Proteins: Structure, Function and Bioinformatics

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An all‐atom structure‐based potential for proteins: Bridging minimal models with all‐atom empirical forcefields
Proteins: Structure, Function and Bioinformatics - Tập 75 Số 2 - Trang 430-441 - 2009
Paul C. Whitford, Jeffrey K. Noel, Shachi Gosavi, Alexander Schug, Karissa Y. Sanbonmatsu, José N. Onuchic
AbstractProtein dynamics take place on many time and length scales. Coarse‐grained structure‐based$ {\bf (G{\overline o})} $models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All‐atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic... hiện toàn bộ
Collective dynamics of the ribosomal tunnel revealed by elastic network modeling
Proteins: Structure, Function and Bioinformatics - Tập 75 Số 4 - Trang 837-845 - 2009
Özge Kürkçüoğlu, Zeynep Kurkcuoglu, Pemra Doruker, Robert L. Jernigan
AbstractThe collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode analysis. The calculated normal modes are considered individually and in linear combinations with different coefficients mimicking the phase angles between modes, in order to follow the mechanistic motions of tunnel wall residues. The lo... hiện toàn bộ
Comparative analysis of the β transducin family with identification of several new members including PWP1, a nonessential gene of Saccharomyces cerevisiae that is divergently transcribed from NMT1
Proteins: Structure, Function and Bioinformatics - Tập 13 Số 1 - Trang 41-56 - 1992
Robert J. Duronio, Jeffrey I. Gordon, Mark S. Boguski
AbstractWhile investigating the expression of the Saccharomyces cerevisiae myristoyl‐CoA:protein N‐myristoyltransferase gene (NMT: E.C. 2.3.1.97) by Northern blot analysis, we observed another RNA transcript whose expression resembled that of NMT1 during meiosis and was derived from a gene located <1 kb immediately upstream of NMT1. This new gene, designated PWP1 (for periodic tryptophan protein),... hiện toàn bộ
Cấu trúc và động lực học của sự liên kết ligand với protein: Escherichia coli dihydrofolate reductase-trimethoprim, một hệ thống thuốc-receptor Dịch bởi AI
Proteins: Structure, Function and Bioinformatics - Tập 4 Số 1 - Trang 31-47 - 1988
Pnina Dauber‐Osguthorpe, Victoria A. Roberts, David J. Osguthorpe, Jon A. Wolff, M. Genest, A. T. Hagler
Tóm tắtMột nghiên cứu về sự liên kết của chất kháng khuẩn trimethoprim với Escherichia coli dihydrofolate reductase đã được thực hiện bằng cách sử dụng các kỹ thuật tối thiểu hóa năng lượng với cả hai trường lực vanh toàn phần và trường lực nguyên tử thống nhất. Các tiêu chí hội tụ đảm bảo rằng không có thay đổi cấu trúc hoặc năng lượng đáng kể nào xảy ra với việc tối thiểu hóa thêm. Các độ lệch c... hiện toàn bộ
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
Proteins: Structure, Function and Bioinformatics - Tập 4 Số 1 - Trang 7-18 - 1988
Michael K. Gilson, Barry Honig
AbstractIn this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms. In addition to the solvation energies of individual molecules, the method can be used to calculate the electrostatic energy associated with conformational changes in prot... hiện toàn bộ
What are the dielectric “constants” of proteins and how to validate electrostatic models?
Proteins: Structure, Function and Bioinformatics - Tập 44 Số 4 - Trang 400-417 - 2001
Claudia Schütz, A. Warshel
AbstractImplicit models for evaluation of electrostatic energies in proteins include dielectric constants that represent effect of the protein environment. Unfortunately, the results obtained by such models are very sensitive to the value used for the dielectric constant. Furthermore, the factors that determine the optimal value of these constants are far from being obvious. This review considers ... hiện toàn bộ
Crystallization and preliminary X‐ray diffraction studies of human salivary α‐amylase
Proteins: Structure, Function and Bioinformatics - Tập 11 Số 3 - Trang 230-232 - 1991
N. Ramasubbu, K. K. Bhandary, Frank A. Scannapieco, M.J. Levine
AbstractNonglycosylated α‐amylase, a major component of human parotid saliva, has been crystallized by the vapor diffusion technique using 2‐methyl‐2,4‐pentanediol as the precipitant in the presence of CaCl2 at pH 9.0. The crystals are orthorhombic, space group P212121 with unit cell dimensions of a = 53.3, b = 75.8, and c = 138.1 Å. The asymmetric unit contains one amylase molecule. The solvent c... hiện toàn bộ
Long timestep dynamics of peptides by the dynamics driver approach
Proteins: Structure, Function and Bioinformatics - Tập 21 Số 4 - Trang 282-302 - 1995
Philippe Derreumaux, Tamar Schlick
AbstractPrevious experience with the Langevin/implicit‐Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5–20 fs range but quenches high‐frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13‐residue oligoalanine) and also develop a new dynamics... hiện toàn bộ
Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study
Proteins: Structure, Function and Bioinformatics - Tập 21 Số 3 - Trang 196-213 - 1995
Philippe H. Hünenberger, Alan E. Mark, Wilfred F. van Gunsteren
AbstractFour methods are compared to drive the unfolding of a protein: (1) high temperature (T‐run), (2) high pressure (P‐run), (3) by imposing a gradual increase in the mean radius of the protein using a penalty function added to the physical interaction function (F‐run, radial force driven unfolding), and (4) by weak coupling of the difference between the temperature of the radially outward movi... hiện toàn bộ
Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long‐time molecular dynamics simulations
Proteins: Structure, Function and Bioinformatics - Tập 23 Số 1 - Trang 49-62 - 1995
Roger M. Brunne, Kurt D. Berndt, Peter Güntert, Kurt Wüthrich, Wilfred F. van Gunsteren
AbstractStructural and dynamic properties of bovine pancreatic trypsin inhibitor (BPTI) in aqueous solution are investigated using two molecular dynamics (MD) simulations: one of 1.4 ns length and one of 0.8 ns length in which atom‐atom distance bounds derived from NMR spectroscopy are included in the potential energy function to make the trajectory satisfy these experimental data more closely. Th... hiện toàn bộ
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