Advances in Protein Chemistry最新文献_第4页

Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results. 蛋白质和蛋白质配体复合物的极化建模:方法和初步结果。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(05)72003-9

Richard A Friesner

{"title":"Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results.","authors":"Richard A Friesner","doi":"10.1016/S0065-3233(05)72003-9","DOIUrl":"https://doi.org/10.1016/S0065-3233(05)72003-9","url":null,"abstract":"This chapter discusses methods for modeling electronic polarization in proteins and protein-ligand complexes. Two different approaches are considered: explicit incorporation of polarization into a molecular mechanics force field and the use of mixed quantum mechanics/molecular mechanics methods to model polarization in a restricted region of the protein or protein-ligand complex. A brief description is provided of the computational methodology and parameterization protocols and then results from two preliminary studies are presented. The first study employs quantum mechanics/molecular mechanics (QM/MM) methods to improve the accuracy of protein-ligand docking; here, incorporation of polarization is shown to dramatically improve the robustness of the accuracy of structural prediction of the protein-ligand docking by enabling qualitative improvement in the selection of the correct hydrogen bonding patterns of the docked ligand. The second study discusses a 2-ns simulation of bovine pancreatic trypsin inhibitor (BPTI) in water using a variety of fixed charge and polarizable models for both the protein and the solvent, analyzing observed root mean square deviations (RMSD), intraprotein hydrogen bonding, and water structure and dynamics. All of these efforts are in a relatively early stage of development, the results are encouraging in that stable methods have been developed, and significant effects of polarization are seen and (in the case of the QM/MM-based docking) improvements have been validated as compared to experiment. With regard to accuracy and robustness of full simulations, a great deal more work needs to be done to quantitate and improve the present models.","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":"72 ","pages":"79-104"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(05)72003-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25945407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 60

Titin and its associated proteins: the third myofilament system of the sarcomere. 肌凝素及其相关蛋白:肌节的第三肌丝系统。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(04)71003-7

Henk L Granzier, Siegfried Labeit

引用次数: 84

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. 肽和蛋白质折叠和构象平衡:用隐式溶剂模型对静电和氢键的理论处理。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(05)72007-6

Wonpil Im, Jianhan Chen, Charles L Brooks

{"title":"Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models.","authors":"Wonpil Im, Jianhan Chen, Charles L Brooks","doi":"10.1016/S0065-3233(05)72007-6","DOIUrl":"https://doi.org/10.1016/S0065-3233(05)72007-6","url":null,"abstract":"Since biomolecules exist in aqueous and membrane environments, the accurate modeling of solvation, and hydrogen bonding interactions in particular, is essential for the exploration of structure and function in theoretical and computational studies. In this chapter, we focus on alternatives to explicit solvent models and discuss recent advances in generalized Born (GB) implicit solvent theories. We present a brief review of the successes and shortcomings of the application of these theories to biomolecular problems that are strongly linked to backbone H-bonding and electrostatics. This discussion naturally leads us to explore existing areas for improvement in current GB theories and our approach towards addressing a number of the key issues that remain in the refinement of these models. Specifically, the critical importance of balancing solvation forces and intramolecular forces in GB models is illustrated by examining the influence of backbone hydrogen bond strength and backbone dihedral energetics on conformational equilibria of small peptids.","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":"72 ","pages":"173-98"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(05)72007-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25944738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 63

Hydrogen bonds in molecular mechanics force fields. 分子力学力场中的氢键。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(05)72004-0

Jan Hermans

引用次数: 9

Microdissection of the sequence and structure of intermediate filament chains. 中间丝链序列和结构的显微解剖。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(05)70005-X

David A D Parry

{"title":"Microdissection of the sequence and structure of intermediate filament chains.","authors":"David A D Parry","doi":"10.1016/S0065-3233(05)70005-X","DOIUrl":"https://doi.org/10.1016/S0065-3233(05)70005-X","url":null,"abstract":"A large number of intermediate filament (IF) chains have now been sequenced. From these data, it has been possible to deduce the main elements of the secondary structure, especially those lying within the central rod domain of the molecule. These conclusions, allied to results obtained from crosslinking studies, have shown that at least four unique but related structures are adopted by the class of structures known generically as intermediate filaments: (1) epidermal and reduced trichocyte keratin; (2) oxidized trichocyte keratin; (3) desmin, vimentin, neurofilaments, and related Type III and IV proteins; and (4) lamin molecules. It would be expected that local differences in sequences of the proteins in these four groups would occur, and that this would ultimately relate to assembly. Site-directed mutagenesis and theoretical methods have now made it possible to investigate these ideas further. In particular, new data have been obtained that allow the role played by some individual amino acids or a short stretch of sequence to be determined. Among the observations catalogued here are the key residues involved in intra- and interchain ionic interactions, as well as those involved in stabilizing some modes of molecular aggregation; the structure and role of subdomains in the head and tail domains; the repeat sequences occurring along the length of the chain and their structural significance; trigger motifs in coiled-coil segments; and helix initiation and termination motifs that terminate the rod domain. Much more remains to be done, not least of which is gaining an increased understanding of the many subtle differences that exist between different IF chains at the sequence level.","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":"70 ","pages":"113-42"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(05)70005-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25063923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 62

Regulation of muscle contraction by tropomyosin and troponin: how structure illuminates function. 原肌凝蛋白和肌钙蛋白对肌肉收缩的调节:结构如何影响功能。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(04)71004-9

Jerry H Brown, Carolyn Cohen

引用次数: 113

Thermodynamics Of alpha-Helix Formation. 螺旋形成的热力学。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(05)72008-8

George I Makhatadze

引用次数: 34

Potential functions for hydrogen bonds in protein structure prediction and design. 氢键在蛋白质结构预测和设计中的潜在功能。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(05)72001-5

Alexandre V Morozov, Tanja Kortemme

{"title":"Potential functions for hydrogen bonds in protein structure prediction and design.","authors":"Alexandre V Morozov, Tanja Kortemme","doi":"10.1016/S0065-3233(05)72001-5","DOIUrl":"https://doi.org/10.1016/S0065-3233(05)72001-5","url":null,"abstract":"Hydrogen bonds are an important contributor to free energies of biological macromolecules and macromolecular complexes, and hence an accurate description of these interactions is important for progress in biomolecular modeling. A simple description of the hydrogen bond is based on an electrostatic dipole-dipole interaction involving hydrogen-donor and acceptor-acceptor base dipoles, but the physical nature of hydrogen bond formation is more complex. At the most fundamental level, hydrogen bonding is a quantum mechanical phenomenon with contributions from covalent effects, polarization, and charge transfer. Recent experiments and theoretical calculations suggest that both electrostatic and covalent components determine the properties of hydrogen bonds. Likely, the level of rigor required to describe hydrogen bonding will depend on the problem posed. Current approaches to modeling hydrogen bonds include knowledge-based descriptions based on surveys of hydrogen bond geometries in structural databases of proteins and small molecules, empirical molecular mechanics models, and quantum mechanics-based electronic structure calculations. Ab initio calculations of hydrogen bonding energies and geometries accurately reproduce energy landscapes obtained from the distributions of hydrogen bond geometries observed in protein structures. Orientation-dependent hydrogen bonding potentials were found to improve the quality of protein structure prediction and refinement, protein-protein docking, and protein design.","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":"72 ","pages":"1-38"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(05)72001-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25945405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 58

Spectrin, alpha-actinin, and dystrophin. 幽灵蛋白，肌动蛋白和肌营养不良蛋白。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(05)70007-3

M J F Broderick, S J Winder

引用次数: 130

Molecular packing in network-forming collagens. 网络形成胶原中的分子堆积。

Advances in Protein Chemistry Pub Date : 2005-01-01 DOI: 10.1016/S0065-3233(05)70011-5

Carlo Knupp, John M Squire

引用次数: 12