Normal mode analysis and applications in biological physics

Dykeman, Eric C.; Sankey, Otto F.

doi:10.1088/0953-8984/22/42/423202

Cited by 93 publications

(115 citation statements)

References 72 publications

(128 reference statements)

Supporting

Mentioning

114

Contrasting

Order By: Relevance

“…Icosahedral viruses are dynamic, with various vibrational modes; transition between antigenically distinct closed and open states of the capsid during a picornavirus breathing cycle has been documented both directly and indirectly (19,20,67,68). The open capsid conformation that occurs during the virus breathing cycle is reversible and exposes segments of VP1 and VP4 that are internalized in the closed state of the capsid.…”

Section: Discussionmentioning

confidence: 99%

Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-Particle

Organtini

Makhov

Conway

et al. 2014

J Virol

View full text Add to dashboard Cite

The coxsackievirus and adenovirus receptor (CAR) has been identified as the cellular receptor for group B coxsackieviruses, including serotype 3 (CVB3). CAR mediates infection by binding to CVB3 and catalyzing conformational changes in the virus that result in formation of the altered, noninfectious A-particle. Kinetic analyses show that the apparent first-order rate constant for the inactivation of CVB3 by soluble CAR (sCAR) at physiological temperatures varies nonlinearly with sCAR concentration. Cryo-electron microscopy (cryo-EM) reconstruction of the CVB3-CAR complex resulted in a 9.0-Å resolution map that was interpreted with the four available crystal structures of CAR, providing a consensus footprint for the receptor binding site. The analysis of the cryo-EM structure identifies important virus-receptor interactions that are conserved across picornavirus species. These conserved interactions map to variable antigenic sites or structurally conserved regions, suggesting a combination of evolutionary mechanisms for receptor site preservation. The CAR-catalyzed A-particle structure was solved to a 6.6-Å resolution and shows significant rearrangement of internal features and symmetric interactions with the RNA genome. IMPORTANCEThis report presents new information about receptor use by picornaviruses and highlights the importance of attaining at least an ϳ9-Å resolution for the interpretation of cryo-EM complex maps. The analysis of receptor binding elucidates two complementary mechanisms for preservation of the low-affinity (initial) interaction of the receptor and defines the kinetics of receptor-catalyzed conformational change to the A-particle.

show abstract

Section: Discussionmentioning

confidence: 99%

Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-Particle

Organtini

Makhov

Conway

et al. 2014

J Virol

View full text Add to dashboard Cite

show abstract

“…Actually, it has been experimentally observed that the large scale conformational changes in a viral capsid can be described by low-frequency modes and are relevant to the fulfillment of viruses' specific functions. [6][7][8][9][10][11] On the other hand, a detailed picture of the enzymes' vibrational modes and frequencies are useful for understanding their cooperative motion and changes in conformation, which can potentially lead to correlated active site opening and/or closure, a phenomenon important for substrate binding and product release. [11][12][13][14][15] No doubt, it is of great significance to study vibration behaviors of bio-related spherical shells and the influence on their biological functions.…”

Section: Introductionmentioning

confidence: 99%

“…Widom et al 18 identified and classified vibration modes of a virus capsid based on a simple mass-andspring model. Dykeman and Sankey 5,8,9,11 calculated low-frequency vibration modes and frequencies of large protein assemblies (such as enzymes and viral capsids), where the vibration modes are modeled with full atomic detail. Yang et al 22 predicted vibrational modes of several icosahedral viruses and an icosahedral enzyme using continuum models, and they estimated the macroscopic material properties such as the Young's modulus or Poisson's ratio by fitting the predictions to an anisotropic network model.…”

Section: Introductionmentioning

confidence: 99%

Free vibration of biopolymer spherical shells of high structural heterogeneity

Zhang

2018

AIP Advances

View full text Add to dashboard Cite

A refined elastic shell model is used to study the effect of high structural heterogeneity on natural frequencies and vibration modes of biopolymer spherical shells. With this model, the structural heterogeneity of a biopolymer spherical shell is characterized by an effective bending thickness (which can be quite different from the average thickness) and the transverse shear modulus (which can be much lower than the in-plane shear modulus). Our results show that actual natural frequencies of axisymmetric spheroidal modes of a biopolymer spherical shell can be much lower than those predicted by the classical homogeneous shell model based on the average thickness, although natural frequencies of axisymmetric torsional modes are close to those predicted by the classical model. For example, with physically realistic parameters for virus capsid STMV, the natural frequencies of spheroidal modes predicted by the present model are about 30-50% lower than those predicted by the classical model, in better agreement with known simulation results. In addition, in the low frequency range of several viral capsids, the number of independent non-axisymmetric vibration modes predicted by the present model is considerably larger than that predicted by the classical homogeneous shell model, in qualitative agreement with known atomistic simulations. These results suggest that the refined shell model could offer a relatively simple model to simulate mechanical behavior of biopolymer spherical shells of high structural heterogeneity.

show abstract

“…During the past three decades NMA has also become a popular alternative to figuring out the large-scale motion of proteins and other macromolecules (see some recent reviews in Refs. [3][4][5][6], and check a recent software tool for NMA in internal coordinates in Ref. [7]).…”

Section: Introductionmentioning

confidence: 99%

Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: an application to protein torsion dynamics

et al. 2012

View full text Add to dashboard Cite

Normal mode analysis (NMA) was introduced in 1930s as a framework to understand the structure of the observed vibration-rotation spectrum of several small molecules. During the past three decades NMA has also become a popular alternative to figuring out the large-scale motion of proteins and other macromolecules. However, the "standard" NMA is based on approximations, which sometimes are unphysical. Especially problematic is the assumption that atoms move only "infinitesimally", which, of course, is an oxymoron when large amplitude motions are concerned. The "infinitesimal" approximation has the further unfortunate side effect of masking the physical importance of the coupling between vibrational and rotational degrees of freedom. Here, we present a novel formulation of the NMA, which is applied for finite motions in non-Eckart body-frame. Contrary to standard normal mode theory, our approach starts by assuming a harmonic potential in generalized coordinates, and tries to avoid the linearization of the coordinates. It also takes explicitly into account the Coriolis terms, which couple vibrations and rotations, and the terms involving Christoffel symbols, which are ignored by default in the standard NMA. We also computationally explore the effect of various terms to the solutions of the NMA equation of motions.

show abstract

Normal mode analysis and applications in biological physics

Cited by 93 publications

References 72 publications

Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-Particle

Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-Particle

Free vibration of biopolymer spherical shells of high structural heterogeneity

Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: an application to protein torsion dynamics

Contact Info

Product

Resources

About