scholarly journals ProMode-Oligomer: Database of Normal Mode Analysis in Dihedral Angle Space for a Full-Atom System of Oligomeric Proteins

2012 ◽  
Vol 6 (1) ◽  
pp. 9-19 ◽  
Author(s):  
Hiroshi Wako ◽  
Shigeru Endo
Keyword(s):  
Normal Mode ◽  
Protein Complexes ◽  
Normal Mode Analysis ◽  
Normal Modes ◽  
Point Of View ◽  
Mode Analysis ◽  
Dihedral Angles ◽  
Oligomeric Proteins ◽  
Displacement Vectors ◽  
Atom System

The database ProMode-Oligomer (http://promode.socs.waseda.ac.jp/promode_oligomer) was constructed by collecting normal-mode-analysis (NMA) results for oligomeric proteins including protein-protein complexes. As in the ProMode database developed earlier for monomers and individual subunits of oligomers (Bioinformatics vol. 20, pp. 2035–2043, 2004), NMA was performed for a full-atom system using dihedral angles as independent variables, and we released the results (fluctuations of atoms, fluctuations of dihedral angles, correlations between atomic fluctuations, etc.). The vibrating oligomer is visualized by animation in an interactive molecular viewer for each of the 20 lowest-frequency normal modes. In addition, displacement vectors of constituent atoms for each normal mode were decomposed into two characteristic motions in individual subunits, i.e., internal and external (deformation and rigid-body movements of the individual subunits, respectively), and then the mutual movements of the subunits and the movement of atoms around the interface regions were investigated. These results released in ProMode-Oligomer are useful for characterizing oligomeric proteins from a dynamic point of view. The analyses are illustrated with immunoglobulin light- and heavy-chain variable domains bound to lysozyme and to a 12-residue peptide.

scholarly journals Normal Mode Analysis as a Routine Part of a Structural Investigation

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3293 ◽  
Author(s):  
Jacob A. Bauer ◽  
Jelena Pavlović ◽  
Vladena Bauerová-Hlinková
Keyword(s):  
Normal Mode ◽  
Structural Study ◽  
Computer Technology ◽  
Structural Investigation ◽  
Normal Mode Analysis ◽  
Computational Cost ◽  
Normal Modes ◽  
Mode Analysis ◽  
Computationally Expensive ◽  
The Web

Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.

scholarly journals STRUCTURE FLUCTUATIONS AND CONFORMATIONAL CHANGES IN PROTEIN BINDING

2012 ◽  
Vol 10 (02) ◽  
pp. 1241002 ◽  
Author(s):  
ANATOLY M. RUVINSKY ◽  
TATSIANA KIRYS ◽  
ALEXANDER V. TUZIKOV ◽  
ILYA A. VAKSER
Keyword(s):  
Conformational Changes ◽  
Protein Complexes ◽  
Normal Mode Analysis ◽  
Distribution Functions ◽  
Mode Analysis ◽  
Amino Acid Type ◽  
Dihedral Angles ◽  
Elastic Network Model ◽  
Centers Of Mass ◽  
Interface Residues

Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may underestimate protein flexibility in solvent. Our classification shows that protein loops and disordered fragments are enriched with highly fluctuating residues and depleted with weakly fluctuating residues. Strategies for engineering thermostable proteins are discussed. To calculate the dihedral angles distribution functions, the configuration space was divided into cells by a cubic grid. The effect of protein association on the distribution functions depends on the amino acid type and a grid step in the dihedral angles space. The changes in the dihedral angles increase from the near-backbone dihedral angle to the most distant one, for most residues. On average, one fifth of the interface residues change the rotamer state upon binding, whereas the rest of the interface residues undergo local readjustments within the same rotamer.

Perturbed normal-mode analysis of induction times, relaxation times, and reaction rates in unimolecular reactions

1979 ◽  
Vol 57 (13) ◽  
pp. 1723-1730 ◽  
Author(s):  
Andrew W. Yau ◽  
Huw O. Pritchard
Keyword(s):  
Normal Mode ◽  
Transition Probabilities ◽  
Normal Mode Analysis ◽  
Relaxation Times ◽  
Normal Modes ◽  
Reaction Rates ◽  
Mode Analysis ◽  
Decomposition Reactions ◽  
Induction Times ◽  
Network Relationship

A perturbed normal-mode analysis is presented of the induction (or incubation) time, the relaxation rate, and the reaction rate of a diluted unimolecular system. At high temperature, the unimolecular rate approaches the Lindemann behaviour and the low-pressure rate is related to the normal modes of relaxation of the reactive states in a simple manner. In a step-ladder model system, the network relationship between the normal modes and the microscopic transition probabilities leads to explicit theoretical correlations between the respective experimental quantities. Illustrative calculations of such correlations are presented for the decomposition reactions of N2O and CO2 diluted in Ar at shock wave temperatures, and are compared with experiment.

scholarly journals Predicting protein functional motions: an old recipe with a new twist

2019 ◽  
Author(s):  
Sergei Grudinin ◽  
Elodie Laine ◽  
Alexandre Hoffmann
Keyword(s):  
Normal Mode ◽  
Conformational Changes ◽  
Normal Mode Analysis ◽  
Normal Modes ◽  
Low Frequency ◽  
Structural Heterogeneity ◽  
Mode Analysis ◽  
Protein Motions ◽  
Wide Range ◽  
Geometrical Constraints

Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. Some of them can be seen experimentally, for example with X-ray crystallography or cryo-electron microscopy. This structural heterogeneity is not occasional and is frequently linked with specific biological function. Thus, the accurate description of macromolecular conformational transitions is crucial for understanding fundamental mechanisms of life’s machinery. We report on a real-time method to predict such transitions by extrapolating from instantaneous eigen-motions, computed using the normal mode analysis, to a series of twists. We demonstrate the applicability of our approach to the prediction of a wide range of motions, including large collective opening-closing transitions and conformational changes induced by partner binding. We also highlight particularly difficult cases of very small transitions between crystal and solution structures. Our method guaranties preservation of the protein structure during the transition and allows to access conformations that are unreachable with classical normal mode analysis. We provide practical solutions to describe localized motions with a few low-frequency modes and to relax some geometrical constraints along the predicted transitions. This work opens the way to the systematic description of protein motions, whatever their degree of collectivity. Our method is available as a part of the NOn-Linear rigid Block (NOLB) package at https://team.inria.fr/nano-d/software/nolb-normal-modes/.Significance StatementProteins perform their biological functions by changing their shapes and interacting with each other. Getting access to these motions is challenging. In this work, we present a method that generates plausible physics-based protein motions and conformations. We model a protein as a network of atoms connected by springs and deform it along the least-energy directions. Our main contribution is to perform the deformations in a nonlinear way, through a series of twists. This allows us to produce a wide range of motions, some of them previously inaccessible, and to preserve the structure of the protein during the motion. We are able to simulate the opening or closing of a protein and the changes it undergoes to adapt to a partner.

Normal-mode linear analysis and initial conditions of capillary jets

2008 ◽  
Vol 602 ◽  
pp. 81-117 ◽  
Author(s):  
F. J. GARCÍA ◽  
H. GONZÁLEZ
Keyword(s):  
Normal Mode ◽  
Initial Conditions ◽  
Normal Mode Analysis ◽  
Normal Modes ◽  
Linear Analysis ◽  
Mode Analysis ◽  
Initial Transient ◽  
Exhaustive Study ◽  
Capillary Jets ◽  
Necessary And Sufficient

The normal-mode linear analysis of an axisymmetric infinite capillary jet is generalized to account for arbitrary initial conditions. An exhaustive study of the dispersion relation reveals the parametric behaviour of all eigenvalues and their corresponding normal modes. The two capillary modes (dominant and subdominant) are found to be necessary and sufficient to describe any possible non-recirculating initial conditions. An infinite set of other modes accounts for initial conditions with recirculating velocity field. The predictions of the normal-mode analysis are contrasted against previous computations of the initial-value problem, previous experiments, and our own one-dimensional numerical simulations. Contrary to the claim of some authors, the normal-mode analysis accurately predicts the initial transient with non-exponential growth of the disturbance amplitude observed in previous works. Simple and accurate formulae for the duration of the initial transient are deduced, with emphasis on improving the growth-rate measurement.

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