Folding & design最新文献

{"title":"The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus","authors":"Zhuyan Guo ,&nbsp;D Thirumalai","doi":"10.1016/S1359-0278(97)00052-7","DOIUrl":"10.1016/S1359-0278(97)00052-7","url":null,"abstract":"<div><p><strong>Background:</strong> Recent experimental and theoretical studies have shown that several small proteins reach the native state by a nucleation-collapse mechanism. Studies based on lattice models have been used to suggest that the critical nucleus is specific, leading to the notion that the transition state may be unique. On the other hand, results of studies using off-lattice models show that the critical nuclei should be viewed as fluctuating mobile structures, thus implying non-unique transition states.</p><p><strong>Results:</strong> The microscopic underpinnings of the nucleation-collapse mechanism in protein folding are probed using minimal off-lattice models and Langevin dynamics. We consider a 46-mer continuum model which has a native <em>β</em>-barrel-like structure. The fast-folding trajectories reach the native state by a nucleation-collapse process. An algorithm based on the self-organized neural nets is used to identify the critical nuclei for a large number of rapidly folding trajectories. This method, which reduces the determination of the critical nucleus to one of ‘pattern recognition’, unambiguously shows that the folding nucleus is not unique. The only common characteristics of the mobile critical nuclei are that they are small (containing on average 15–22 residues) and are largely composed of residues near the loop regions of the molecule. The structures of the transition states, corresponding to the critical nuclei, show the existence of spatially localized ordered regions that are largely made up of residues that are close to each other. These structures are stabilized by a few long-range contacts. The structures in the ensemble of transition states exhibit a rather diverse degree of similarity to the native conformation.</p><p><strong>Conclusions:</strong> The multiplicity of delocalized nucleation regions can explain the two-state folding by a nucleation-collapse mechanism for small single-domain proteins (such as chymotrypsin inhibitor 2) and their mutants. Because there are many distinct critical nuclei, we predict that the folding kinetics of fast-folding proteins will not be drastically changed even if some of the residues in a ‘typical’ nucleus are altered.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 6","pages":"Pages 377-391"},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00052-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20354907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and mechanistic consequences of polypeptide binding by GroEL","authors":"Joseph E Coyle ,&nbsp;Joachim Jaeger ,&nbsp;Michael Groß ,&nbsp;Carol V Robinson ,&nbsp;Sheena E Radford","doi":"10.1016/S1359-0278(97)00046-1","DOIUrl":"10.1016/S1359-0278(97)00046-1","url":null,"abstract":"<div><p>The remarkable ability of the chaperonin GroEL to recognise a diverse range of non-native states of proteins constitutes one of the most fascinating molecular recognition events in protein chemistry. Recent structural studies have revealed a possible model for substrate binding by GroEL and a high-resolution image of the GroEL–GroES folding machinery has provided important new insights into our understanding of the mechanism of action of this chaperonin. Studies with a variety of model substrates reveal that the binding of substrate proteins to GroEL is not just a passive event, but can result in significant changes in the structure and stability of the bound polypeptide. The potential impact of this on the mechanism of chaperonin-assisted folding is not fully understood, but provides exciting scope for further experiment.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 6","pages":"Pages R93-R104"},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00046-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20354400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Folding α-helical membrane proteins: kinetic studies on bacteriorhodopsin","authors":"Paula J Booth","doi":"10.1016/S1359-0278(97)00045-X","DOIUrl":"10.1016/S1359-0278(97)00045-X","url":null,"abstract":"<div><p>The correct folding and assembly of proteins within biological membranes is essential for membrane biogenesis and function. In contrast to the large body of work on water-soluble protein folding, however, very little is known about how membrane proteins fold to their final structures. Recent biophysical studies on membrane-protein folding <em>in vitro</em> are beginning to shed light on this problem. In particular, the forces that the membrane lipids impose on the folding protein appear to control certain events. The seven-helix transmembrane protein bacteriorhodopsin has been the focus of much attention and kinetic studies on the folding of this protein form the basis of this review.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 6","pages":"Pages R85-R92"},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00045-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20354399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chiral N-substituted glycines can form stable helical conformations","authors":"Philippe Armand ,&nbsp;Kent Kirshenbaum ,&nbsp;Alexis Falicov ,&nbsp;Roland L Dunbrack Jr ,&nbsp;Ken A Dill ,&nbsp;Ronald N Zuckermann ,&nbsp;Fred E Cohen","doi":"10.1016/S1359-0278(97)00051-5","DOIUrl":"10.1016/S1359-0278(97)00051-5","url":null,"abstract":"<div><h3>Background:</h3><p>Short sequence-specific heteropolymers of N-substituted glycines (peptoids) have emerged as promising tools for drug discovery. Recent work on medium-length peptoids containing chiral centers in their sidechains has demonstrated the existence of stable chiral conformations in solution. In this report, we explore the conformational properties of these N<em>α</em> chiral peptoids by molecular mechanics calculations and we propose a model for the solution conformation of an octamer of (<em>S)</em>-N-(1-phenylethyl)glycine.</p></div><div><h3>Results:</h3><p>Molecular mechanics calculations indicate that the presence of N-substituents in which the N<em>α</em> carbons are chiral centers has a dramatic impact on the available backbone conformations. These results are supported by semi-empirical quantum mechanical calculations and coincide qualitatively with simple steric considerations. They suggest that an octamer of (<em>S)</em>-N-(phenylethyl)glycine should form a right-handed helix with <em>cis</em> amide bonds, similar to the polyproline type I helix. This model is consistent with circular dichroism studies of these molecules.</p></div><div><h3>Conclusions:</h3><p>Peptoid oligomers containing chiral centers in their sidechains present a new structural paradigm that has promising implications for the design of stably folded molecules. We expect that their novel structure may provide a scaffold to create heteropolymers with useful functionality.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 6","pages":"Pages 369-375"},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00051-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20354906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications","authors":"Anastassis Perrakis ,&nbsp;Christos Ouzounis ,&nbsp;Keith S Wilson","doi":"10.1016/S1359-0278(97)00040-0","DOIUrl":"10.1016/S1359-0278(97)00040-0","url":null,"abstract":"<div><p><strong>Background:</strong> Chitinase A from <em>Serratia marcescens</em> is a glycosyl hydrolase consisting of three distinct domains. The N-terminal domain (ChiN domain, amino acids 24–137) has an immunoglobulin-like fold. This ChiN domain is structurally similar to fibronectin type III domains (FnIII domains), which exist in other chitinases, but does not share any sequence similarity with them.</p><p><strong>Results:</strong> Structure comparisons of the ChiN domain and FnIII domains confirm the similar fold, but fail to establish any sequence similarity. Sequence searches and comparisons between ChiN and FnIII domain sequences show a remarkable difference between the two domains in chitinases from an evolutionary point of view. A low temperature structure of chitinase A shows that the ChiN module is flexible with respect to the catalytic body of the protein.</p><p><strong>Conclusions:</strong> We postulate that the ChiN and FnIII domains evolved independently in chitinases which share otherwise homologous catalytic domains. The flexibility of the ChiN domain, together with biochemical knowledge of the function of similar domains, leads us to propose that immunoglobulin-like folds in chitinases are involved in interactions with the chitin chain during catalysis.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 5","pages":"Pages 291-294"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00040-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20309510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The pH-dependent tertiary structure of a designed helix–loop–helix dimer","authors":"Gunnar T Dolphin ,&nbsp;Lars Baltzer","doi":"10.1016/S1359-0278(97)00043-6","DOIUrl":"10.1016/S1359-0278(97)00043-6","url":null,"abstract":"<div><p><strong>Background:</strong> <em>De novo</em> designed helix–loop–helix motifs can fold into well-defined tertiary structures if residues or groups of residues are incorporated at the helix–helix boundary to form helix-recognition sites that restrict the conformational degrees of freedom of the helical segments. Understanding the relationship between structure and function of conformational constraints therefore forms the basis for the engineering of non-natural proteins. This paper describes the design of an interhelical HisH⁺–Asp^- hydrogen-bonded ion pair and the conformational stability of the folded helix–loop–helix motif.</p><p><strong>Results:</strong> GTD-C, a polypeptide with 43 amino acid residues, has been designed to fold into a hairpin helix–loop–helix motif that can dimerise to form a four-helix bundle. The folded motif is in slow conformational exchange on the NMR timescale and has a well-dispersed ¹H NMR spectrum, a narrow temperature interval for thermal denaturation and a near-UV CD spectrum with some fine structure. The conformational stability is pH dependent with an optimum that corresponds to the pH for maximum formation of a hydrogen-bonded ion pair between HisH17⁺ in helix I and Asp27^- in helix II.</p><p><strong>Conclusions:</strong> The formation of an interhelical salt bridge is strongly suggested by the pH dependence of a number of spectroscopic probes to generate a well-defined tertiary structure in a designed helix–loop–helix motif. The thermodynamic stability of the folded motif is not increased by the formation of the salt bridge, but neighbouring conformations are destabilised. The use of this novel design principle in combination with hydrophobic interactions that provide sufficient binding energy in the folded structure should be of general use in <em>de novo</em> design of native-like proteins.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 5","pages":"Pages 319-330"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00043-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20309513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force","authors":"Aderonke Babajide ,&nbsp;Ivo L Hofacker ,&nbsp;Manfred J Sippl ,&nbsp;Peter F Stadler","doi":"10.1016/S1359-0278(97)00037-0","DOIUrl":"10.1016/S1359-0278(97)00037-0","url":null,"abstract":"<div><p><strong>Background:</strong> Many protein sequences, often unrelated, adopt similar folds. Sequences folding into the same shape thus form subsets of sequence space. The shape and the connectivity of these sets have implications for protein evolution and <em>de novo</em> design.</p><p><strong>Results:</strong> We investigate the topology of these sets for some proteins with known three-dimensional structure using inverse folding techniques. First, we find that sequences adopting a given fold do not cluster in sequence space and that there is no detectable sequence homology among them. Nevertheless, these sequences are connected in the sense that there exists a path such that every sequence can be reached from every other sequence while the fold remains unchanged. We find similar results for restricted amino acid alphabets in some cases (e.g. ADLG). In other cases, it seems impossible to find sequences with native-like behavior (e.g. QLR). These findings seem to be independent of the particular structure considered.</p><p><strong>Conclusions:</strong> Amino acid sequences folding into a common shape are distributed homogeneously in sequence space. Hence, the connectivity of the set of these sequences implies the existence of very long neutral paths on all examined protein structures. Regarding protein design, these results imply that sequences with more or less arbitrary chemical properties can be attached to a given structural framework. But we also observe that designability varies significantly among native structures. These features of protein sequence space are similar to what has been found for nucleic acids.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 5","pages":"Pages 261-269"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00037-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20203910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of the free energy spectrum of peptostreptococcal protein L","authors":"Qian Yi ,&nbsp;Michelle L Scalley ,&nbsp;Kim T Simons ,&nbsp;Sharon T Gladwin ,&nbsp;David Baker","doi":"10.1016/S1359-0278(97)00038-2","DOIUrl":"10.1016/S1359-0278(97)00038-2","url":null,"abstract":"<div><p><strong>Background:</strong> Native state hydrogen/deuterium exchange studies on cytochrome <em>c</em> and RNase H revealed the presence of excited states with partially formed native structure. We set out to determine whether such excited states are populated for a very small and simple protein, the IgG-binding domain of peptostreptococcal protein L.</p><p><strong>Results:</strong> Hydrogen/deuterium exchange data on protein L in 0–1.2 M guanidine fit well to a simple model in which the only contributions to exchange are denaturant-independent local fluctuations and global unfolding. A substantial discrepancy emerged between unfolding free energy estimates from hydrogen/deuterium exchange and linear extrapolation of earlier guanidine denaturation experiments. A better determined estimate of the free energy of unfolding obtained by global analysis of a series of thermal denaturation experiments in the presence of 0–3 M guanidine was in good agreement with the estimate from hydrogen/deuterium exchange.</p><p><strong>Conclusions:</strong> For protein L under native conditions, there do not appear to be partially folded states with free energies intermediate between that of the folded and unfolded states. The linear extrapolation method significantly underestimates the free energy of folding of protein L due to deviations from linearity in the dependence of the free energy on the denaturant concentration.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 5","pages":"Pages 271-280"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00038-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20307626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emerging themes in RNA folding","authors":"Jennifer A Doudna ,&nbsp;Elizabeth A Doherty","doi":"10.1016/S1359-0278(97)00035-7","DOIUrl":"10.1016/S1359-0278(97)00035-7","url":null,"abstract":"<div><p>RNAs, like proteins, readily form specific structures adapted for ligand binding and catalysis. Since they are composed of completely different chemical building blocks, however, RNAs and proteins necessarily use distinct strategies to assemble complex architectures. While burial of hydrophobic residues drives protein folding, the hydrophobic effect in RNA contributes primarily to the formation of secondary structure. To form tertiary structure, RNA must overcome electrostatic repulsions from the phosphate backbone. How do negatively charged double helices pack together to produce catalytic centers and ligand binding surfaces? Here, we review our understanding of the principles that underlie RNA folding based on the structural information currently available.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 5","pages":"Pages R65-R70"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00035-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20307624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a conserved hydrophobic cluster in partially folded bovine β-lactoglobulin at pH 2","authors":"Laura Ragona ,&nbsp;Francesca Pusterla ,&nbsp;Lucia Zetta ,&nbsp;Hugo L Monaco ,&nbsp;Henriette Molinari","doi":"10.1016/S1359-0278(97)00039-4","DOIUrl":"10.1016/S1359-0278(97)00039-4","url":null,"abstract":"<div><p><strong>Background:</strong> NMR studies of denaturated states, both fully unfolded and partially folded, give insight into the conformations and interactions formed during folding. Although the complete structural characterization of partially folded proteins is a very difficult task, the identification of structured subsets, such as hydrophobic clusters, is of value in understanding the structural organization of such states. Here, we report the NMR characterization, in acidic conditions (pH 2), of a well-defined hydrophobic cluster localized in the core of bovine <em>β</em>-lactoglobulin.</p><p><strong>Results:</strong> The existence of a small hydrophobic cluster present in the lipocalin protein family has been assessed on the basis of structural alignment and NMR data obtained for the partially folded bovine <em>β</em>-lactoglobulin. The presence of the cluster had been predicted identifying those residues that are highly conserved in most members of the family. An NMR study conducted at pH 2, where the protein exhibits a very stable <em>β</em>-core together with disordered regions, reveals the presence of NOEs among sidechains of 11 hydrophobic residues centered around Trp19 and pointing towards the interior of the protein. This buried cluster is found to be unusually stable at pH 2, not only at room temperature but also at 323K. Furthermore, conserved hydrophobic residues pointing towards the surface of the protein define a hydrophobic surface patch located in a groove between the strands and the helix.</p><p><strong>Conclusions:</strong> The detected buried cluster most likely plays an important role in <em>β</em>-lactoglobulin stability. The analysis of five structurally related proteins reveals that the same extended cluster is present in these structures. We propose that the buried cluster may represent the internal binding site as well and that the hydrophobic surface patch is involved in a second external binding site.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 5","pages":"Pages 281-290"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00039-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20309509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}