in hydrogen bond interactions and secondary structures in composite gels, leading to the formation of loose or compact gel networks. The pH 2‐shifting modified protein and starch molecules with shorter chains tended to form smaller intermolecular aggregates, resulting in the formation of a looser gel network. For pH 12‐shifting treatment, conformational change of FP caused the unfolding of protein and the exposure of more hydrophobic groups, which enhanced the hydrogen bond and hydrophobic interactions between polymers, contributing to the formation of a compact gel network. Furthermore, pH 12‐shifting improved the water‐holding capacity (WHC), storage modulus, and strength of gels, while pH 2‐treated gels exhibited lower WHC, hardness, and gumminess due to the degradation of MBS and denaturation of FP caused by extreme acid condition. These findings suggest that pH‐shifting can alter the gel properties of bi‐polymeric starch‐protein composite systems by affecting the secondary structures of proteins and the hydrogen bonding between the polymers, and provide a promising way for a wide application of FP in soft gel‐type food production. [ABSTRACT FROM AUTHOR]

Flaxseed is one of the main cultivated economic oil crops in the world, with a global output of ~3.06 million tons. Its residual meal, after oil industrial processing, is rich in protein (35%–40%). However, flaxseed protein is mainly used for feed and its processing efficiency is low. The potential for high‐value utilization of flaxseed protein is far from being excavated. Interface dominated‐colloidal systems, such as emulsions and foams, are widely available and have extensive applications in food products. Flaxseed protein possesses high contents of hydrophobic amino acids and sulfur‐containing amino acids, relatively ordered secondary structures, tunable structural properties, and acceptable interfacial behaviors. These characteristics give it the potential to effectively stabilize food emulsions and foams. By modifications of flaxseed proteins, such as physical treatment and the complexation with polysaccharides and polyphenols, their structural properties and interfacial behaviors can be regulated, therefore, leading to the enhancement of emulsifying and foaming properties. In this review article, the fractionation, composition, and structure of flaxseed protein are detailed summarized. Then, the interfacial behaviors of flaxseed protein and their control approach are highlighted. Additionally, the emulsions and foams stabilized by flaxseed protein‐based amphiphilic systems and their applications in food processing are emphasized. [ABSTRACT FROM AUTHOR]

Ts3 is an alpha scorpion toxin from the venom of the Brazilian scorpion Tityus serrulatus. Ts3 binds to the domain IV voltage sensor of voltage-gated sodium channels (Nav) and slows down their fast inactivation. The covalent structure of the Ts3 toxin is uncertain, and the structure of the folded protein molecule is unknown. Herein, we report the total chemical synthesis of four candidate Ts3 toxin protein molecules and the results of structure-activity studies that enabled us to establish the covalent structure of biologically active Ts3 toxin. We also report the synthesis of the mirror image form of the Ts3 protein molecule, and the use of racemic protein crystallography to determine the folded (tertiary) structure of biologically active Ts3 toxin by X-ray diffraction. [ABSTRACT FROM AUTHOR]

The quality of protein crystals is an important parameter for structural determination with X-ray crystallography. Indeed, a prerequisite for obtaining high-resolution diffraction data is that the crystals be of sufficient quality. However, obtaining high-quality protein crystals is a well known bottleneck to protein structural determination that remains a difficult task. In this paper, it is demonstrated that recrystallization can be an effective method of improving the quality of protein crystals. Five proteins, lysozyme, proteinase K, concanavalin A, thaumatin and catalase, were used for this investigation, and the crystal quality of these proteins was examined using X-ray diffraction before and after recrystallization. Comparisons of the crystals before and after recrystallization verified that recrystallization not only enhanced the morphology of the crystals but also improved crystal quality. Therefore, it is proposed that recrystallization might be a useful alternative method for obtaining protein crystals with enhanced diffraction. [ABSTRACT FROM AUTHOR]

Current demand of consumers for healthy and sustainable food products has led the industry to search for different sources of plant protein isolates and concentrates. Legumes represent an excellent nonanimal protein source with high‐protein content. Legume species are distributed in a wide range of ecological conditions, including regions with drought conditions, making them a sustainable crop in a context of global warming. However, their use as human food is limited by the presence of antinutritional factors, such as protease inhibitors, lectins, phytates, and alkaloids, which have adverse nutritional effects. Antitechnological factors, such as fiber, tannins, and lipids, can affect the purity and protein extraction yield. Although most are removed or reduced during alkaline solubilization and isoelectric precipitation processes, some remain in the resulting protein isolates. Selection of appropriate legume genotypes and different emerging and sustainable facilitating technologies, such as high‐power ultrasound, pulsed electric fields, high hydrostatic pressure, microwave, and supercritical fluids, can be applied to increase the removal of unwanted compounds. Some technologies can be used to increase protein yield. The technologies can also modify protein structure to improve digestibility, reduce allergenicity, and tune technological properties. This review summarizes recent findings regarding the use of emerging technologies to obtain high‐purity protein isolates and the effects on techno‐functional properties and health. [ABSTRACT FROM AUTHOR]

Coarse‐grained normal mode analyses of protein dynamics rely on the idea that the geometry of a protein structure contains enough information for computing its fluctuations around its equilibrium conformation. This geometry is captured in the form of an elastic network (EN), namely a network of edges between its residues. The normal modes of a protein are then identified with the normal modes of its EN. Different approaches have been proposed to construct ENs, focusing on the choice of the edges that they are comprised of, and on their parameterizations by the force constants associated with those edges. Here we propose new tools to guide choices on these two facets of EN. We study first different geometric models for ENs. We compare cutoff‐based ENs, whose edges have lengths that are smaller than a cutoff distance, with Delaunay‐based ENs and find that the latter provide better representations of the geometry of protein structures. We then derive an analytical method for the parameterization of the EN such that its dynamics leads to atomic fluctuations that agree with experimental B‐factors. To limit overfitting, we attach a parameter referred to as flexibility constant to each atom instead of to each edge in the EN. The parameterization is expressed as a non‐linear optimization problem whose parameters describe both rigid‐body and internal motions. We show that this parameterization leads to improved ENs, whose dynamics mimic MD simulations better than ENs with uniform force constants, and reduces the number of normal modes needed to reproduce functional conformational changes. [ABSTRACT FROM AUTHOR]

BACKGROUND: Channel catfish farming is very important aquaculture industry in the southern states of the USA. However, huge amounts of by-products are generated from catfish fillet-processing. The by-products (mostly heads and bone frames) are excellent sources of proteins. Currently, catfish by-product has little value, and is regarded as a 'waste', which if not utilized properly could cause serious environmental pollution. Therefore, to find a way to utilize those by-products is critical for the economy of aquaculture. METHOD: Protein isolates were extracted from the mixture of catfish by-products (heads and frames) under different alkaline conditions (pH 7.5-11) and made into protein gels. Secondary structures of extracted protein isolates were studied. Microbial transglutaminase (MTGase, 0-4 U g-1 proteins) was incorporated to improve gel structure. Gelling, physicochemical, textural and thermal properties of protein gels treated with/without MTGase were investigated. Protein pattern changes of MTGasetreated protein gels were studied and the microstructure of the protein gels was analyzed. RESULTS: Alpha-helicity of protein isolates made at pH 11 was 21.5% lower than that extracted at pH 8.5. Storage modulus (G0) of protein gel decreased with increasing extraction pH (pH > 9) of the corresponding protein isolate. MTGase treatment exhibited significant effects on denaturation temperature and enthalpy of protein gels. Excessive MTGase (>2 U g-1) could weaken the gel structure. CONCLUSION: Protein isolates can be extracted from catfish by-products and made into protein gels, which are a value-added product. [ABSTRACT FROM AUTHOR]

Human guanylate‐binding protein 1 (hGBP‐1) shows a dimer‐induced acceleration of the GTPase activity yielding GDP as well as GMP. While the head‐to‐head dimerization of the large GTPase (LG) domain is well understood, the role of the rest of the protein, particularly of the GTPase effector domain (GED), in dimerization and GTP hydrolysis is still obscure. In this study, with truncations and point mutations on hGBP‐1 and by means of biochemical and biophysical methods, we demonstrate that the intramolecular communication between the LG domain and the GED (LG:GED) is crucial for protein dimerization and dimer‐stimulated GTP hydrolysis. In the course of GTP binding and γ‐phosphate cleavage, conformational changes within hGBP‐1 are controlled by a chain of amino acids ranging from the region near the nucleotide‐binding pocket to the distant LG:GED interface and lead to the release of the GED from the LG domain. This opening of the structure allows the protein to form GED:GED contacts within the dimer, in addition to the established LG:LG interface. After releasing the cleaved γ‐phosphate, the dimer either dissociates yielding GDP as the final product or it stays dimeric to further cleave the β‐phosphate yielding GMP. The second phosphate cleavage step, that is, the formation of GMP, is even more strongly coupled to structural changes and thus more sensitive to structural restraints imposed by the GED. Altogether, we depict a comprehensive mechanism of GTP hydrolysis catalyzed by hGBP‐1, which provides a detailed molecular understanding of the enzymatic activity connected to large structural rearrangements of the protein. Database: Structural data are available in RCSB Protein Data Bank under the accession numbers: 1F5N, 1DG3, 2B92. [ABSTRACT FROM AUTHOR]

Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved inter‐residue contact prediction, contact‐based structure prediction has gradually reached the performance ceiling. New methods have been proposed to predict the inter‐residue distance, but unanimously by simplifying the real‐valued distance prediction into a multiclass classification problem. Here, a lightweight regression‐based distance prediction method is shown, which adopts the generative adversarial network to capture the delicate geometric relationship between residue pairs and thus could predict the continuous, real‐valued inter‐residue distance rapidly and satisfactorily. The predicted residue distance map allows quick structure modeling by the CNS suite, and the constructed models approach the same level of quality as the other state‐of‐the‐art protein structure prediction methods when tested on CASP13 targets. Moreover, this method can be used directly for the structure prediction of membrane proteins without transfer learning. [ABSTRACT FROM AUTHOR]

Molecular chaperones are diverse families of proteins that play key roles in protein homeostasis. They assist the folding of client proteins or prevent them from irreversible aggregation under stress conditions. Diverse chaperone families contribute to different aspects of protein homeostasis by interacting with a wide range of client proteins. Despite the vital roles of chaperones in cell survival, the molecular mechanisms underlying chaperone functions remain elusive, due to the non‐specificity of chaperone‐client interactions and the intrinsic flexibility of the clients. Our understanding of the chaperone functional mechanisms, especially regarding chaperone‐client interactions, has greatly expanded in recent years, thanks to the significant contribution from various NMR studies. Solution NMR methods have unique advantages in characterizing disordered protein structures, detecting weak and non‐specific interactions, and probing conformational dynamics of proteins and protein complexes, etc., and therefore are especially powerful in the studies of chaperone structure‐function relationships. In this review, we summarize some of the current knowledge of molecular chaperones, with emphasis on common features of chaperone‐client interactions and examples on a number of specific systems in which solution NMR methods were used to provide essential insights into their functional mechanisms. [ABSTRACT FROM AUTHOR]

Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron‐sulfur‐oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox‐titrated samples. Both proteins contain a [4Fe‐4S]‐cluster as well as a [4Fe‐2O‐2S]‐hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry‐based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S‐nitrosylation in bacteria. [ABSTRACT FROM AUTHOR]

15N R1ρ relaxation experiments in solid-state NMR spectroscopy are sensitive to timescales and amplitudes of internal protein motions in the hundreds of nano- to microsecond time window, which is difficult to probe by solution-state NMR spectroscopy. By using 15N R1ρ relaxation experiments, a simplified approach to detect low microsecond protein dynamics is described and residue-specific correlation times are determined from the ratio of 15N R1ρ rate constants at different magic angle spinning frequencies. Microcrystalline ubiquitin exhibits small-amplitude dynamics on a timescale of about 1 μs across the entire protein, and larger amplitude motions, also on the 1 μs timescale, for several sites, including the β1-β2 turn and the N terminus of the α helix. According to the analysis, the microsecond protein backbone dynamics are of lower amplitude than that concluded in previous solid-state NMR spectroscopy studies, but persist across the entire protein with a rather uniform timescale of 1 μs. [ABSTRACT FROM AUTHOR]

NMR is a powerful tool for studying structural details of protein/peptide complexes exhibiting weak to medium binding ( KD > 10 μ m). However, it has been assumed that intermolecular nuclear Overhauser effect ( NOE) interactions are difficult to observe in such complexes. We demonstrate that intermolecular NOEs can be revealed by combining the 13C-edited/13C-filtered experiment with the transferred NOE effect ( TRNOE). Due to the TRNOE phenomenon, intermolecular NOE cross peaks are characterized by both the chemical shifts (CSs) of the protein protons and the average CSs of the peptide protons, which are dominated by the CSs of the protons of the free peptide. Previously, the TRNOE phenomenon was used almost exclusively to investigate the conformation of small ligands bound to large biomolecules. Here, we demonstrate that TRNOE can be extended to enable the study of intermolecular interactions in small- and medium-sized protein complexes. We used the 13C-edited/13C-filtered TRNOE experiment to study the interactions of the chemokine regulated upon activation, normal T cell, expressed and secreted ( RANTES) with a 27-residue peptide, containing two sulfotyrosine residues, representing the N-terminal segment of the CCR5 receptor ((Nt- CCR5(1-27). The TRNOE phenomenon led to more than doubling of the signal-to-noise ratios ( SNRs) for the intermolecular NOEs observed in the 13C-edited/13C-filtered experiment for the 11.5-kDa monomeric RANTES/Nt- CCR5(1-27) complex. An even better improvement in the SNR was achieved with dimeric Nt- CCR5(1-27)/ RANTES (23 kDa), especially in comparison with the spectra measured with a 1 : 1 protein to peptide ratio. In principle, the isotope-edited/isotope-filtered TRNOE spectrum can discern all intermolecular interactions involving nonexchangeable protons in the complex. [ABSTRACT FROM AUTHOR]

To explore the influence of nearest neighbors on conformational biases in unfolded peptides, we combined vibrational and 2D NMR spectroscopy to obtain the conformational distributions of selected 'GxyG' host-guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y=A, K, L, V. Large changes of conformational propensities were observed due to nearest-neighbor interactions, at variance with the isolated pair hypothesis. We found that protonated aspartic acid and serine lose their above-the-average preference for turn-like structures in favor of polyproline II (pPII) populations in the presence of neighbors with bulky side chains. Such residues also decrease the above-the-average pPII preference of alanine. These observations suggest that the underlying mechanism involves a disruption of the hydration shell. Thermodynamic analysis of 3 J(HN,Hα) ( T) data for each x,y residue reveals that modest changes in the conformational ensemble masks larger changes of enthalpy and entropy governing the pPII↔β equilibrium indicating a significant residue dependent temperature dependence of the peptides' conformational ensembles. These results suggest that nearest-neighbor interactions between unlike residues act as conformational randomizers close to the enthalpy-entropy compensation temperature, eliminating intrinsic biases in favor of largely balanced pPII/β dominated ensembles at physiological temperatures. [ABSTRACT FROM AUTHOR]

Mammalian metallothioneins are cysteine rich metal-binding proteins comprising, when fully metalated, two metal-binding domains: the α-domain binds with ${{\rm M}{{{\rm II}\hfill \atop 4\hfill}}}$S [ABSTRACT FROM AUTHOR]

The analyte signal enhancements of polymers and proteins were investigated using ionic liquid (IL) matrix-enhanced SIMS. The molecular weight of the polymer does not play a significant role in determining the magnitude of the n-mer and oligomer ion intensity enhancements. The analyte ion intensities enhancements are strongly dependent on the chemistry of the polymer side and terminal groups. Further, it was observed that ILs based on the matrix-assisted laser desorption/ionization matrix 2,5 dihydroxybenzoic acid were the most effective matrices. The molecular ion intensity enhancements of peptides including bradykinin were also investigated. Using bradykinins with different terminal amino acids, it is observed that molecular ion intensities are significantly enhanced using IL matrices if the N or C terminal amino acid can accept (or donate) a proton. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]