Folding & design最新文献_第5页

Energy strain in three-dimensional protein structures 三维蛋白质结构中的能量应变

Folding & design Pub Date : 1998-08-01 DOI: 10.1016/S1359-0278(98)00037-6

Vladimir Maiorov , Ruben Abagyan

{"title":"Energy strain in three-dimensional protein structures","authors":"Vladimir Maiorov , Ruben Abagyan","doi":"10.1016/S1359-0278(98)00037-6","DOIUrl":"10.1016/S1359-0278(98)00037-6","url":null,"abstract":"<div>Background: Steric strain in protein three-dimensional structures is related to unfavorable inter-atomic interactions. The steric strain may be a result of packing or functional requirements, or may indicate an error in the coordinates of a structure. Detailed energy functions are, however, usually considered too noisy for error detection.Results: After a short energy refinement, a full-atom, detailed energy function becomes a sensitive indicator of errors. The statistics of the energy distribution of amino acid residues in high-resolution crystal structures, represented by models with idealized covalent geometry, were calculated. The interaction energy of each residue with the whole protein structure and with the solvent was considered. Normalized deviations of amino acid residue energies from their average values were used for detecting energy-strained and, therefore, potentially incorrect fragments of a polypeptide chain. Protein three-dimensional structures of different origin (X-ray crystallography, NMR spectroscopy, theoretical models and deliberately misfolded decoys) were compared. Examples of the applications to loop and homology modeling are provided.Conclusions:Elevated levels of energy strain may point at a problematic fragment in a protein three-dimensional structure of either experimental or theoretical origin. The approach may be useful in model building and refinement, modeling by homology, protein design, folding calculations, and protein structure analysis.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 4","pages":"Pages 259-269"},"PeriodicalIF":0.0,"publicationDate":"1998-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00037-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20626460","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}

引用次数: 37

Site-selective control of the reactivity of surface-exposed histidine residues in designed four-helix-bundle catalysts 设计的四螺旋束催化剂中表面暴露组氨酸残基反应性的位点选择性控制

Folding & design Pub Date : 1998-08-01 DOI: 10.1016/S1359-0278(98)00041-8

Kerstin S. Broo , Lars Brive , Richard S. Sott , Lars Baltzer

{"title":"Site-selective control of the reactivity of surface-exposed histidine residues in designed four-helix-bundle catalysts","authors":"Kerstin S. Broo , Lars Brive , Richard S. Sott , Lars Baltzer","doi":"10.1016/S1359-0278(98)00041-8","DOIUrl":"10.1016/S1359-0278(98)00041-8","url":null,"abstract":"<div>Background: The structure and function of native proteins often depend on the interplay between ionisable residues with physical properties that have been fine tuned by interactions with neighbouring groups. Here, we systematically vary the environment of histidines in designed helix–loop–helix motifs to modulate histidine pKa values and reactivities.Results: 25 helix–loop–helix motifs were designed in which surface-exposed histidine residues were flanked by neutral, negatively charged and positively charged groups and the histidine's proximity to the hydrophobic core was varied. The 57 histidine pKa values were determined by 1H NMR spectroscopy and found to be in the interval 5.2–7.2 with changes ranging from a decrease of 1.3 pKa units to an increase of 0.7 pKa units compared with the pKa for an unperturbed histidine residue.Conclusions:A decrease in the pKa of His34 by 1.3 units was accomplished by placing it in close proximity to the hydrophobic core and flanking it by positively charged residues in positions (i, i + 3) and (i, i – 4). Flanking a histidine residue with a lysine or a histidine in positions (i, i + 3), (i, i + 4) or (i, i – 4) resulted in pKa depressions of ∼0.5 pKa units per residue and additivity was observed. The increase of the histidine pKa by glutamate residues was the most efficient in position (i, i + 3), but less efficient in position (i, i + 4). These principles should be useful in the engineering of novel catalysts.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 4","pages":"Pages 303-312"},"PeriodicalIF":0.0,"publicationDate":"1998-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00041-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20625085","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}

引用次数: 13

Amide protection in an early folding intermediate of cytochrome c 细胞色素c早期折叠中间体的酰胺保护作用

Folding & design Pub Date : 1998-08-01 DOI: 10.1016/S1359-0278(98)00040-6

J Michael Sauder , Heinrich Roder

{"title":"Amide protection in an early folding intermediate of cytochrome c","authors":"J Michael Sauder , Heinrich Roder","doi":"10.1016/S1359-0278(98)00040-6","DOIUrl":"10.1016/S1359-0278(98)00040-6","url":null,"abstract":"<div>Background: For many proteins, compact states appear long before the rate-limiting step in the formation of the native structure. A key issue is whether the initial collapse of the chain is driven by random or more specific hydrophobic interactions.Results: Hydrogen-exchange labeling coupled with NMR was used to monitor the formation of stable hydrogen-bonded and solvent-excluded structure in horse cytochrome c (cyt c). Protection was measured using a hydrogen exchange/folding competition protocol at variable pH and short competition time (2 ms). Protection factors of threefold to eightfold were observed in all three α helices of cyt c, whereas other regions showed no significant protection. This suggests that the compact states that are present contain segments of marginally stable hydrogen-bonded structure. When the intermediate(s) are destabilized, only amide protons from Cys14, Ala15 and His18 show significant protection, indicating a region of persistent residual structure near the covalently bound heme group in the unfolded protein. Fluorescence-detected stopped-flow studies showed that the maximum protection factor in the early intermediate is consistent with its unfolding equilibrium constant.Conclusions:Together with previous fluorescence and CD results, the observed pattern of amide protection is consistent with the early formation of an α-helical core domain in an ensemble of compact states, indicating that efficient folding is facilitated by stepwise acquisition of native structural elements. These specific early interactions are established on the sub-millisecond time scale, prior to the rate-limiting step for folding.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 4","pages":"Pages 293-301"},"PeriodicalIF":0.0,"publicationDate":"1998-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00040-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20625084","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}

引用次数: 51

A protein engineering analysis of the transition state for protein folding: simulation in the lattice model 蛋白质折叠过渡态的蛋白质工程分析:在晶格模型中的模拟

Folding & design Pub Date : 1998-06-01 DOI: 10.1016/S1359-0278(98)00026-1

Alexander M Gutin , Victor I Abkevich , Eugene I Shakhnovich

{"title":"A protein engineering analysis of the transition state for protein folding: simulation in the lattice model","authors":"Alexander M Gutin , Victor I Abkevich , Eugene I Shakhnovich","doi":"10.1016/S1359-0278(98)00026-1","DOIUrl":"10.1016/S1359-0278(98)00026-1","url":null,"abstract":"<div>Background: Protein engineering has been used extensively to evaluate the properties of transition states in protein folding. Although the method has proved useful, its limitations and the details of interpretation of the obtained results remain largely unexplored.Results: Lattice model simulations are used to test and verify the protein engineering analysis of the transition state in protein folding. It is shown that in some cases – but not always – this method is able to determine the transition state with reasonable accuracy. Limitations of protein engineering are revealed and analyzed. In particular, the change in non-native interactions as a result of mutations is shown to influence the results of the protein engineering analysis. Furthermore, the temperature dependencies of ϕ values (which are a measure of the participation of a residue in the transition state) and the character of the transition state ensemble are studied. It is shown that as a general trend ϕ values decrease when the temperature decreases, a finding consistent with recent experimental results. Our analysis suggests that this trend results primarily from the formation of some contacts (native and non-native) in the unfolded state at a lower temperature, when the barrier for folding is energetic.Conclusions: Our analysis helps to interpret the results of protein engineering and allows observed ϕ values to be directly related to structural features of the unfolded state, the transition state and the native state.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 3","pages":"Pages 183-194"},"PeriodicalIF":0.0,"publicationDate":"1998-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00026-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20483361","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}

引用次数: 36

A single dipeptide sequence modulates the redox properties of a whole enzyme family 单个二肽序列调节整个酶家族的氧化还原特性

Folding & design Pub Date : 1998-06-01 DOI: 10.1016/S1359-0278(98)00024-8

Martina Huber-Wunderlich , Rudi Glockshuber

{"title":"A single dipeptide sequence modulates the redox properties of a whole enzyme family","authors":"Martina Huber-Wunderlich , Rudi Glockshuber","doi":"10.1016/S1359-0278(98)00024-8","DOIUrl":"10.1016/S1359-0278(98)00024-8","url":null,"abstract":"<div>Background: Disulfide exchange reactions are catalyzed by thiol/disulfide oxidoreductases. These enzymes possess a thioredoxin fold and contain a catalytic disulfide with the sequence Cys–X–X–Cys at the N terminus of an α helix. Despite these similarities, the various members differ strongly in their redox potentials (-122 mV to -270 mV). Using the strong oxidant DsbA from Escherichia coli as a model system, we investigated whether the redox properties of these enzymes can be modulated rationally by exchange of the X–X dipeptide.Results: The X–X dipeptide of DsbA (Cys30–Pro31–His32–Cys33) was exchanged by the dipeptides of eukaryotic protein disulfide isomerase (PDI; Gly–His), glutaredoxin (Pro–Tyr), and thioredoxin (Gly–Pro) from E. coli. All variants were less oxidizing than wild-type DsbA and their redox potentials were in the order of the related natural enzymes (DsbA > PDI > glutaredoxin > thioredoxin). The equilibrium constant between glutathione and the thioredoxin-like variant increased 1200-fold compared with wild-type DsbA. The variants also showed a strong increase in the pKa of the nucleophilic cysteine (Cys30). As for glutaredoxin and thioredoxin, the catalytic disulfide stabilized the corresponding variants while destabilizing wild-type DsbA and the PDI-like variant.Conclusions: The X–X dipeptide in the active site of thiol/disulfide oxidoreductases appears to be the main determinant of the redox properties of these enzymes. This empirical finding should be very useful for the design of new thiol/disulfide oxidoreductases with altered redox potentials and for studying the function of these enzymes in vivo.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 3","pages":"Pages 161-171"},"PeriodicalIF":0.0,"publicationDate":"1998-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00024-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20483360","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}

引用次数: 185

Computational analysis of thermal stability: effect of Ile→Val mutations in human lysozyme 溶菌酶热稳定性的计算分析:Ile→Val突变的影响

Folding & design Pub Date : 1998-06-01 DOI: 10.1016/S1359-0278(98)00025-X

Yuji Sugita , Akio Kitao , Nobuhiro Go

{"title":"Computational analysis of thermal stability: effect of Ile→Val mutations in human lysozyme","authors":"Yuji Sugita , Akio Kitao , Nobuhiro Go","doi":"10.1016/S1359-0278(98)00025-X","DOIUrl":"10.1016/S1359-0278(98)00025-X","url":null,"abstract":"<div>Background: Free energy calculations are carried out to study the change of thermal stability caused by Ile23→Val, Ile56→Val, Ile89→Val and Ile106→Val mutations in human lysozyme. In order to examine the dependence of the free energy difference, ΔΔG, on the denatured-state structure, extended and native-like conformations are employed as initial conformations in the denatured-state simulations.Results: Calculated values of ΔΔG for the mutations, Ile56→Val, Ile89→Val and Ile106→Val, were in good agreement with experimental values when the native-like structure was employed in the respective denatured-state simulations. In the case of Ile23→Val, a considerable difference between the calculated and experimental values of ΔΔG was observed.Conclusions: The physical nature of Ile56→Val, Ile89→Val and Ile106→Val mutations was rationally characterized by a free energy component analysis. It is suggested that the α domain in which Ile23 is included is considerably structured even in the denatured state.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 3","pages":"Pages 173-181"},"PeriodicalIF":0.0,"publicationDate":"1998-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00025-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20483362","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}

引用次数: 13

Initial hydrophobic collapse is not necessary for folding RNase A 最初的疏水坍缩对于rna酶A的折叠是不必要的

Folding & design Pub Date : 1998-06-01 DOI: 10.1016/S1359-0278(98)00029-7

Angela Nöppert , Klaus Gast , Dietrich Zirwer , Gregor Damaschun

{"title":"Initial hydrophobic collapse is not necessary for folding RNase A","authors":"Angela Nöppert , Klaus Gast , Dietrich Zirwer , Gregor Damaschun","doi":"10.1016/S1359-0278(98)00029-7","DOIUrl":"10.1016/S1359-0278(98)00029-7","url":null,"abstract":"<div>Background: One of the main distinctions between different theories describing protein folding is the predicted sequence of secondary structure formation and compaction during the folding process. Whether secondary structure formation precedes compaction of the protein molecules or secondary structure formation is driven by a hydrophobic collapse cannot be decided unequivocally on the basis of existing experimental data.Results: In this study, we investigate the refolding of chemically denatured, disulfide-intact ribonuclease A (RNase A) by monitoring compaction and secondary structure formation using stopped-flow dynamic light scattering and stopped-flow CD, respectively. Our data reveal the formation of a considerable amount of secondary structure early in the refolding of the slow folding species of RNase A without a significant compaction of the molecules. A simultaneous formation of secondary structure and compaction is observed in the subsequent rate-limiting step of folding.Conclusions: During folding of RNase A an initial global hydrophobicity is not observed, which contradicts the view that this is a general requirement for protein folding. This folding behavior could be typical of similar, moderately hydrophobic proteins.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 3","pages":"Pages 213-221"},"PeriodicalIF":0.0,"publicationDate":"1998-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00029-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20483365","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}

引用次数: 21

Protein design: a perspective from simple tractable models 蛋白质设计:从简单可处理模型的视角

Folding & design Pub Date : 1998-06-01 DOI: 10.1016/S1359-0278(98)00021-2

Eugene I Shakhnovich

引用次数: 144

A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure 从已知二级结构预测蛋白质三级模型的组合距离约束方法

Folding & design Pub Date : 1998-06-01 DOI: 10.1016/S1359-0278(98)00023-6

Gareth Chelvanayagam , Lukas Knecht , Thomas Jenny , Steven A Benner , Gaston H Gonnet

{"title":"A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure","authors":"Gareth Chelvanayagam , Lukas Knecht , Thomas Jenny , Steven A Benner , Gaston H Gonnet","doi":"10.1016/S1359-0278(98)00023-6","DOIUrl":"10.1016/S1359-0278(98)00023-6","url":null,"abstract":"<div>Background: Distance geometry methods allow protein structures to be constructed using a large number of distance constraints, which can be elucidated by experimental techniques such as NMR. New methods for gleaning tertiary structural information from multiple sequence alignments make it possible for distance constraints to be predicted from sequence information alone. The basic distance geometry method can thus be applied using these empirically derived distance constraints. Such an approach, which incorporates a novel combinatoric procedure, is reported here.Results: Given the correct sheet topology and disulfide formations, the fully automated procedure is generally able to construct native-like Cα models for eight smallβ-protein structures. When the sheet topology was unknown but disulfide connectivities were included, all sheet topologies were explored by the combinatorial procedure. Using a simple geometric evaluation scheme, models with the correct sheet topology were ranked first in four of the eight example cases, second in three examples and third in one example. If neither the sheet topology nor the disulfide connectivities were givena priori, all combinations of sheet topologies and disulfides were explored by the combinatorial procedure. The evaluation scheme ranked the correct topology within the top five folds for half the example cases.Conclusions: The combinatorial procedure is a useful technique for identifying a limited number of low-resolution candidate folds for small, disulfide-rich, β-protein structures. Better results are obtained, however, if correct disulfide connectivities are known in advance. Combinatorial distance constraints can be applied whenever there are a sufficiently small number of finite connectivities.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 3","pages":"Pages 149-160"},"PeriodicalIF":0.0,"publicationDate":"1998-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00023-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20483359","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}

引用次数: 14

Chain-like conformation of heat-denatured ribonuclease A and cytochromec as evidenced by solution X-ray scattering 热变性核糖核酸酶A的链状构象和细胞染色剂的溶液x射线散射

Folding & design Pub Date : 1998-06-01 DOI: 10.1016/S1359-0278(98)00027-3

Yoshihisa Hagihara , Masaru Hoshino , Daizo Hamada , Mikio Kataoka , Yuji Goto

{"title":"Chain-like conformation of heat-denatured ribonuclease A and cytochromec as evidenced by solution X-ray scattering","authors":"Yoshihisa Hagihara , Masaru Hoshino , Daizo Hamada , Mikio Kataoka , Yuji Goto","doi":"10.1016/S1359-0278(98)00027-3","DOIUrl":"10.1016/S1359-0278(98)00027-3","url":null,"abstract":"<div>Background: Although the characterization of heat-denatured proteins is essential for understanding the thermodynamic mechanism of protein folding, their structural features are still unclear and controversial. In order to address this problem, we studied the size and shape of the heat-denatured states of bovine ribonuclease A (RNase A) and horse ferricytochrome c (cytochrome c) by solution X-ray scattering.Results: RNase A has four disulfide bonds, whereas cytochrome c, with a covalently bound heme group, has no disulfide bond. Guinier plots show that the heat-denatured RNase A is relatively compact, but the heat-denatured cytochrome c is expanded. On the other hand, the Kratky plots of the two proteins are similar, indicating that the heat-denatured proteins assume a chain-like disordered conformation. The X-ray scattering of RNase A and cytochrome c at various temperatures confirmed that their thermal transitions from a globular native state to a chain-like extended conformation can be approximated well by a two-state transition.Conclusions: These results indicate that the heat-denatured RNase A and cytochrome c are substantially unfolded according to the criteria of solution X-ray scattering, although the heat-denatured RNase A remains compact because of the presence of the disulfide bonds. The results also confirm that the thermal denaturation occurs cooperatively with the breakdown of secondary and tertiary structure.</div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 3","pages":"Pages 195-201"},"PeriodicalIF":0.0,"publicationDate":"1998-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00027-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20483363","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}

引用次数: 29