Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures

Occurrence and accommodation of charged amino acid residues in proteins that are structurally equivalent to buried non-polar residues in homologues have been investigated. Using a dataset of 1,852 homologous pairs of crystal structures of proteins available at 2A or better resolution, 14,024 examples of apolar residues in the structurally conserved regions replaced by charged residues in homologues have been identified. Out of 2,530 cases of buried apolar residues, 1,677 of the equivalent charged residues in homologues are exposed and the rest of the charged residues are buried. These drastic substitutions are most often observed in homologous protein pairs with low sequence identity (<30%) and in large protein domains (>300 residues). Such buried charged residues in the large proteins are often located in the interface of sub-domains or in the interface of structural repeats, Beyond 7A of residue depth of buried apolar residues, or less than 4% of solvent accessibility, almost all the substituting charged residues are buried. It is also observed that acidic sidechains have higher preference to get buried than the positively charged residues. There is a preference for buried charged residues to get accommodated in the interior by forming hydrogen bonds with another sidechain than the main chain. The sidechains interacting with a buried charged residue are most often located in the structurally conserved regions of the alignment. About 50% of the observations involving hydrogen bond between buried charged sidechain and another sidechain correspond to salt bridges. Among the buried charged residues interacting with the main chain, positively charged sidechains form hydrogen bonds commonly with main chain carbonyls while the negatively charged residues are accommodated by hydrogen bonding with the main chain amides. These carbonyls and amides are usually located in the loops that are structurally variable among homologous proteins.     

Predicting amino acid residues responsible for enzyme specificity solely from protein sequences

We describe a general, modular method for developing protocols to identify the amino acid residues that most likely define the division of a protein superfamily into two subsets. As one possibility, we use PROBE to gather superfamily members and perform an ungapped alignment. We then use a modified BLOSUM62 substitution matrix to determine the discriminating power of each column of aligned residues. The overall method is particularly useful for predicting amino acids responsible for substrate or binding specificity when no structures are available. We apply our method to three pairs of protein classes in three different superfamilies, and present our results, some of which have been experimentally verified. This approach may accelerate the elucidation of enzymic substrate specificity, which is critical for both mechanistic insights into biocatalysis and ultimate application.     

Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues

The structural organization of the B1 domain of streptococcal protein G (PGA) has been probed using molecular dynamics simulations, with a particular emphasis on the role of the solvent exposed Ile6 residue. In addition to the native protein (WT-PGA), three single-mutants (I6G-PGA, I6F-PGA, and I6T-PGA), one double-mutant (I6T,T53G-PGA), and three isolated peptide fragments (corresponding to the helix and the two beta-hairpins) were studied in the presence of explicit water molecules. Comparative analysis of the various systems showed that the level of perturbation was directly related to the hydrophobicity and the size of the side chain of residue 6, the internal rigidity of the proteins decreasing in the order I6T-PGA > I6G-PGA > WT-PGA > I6F-PGA. The results emphasized the importance of residue 6 in controlling both the integrity of the sheet's surface and the orientation of the helix in relation to the sheet by modulation of surface/core interactions. The effects of mutations were delocalized across the structure, and glycine residues, in particular, absorbed most of the introduced strain. A qualitative structural decomposition of the native fold into elementary building-blocks was achieved using principal component analysis and mechanical response matrices. Within this framework, internal motions of the protein were described as coordinated articulations of these structural units, mutations affecting mostly the amplitude of the motions rather than the structure/location of the building-blocks. Analysis of the isolated peptidic fragments suggested that packing did not play a determinant role in defining the elementary building-blocks, but that chain topology was mostly responsible.     

Potential for biochar carbon sequestration from crop residues: A global spatially explicit assessment

Global warming necessitates urgent action to reduce carbon dioxide (CO₂) emissions and remove CO₂ from the atmosphere. Biochar, a type of carbonized biomass which can be produced from crop residues (CRs), offers a promising solution for carbon dioxide removal (CDR) when it is used to sequester photosynthetically fixed carbon that would otherwise have been returned to atmospheric CO₂ through respiration or combustion. However, high-resolution spatially explicit maps of CR resources and their capacity for climate change mitigation through biochar production are currently lacking, with previous global studies relying on coarse (mostly country scale) aggregated statistics. By developing a comprehensive high spatial resolution global dataset of CR production, we show that, globally, CRs generate around 2.4 Pg C annually. If 100% of these residues were utilized, the maximum theoretical technical potential for biochar production from CRs amounts to 1.0 Pg C year⁻¹ (3.7 Pg CO₂e year⁻¹). The permanence of biochar differs across regions, with the fraction of initial carbon that remains after 100 years ranging from 60% in warm climates to nearly 100% in cryosols. Assuming that biochar is sequestered in soils close to point of production, approximately 0.72 Pg C year⁻¹ (2.6 Pg CO₂e year⁻¹) of the technical potential would remain sequestered after 100 years. However, when considering limitations on sustainable residue harvesting and competing livestock usage, the global biochar production potential decreases to 0.51 Pg C year⁻¹ (1.9 Pg CO₂e year⁻¹), with 0.36 Pg C year⁻¹ (1.3 Pg CO₂e year⁻¹) remaining sequestered after a century. Twelve countries have the technical potential to sequester over one fifth of their current emissions as biochar from CRs, with Bhutan (68%) and India (53%) having the largest ratios. The high-resolution maps of CR production and biochar sequestration potential provided here will provide valuable insights and support decision-making related to biochar production and investment in biochar production capacity.     

Involvement of lysine and arginine residues in the binding of yeast ribosomal protein YL3 to 5S RNA

The contribution of lysine and arginine residues to the formation of yeast ribonucleoprotein complex 5S RNA. protein YL3 has been investigated by determining the effects on complex formation of modification with chemical reagents specific for either lysine or arginine. Treatment of protein YL3 with acetic anhydride, malefic anhydride or phenylglyoxal is accompanied by loss of its capacity to bind to 5S RNA. This effect is accomplished by modification with phenylglyoxal of only 3 arginine residues per YL3 molecule. In contrast, a large number of protein YL3 amino groups [16] must be modified by acetic anhydride to prevent complex formation.     

Role of conserved residues in structure and stability: tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily

Serum retinol binding protein (RBP) is a member of the lipocalin family, proteins with up-and-down beta-barrel folds, low levels of sequence identity, and diverse functions. Although tryptophan 24 of RBP is highly conserved among lipocalins, it does not play a direct role in activity. To determine if Trp24 and other conserved residues have roles in stability and/or folding, we investigated the effects of conservative substitutions for the four tryptophans and some adjacent residues on the structure, stability, and spectroscopic properties of apo-RBP. Crystal structures of recombinant human apo-RBP and of a mutant with substitutions for tryptophans 67 and 91 at 1.7 A and 2.0 A resolution, respectively, as well as stability measurements, indicate that these relatively exposed tryptophans have little influence on structure or stability. Although Trp105 is largely buried in the wall of the beta-barrel, it can be replaced with minor effects on stability to thermal and chemical unfolding. In contrast, substitutions of three different amino acids for Trp24 or replacement of Arg139, a conserved residue that interacts with Trp24, lead to similar large losses in stability and lower yields of native protein generated by in vitro folding. The results and the coordinated nature of natural substitutions at these sites support the idea that conserved residues in functionally divergent homologs have roles in stabilizing the native relative to misfolded structures. They also establish conditions for studies of the kinetics of folding and unfolding by identifying spectroscopic signals for monitoring the formation of different substructures.     

华东三省转Bt基因棉花种植对边际水体中Cry1Ab/c蛋白残留的影响

为调查转基因棉花种植地区边际水体中的Cry1Ab/c蛋白残留情况, 在华东地区的山东、江苏、安徽三省棉田设置采样点, 连续3年在棉花的花铃期和收获季节, 对棉区地块内部及周围边际水体随机采样, 进行去杂及纯化处理后, 利用ELISA (酶联免疫吸附测定)方法检测水样中的Cry1Ab/c蛋白含量。结果表明: (1)在花铃期和收获季前后两周, 分别在5个布控点边际水体中检出Cry1Ab/c蛋白, 其中1个布控点阳性蛋白残留浓度最高达到0.4 ppb, 另外4个布控点检测出的阳性蛋白量均在0.04 ppb以下; (2)距离棉田越近, 蛋白检出阳性率越高, 其中棉田内水渠阳性率为13.3%; (3)连续种植时间超过7年的田地周围水体中蛋白阳性率为12.4%。在所有取样时间点中, 与花铃期相比, 收获季更容易检测到阳性结果。这表明在转基因棉花产区, 应在收获季进行适当的指导和监控, 以预防和降低转基因棉花中Cry1Ab/c蛋白对边际水体的潜在影响。     

Interatomic potentials and solvation parameters from protein engineering data for buried residues

Van der Waals (vdW) interaction energies between different atom types, energies of hydrogen bonds (H-bonds), and atomic solvation parameters (ASPs) have been derived from the published thermodynamic stabilities of 106 mutants with available crystal structures by use of an originally designed model for the calculation of free-energy differences. The set of mutants included substitutions of uncharged, inflexible, water-inaccessible residues in alpha-helices and beta-sheets of T4, human, and hen lysozymes and HI ribonuclease. The determined energies of vdW interactions and H-bonds were smaller than in molecular mechanics and followed the "like dissolves like" rule, as expected in condensed media but not in vacuum. The depths of modified Lennard-Jones potentials were -0.34, -0.12, and -0.06 kcal/mole for similar atom types (polar-polar, aromatic-aromatic, and aliphatic-aliphatic interactions, respectively) and -0.10, -0.08, -0.06, -0.02, and nearly 0 kcal/mole for different types (sulfur-polar, sulfur-aromatic, sulfur-aliphatic, aliphatic-aromatic, and carbon-polar, respectively), whereas the depths of H-bond potentials were -1.5 to -1.8 kcal/mole. The obtained solvation parameters, that is, transfer energies from water to the protein interior, were 19, 7, -1, -21, and -66 cal/moleA(2) for aliphatic carbon, aromatic carbon, sulfur, nitrogen, and oxygen, respectively, which is close to the cyclohexane scale for aliphatic and aromatic groups but intermediate between octanol and cyclohexane for others. An analysis of additional replacements at the water-protein interface indicates that vdW interactions between protein atoms are reduced when they occur across water.     

植物源过敏蛋白

植物过敏原是最普遍的一类过敏原,也是与人类关系最密切的一类过敏原。本文简单介绍了植物中蛋白质类过敏原的种类、特性及低敏植物性食品开发等研究新进展。     

Prediction of protein domain boundaries from statistics of appearance of amino acid residues

A database of 452 two-domain proteins with less than 25% homology was constructed. One half of the database was used to obtain statistics on the appearance of amino acid residues at domain boundaries. Small and hydrophilic residues (proline, glycine, asparagine, glutamic acid, arginine, etc.) occurred more often at domain boundaries than in total proteins. Hydrophobic residues (tryptophan, methionine, phenylalanine, etc.) were rarer at domain boundaries than in total proteins. Probability scales of amino acid appearance in boundary-flanking regions were constructed with these statistics and used to predict the domain boundaries in proteins of the other half of the database. The probability scale obtained by averaging the appearance of amino acids over an 8-residue region (±4 residues from the real domain boundaries) yielded the best results: domain boundaries were predicted within 40 residues of the real boundary in 57% of proteins and within 20 residues of the real boundary in 41% of proteins. The probability scale was used to predict the domain boundaries in proteins with unknown structures (CASP6).     

Microbiota and food residues including possible evidence of pre‐mammalian hair in Upper Permian coprolites from Russia

Coprolites (fossil faeces) provide direct evidence on the diet of its producer and unique insights on ancient food webs and ecosystems. We describe the contents of seven coprolites, collected from the Late Permian Vyazniki site of the European part of Russia. Two coprolite morphotypes (A, B) contain remains of putative bacteria, cyanobacteria, fungi, protists, invertebrate eggs, arthropod elements, undigested bone and tooth fragments, fish scales and elongated hair‐like structures with hollow interiors. Content, size and shape of the coprolites together with the associated body fossil record suggest that the most probable scat‐producers were carnivorous tetrapods; the bone‐rich morphotype A reveals short food retention time and a fast metabolism and is therefore assigned to therapsid carnivores whereas morphotype B with rarer and degraded bones are assigned to archosauromorphs or other non‐therapsid carnivores. The general coprolite matrix contains abundant micron‐sized spheres and thin‐walled vesicles which are interpreted as oxide and phosphatic pseudomorphs after microbial cells. From analyses of the undigested bones, we infer that they represent remains of actinopterygian fish, a therapsid and unrecognizable parts of amphibians and/or reptiles. Additionally, hair‐like structures found in one coprolite specimen occur as diagenetically altered (oxide‐replaced) structures and moulds (or partly as pseudomorphs) in a microcrystalline carbonate‐fluoride‐bearing calcium phosphate. This suggests that the latest Permian therapsids probably were equipped with hair‐like integument or hairsuit. If true, this is by far the oldest evidence of this mammalian character in the stem group of mammals.     

Proline and lysine residues provide modulatory switches in amyloid formation: Insights from prion protein

Amyloidogenic proteins have an increased propensity to reorganize into the highly structured, β sheet rich structures that characterize amyloid. The probability of attaining these highly structured assemblies is influenced by multiple factors, including amino acid composition and environmental conditions. Evolutionary selection for amino acid sequences that prevent amyloid formation could further modulate amyloid-forming propensity. Indeed, we have recently identified specific proline and lysine residues, contained within a highly conserved central region of prion protein (PrP), that impede PrP amyloid formation in vitro. These prolines are mutated in certain forms of the human familial genetic disease, Gerstmann-Straüssler-Schneiker (GSS) syndrome. Here, I discuss the influence of these proline and lysine residues on PrP amyloid formation and how such anti-amyloidogenic primary amino acid sequences might be modulated to influence protein amyloidogenicity.     

Identification of catalytic residues from protein structure using support vector machine with sequence and structural features

Identification of catalytic residues can provide valuable insights into protein function. With the increasing number of protein 3D structures having been solved by X-ray crystallography and NMR techniques, it is highly desirable to develop an efficient method to identify their catalytic sites. In this paper, we present an SVM method for the identification of catalytic residues using sequence and structural features. The algorithm was applied to the 2096 catalytic residues derived from Catalytic Site Atlas database. We obtained overall prediction accuracy of 88.6% from 10-fold cross validation and 95.76% from resubstitution test. Testing on the 254 catalytic residues shows our method can correctly predict all 254 residues. This result suggests the usefulness of our approach for facilitating the identification of catalytic residues from protein structures.     

Prostatic epithelial cells in culture: phosphorylation of protein tyrosyl residues and tyrosine protein kinase activity.

The ability of dividing canine prostatic epithelial cells in primary monolayers to phosphorylate protein tyrosyl residues was evaluated by metabolic studies performed through incorporation of [32P]-phosphate into alkali-resistant phosphoproteins and by the assay of their tyrosine protein kinase activity. The presence of sodium orthovanadate during cell incubation with [32P]-phosphate greatly enhanced the relative labelling intensity of a 44 kDa alkali-resistant phosphoprotein and the total cellular content of phosphotyrosine in proteins; in this respect, growth factors such as epidermal growth factor, insulin, and insulin-like growth factor I, and the steroids dihydrotestosterone and estradiol were inactive. When the cells were solubilized, sodium orthovanadate stimulated their tyrosine protein kinase activity and inhibited their phosphotyrosine phosphatase activity. To characterize the tyrosine protein kinase of these cultured cells, conditions for optimal activity were established using the substrate poly [Glu80Na, Tyr20]. The subcellular localization of the enzyme was determined upon cell fractionation: 88% of the kinase activity was associated with the particulate fraction and 30% of this activity was partially solubilized with 0.5% Triton X-100; this solubilization was improved to 83% in the presence of 0.25 M KCI. The enzyme directly solubilized from prostatic cells with Triton X-100 (38% of activity) mainly catalyzed the alkali-resistant phosphorylation of pp63, pp59, and pp44, which contained phosphotyrosine. These proteins were also phosphorylated by the major peak of kinase activity which was eluted at an apparent molecular weight of 300-350 kDa upon gel filtration.(ABSTRACT TRUNCATED AT 250 WORDS)     

Charged residues at protein interaction interfaces: unexpected conservation and orchestrated divergence

Protein-protein interactions play an essential role in the functioning of cell. The importance of charged residues and their diverse role in protein-protein interactions have been well studied using experimental and computational methods. Often, charged residues located in protein interaction interfaces are conserved across the families of homologous proteins and protein complexes. However, on a large scale, it has been recently shown that charged residues are significantly less conserved than other residue types in protein interaction interfaces. The goal of this work is to understand the role of charged residues in the protein interaction interfaces through their conservation patterns. Here, we propose a simple approach where the structural conservation of the charged residue pairs is analyzed among the pairs of homologous binary complexes. Specifically, we determine a large set of homologous interactions using an interaction interface similarity measure and catalog the basic types of conservation patterns among the charged residue pairs. We find an unexpected conservation pattern, which we call the correlated reappearance, occurring among the pairs of homologous interfaces more frequently than the fully conserved pairs of charged residues. Furthermore, the analysis of the conservation patterns across different superkingdoms as well as structural classes of proteins has revealed that the correlated reappearance of charged residues is by far the most prevalent conservation pattern, often occurring more frequently than the unconserved charged residues. We discuss a possible role that the new conservation pattern may play in the long-range electrostatic steering effect.     

Mutation of active site residues of the puromycin-sensitive aminopeptidase: conversion of the enzyme into a catalytically inactive binding protein

The active site glutamate, Glu 309, of the puromycin-sensitive aminopeptidase was mutated to glutamine, alanine, and valine. These mutants were characterized with amino acid beta-naphthylamides as substrates and dynorphin A(1-9) as an alternate substrate inhibitor. Conversion of glutamate 309 to glutamine resulted in a 5000- to 15,000-fold reduction in catalytic activity. Conversion of this residue to alanine caused a 25,000- to 100,000-fold decrease in activity, while the glutamate to valine mutation was the most dramatic, reducing catalytic activity 300,000- to 500,000-fold. In contrast to the dramatic effect on catalysis, all three mutations produced relatively small (1.5- to 4-fold) effects on substrate binding affinity. Mutation of a conserved tyrosine, Y394, to phenylalanine resulted in a 1000-fold decrease in k(cat), with little effect on binding. Direct binding of a physiological peptide, dynorphin A(1-9), to the E309V mutant was demonstrated by gel filtration chromatography. Taken together, these data provide a quantitative assessment of the effect of mutating the catalytic glutamate, show that mutation of this residue converts the enzyme into an inactive binding protein, and constitute evidence that this residue acts a general acid/base catalyst. The effect of mutating tyrosine 394 is consistent with involvement of this residue in transition state stabilization.     

Cyclic enterobacterial common antigen: Potential contaminant of bacterially expressed protein preparations

We have previously reported the identification of the cyclic enterobacterial common antigen (ECA(CYC)) polysaccharide in E. coli strains commonly used for heterologous protein expression (PJA Erbel et al., J. Bacteriol. 185 (2003): 1995). Following this initial report, interactions among several NMR groups established that characteristic N -acetyl signals of ECA(CYC) have been observed in (15)N-(1)H HSQC spectra of samples of various bacterially-expressed proteins suggesting that this water-soluble carbohydrate is a common contaminant. We provide NMR spectroscopic tools to recognize ECA(CYC) in protein samples, as well as several methods to remove this contaminant. Early recognition of ECA-based NMR signals will prevent time-consuming analyses of this copurifying carbohydrate.     

Butanol production from agricultural residues: Impact of degradation products on Clostridium beijerinckii growth and butanol fermentation

During pretreatment and hydrolysis of fiber-rich agricultural biomass, compounds such as salts, furfural, hydroxymethyl furfural (HMF), acetic, ferulic, glucuronic, rho-coumaric acids, and phenolic compounds are produced. Clostridium beijerinckii BA101 can utilize the individual sugars present in lignocellulosic [e.g., corn fiber, distillers dry grain solubles (DDGS), etc] hydrolysates such as cellobiose, glucose, mannose, arabinose, and xylose. In these studies we investigated the effect of some of the lignocellulosic hydrolysate inhibitors associated with C. beijerinckii BA101 growth and acetone-butanol-ethanol (ABE) production. When 0.3 g/L rho-coumaric and ferulic acids were introduced into the fermentation medium, growth and ABE production by C. beijerinckii BA101 decreased significantly. Furfural and HMF are not inhibitory to C. beijerinckii BA101; rather they have stimulatory effect on the growth of the microorganism and ABE production.     

Single-spanning membrane protein insertion in membrane mimetic systems: role and localization of aromatic residues

Membrane protein insertion in the lipid bilayer is determining for their activity and is governed by various factors such as specific sequence motifs or key amino-acids. A detailed fluorescence study of such factors is exemplified with PMP1, a small (38 residues) single-membrane span protein that regulates the plasma membrane H⁺-ATPase in yeast and specifically interacts with phosphatidylserines. Such interactions may stabilize raft domains that have been shown to contain H⁺-ATPase. Previous NMR studies of various fragments have focused on the critical role of interfacial residues in the PMP1 structure and intermolecular interactions. The C-terminal domain contains a terminal Phe (F38), a single Trp (W28) and a single Tyr (Y25) that may act together to anchor the protein in the membrane. In order to describe the location and dynamics of W28 and the influence of Y25 on protein insertion within membrane, we carried out a detailed steady-state and time-resolved fluorescence study of the synthetic G13-F38 fragment and its Tyr-less mutant, Y25L in various membrane mimetic systems. Detergent micelles are conveniently used for this purpose. We used dodecylphosphocholine (DPC) in order to compare with and complement previous NMR results. In addition, dodecylmaltoside (DM) was used so that we could apply our recently described new quenching method by two brominated analogs of DM (de Foresta et al. 2002, Eur. Biophys. J. 31:185–97). In both systems, and in the presence and absence of Y25, W28 was shown to be located below but close to the polar headgroup region, as shown by its maximum emission wavelengths (λ_max), curves for the quenching of Trp by the brominated analogs of DM and bimolecular constants for quenching (k_q) by acrylamide. Results were interpreted by comparison with calibration data obtained with fluorescent model peptides. Time-resolved anisotropy measurements were consistent with PMP1 fragment immobilization within peptide-detergent complexes. We tentatively assigned the two major Trp lifetimes to the Trp (χ₁=60° and 180°) rotamers, based on the recent lifetime–rotamer correlation proposed for model cyclic peptides (Pan and Barkley 2004, Biophys J 86:3828–35). We also analyzed the role of the hydrophobic anchor, by comparing the micelle binding of fragments of various lengths including the synthesized full-length protein and detected peculiar differences for protein interaction with the polar headgroups of DM or DPC.