Building-block approach for determining low-frequency normal modes of macromolecules

Tama, Florence; Gadéa, Florent Xavier; Marques, Osni; Sanejouand, Yves‐Henri

doi:10.1002/1097-0134(20001001)41:1<1::aid-prot10>3.0.co;2-p

Cited by 446 publications

(468 citation statements)

References 38 publications

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“…24 Further computational efficiency can be gained without significant loss in information through the addition of the rotation-translation block (RTB) method for the diagonalization of the matrix of second derivatives. 25 In the present calculations we have used a Cα-only representation in constructing the elastic network models of the virus capsids and the RTB approach with individual blocks corresponding the each protein in the viral capsid for the normal mode calculations. Details of the elastic network models and associated normal mode methods can be found in the recent review by Tama and Brooks.…”

Section: Theorymentioning

confidence: 99%

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

et al. 2005

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Electrostatic properties of cowpea chlorotic mottle virus (CCMV) and cucumber mosaic virus (CMV) were investigated using numerical solutions to the Poisson-Boltzmann equation. Experimentally, it has been shown that CCMV particles swell in the absence of divalent cations when the pH is raised from 5 to 7. CMV, although structurally homologous, does not undergo this transition. An analysis of the calculated electrostatic potential confirms that a strong electrostatic repulsion at the calcium binding sites in the CCMV capsid is most likely the driving force for the capsid swelling process during the release of calcium. The binding interaction between the encapsulated genome material (RNA) inside of the capsid and the inner capsid shell is weakened during the swelling transition. This probably aids in the RNA release process, but it is unlikely that the RNA is released through capsid openings due to unfavorable electrostatic interaction between the RNA and capsid inner shell residues at these openings. Calculations of the calcium binding energies show that Ca 2+ can bind both to the native and swollen forms of the CCMV virion. Favorable binding to the swollen form suggests that Ca 2+ ions can induce the capsid contraction and stabilize the native form.

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Section: Theorymentioning

confidence: 99%

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

et al. 2005

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“…Block choice [C α ] 1 was proposed by Tama et al [2]; it has no linked blocks. In the other block choices, the C α carbon …”

Section: Validation Of Mobile Block Hessian (Mbh) Methodsmentioning

confidence: 99%

“…1. The internal structure of a block need not be optimized, so a partial geometry optimization is sufficient to apply MBH, in contrast to the plain Rotation-Translation Block (RTB) method by Tama et al [2]. The block choice determines whether the low or high frequency modes, or the coupling between both groups, are reproduced.…”

Section: Introductionmentioning

confidence: 99%

Normal mode analysis of macromolecular systems with the mobile block Hessian method

Ghysels¹,

Speybroeck²,

Neck³

et al. 2015

AIP Conference Proceedings

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Abstract. Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N a × 3N a matrix with N a the number of atoms. A series of simplified models has been proposed, in particular the RotationTranslation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each.Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible -but not necessarily optimized -geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian.In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.

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“…Popular approaches include the Rotational Translational Blocks (RTB) procedure [9], which requires atomic coordinates for the underlying protein structure, the Gaussian [10][11][12][13] and Elastic Network Model (ENM) [14], the Rigid-Cluster Model [15][16][17], and more recently the Finite Element Method (FEM) [18]. The FEM is a well established numerical procedure with solid theoretical foundations that has been developed over several decades to be applied to a broad range of continuum and molecular-level dynamical phenomena [19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Conformational dynamics of supramolecular protein assemblies

Kim

Nguyen

Bathe

2011

Journal of Structural Biology

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Supramolecular protein assemblies including molecular motors, cytoskeletal filaments, chaperones, and ribosomes play a central role in a broad array of cellular functions ranging from cell division and motility to RNA and protein synthesis and folding. Single-particle reconstructions of such assemblies have been growing rapidly in recent years, providing increasingly high resolution structural information under native conditions. While the static structure of these assemblies provides essential insight into their mechanism of biological function, their dynamical motions provide additional important information that cannot be inferred from structure alone. Here we present an unsupervised computational framework for the analysis of high molecular weight assemblies and use it to analyze the conformational dynamics of structures deposited in the Electron Microscopy Data Bank. Protein assemblies are modeled using a recently introduced coarse-grained modeling framework based on the finite element method, which is used to compute equilibrium thermal fluctuations, elastic strain energy distributions associated with specific conformational transitions, and dynamical correlations in distant molecular domains. Results are presented in detail for the ribosome-bound termination factor RF2 from Escherichia coli, the nuclear pore complex from Dictyostelium discoideum, and the chaperonin GroEL from E. coli. Elastic strain energy distributions reveal hinge-regions associated with specific conformational change pathways, and correlations in collective molecular motions reveal dynamical coupling between distant molecular domains that suggest new, as well as confirm existing, allosteric mechanisms. Results are publically available for use in further investigation and interpretation of biological function including cooperative transitions, allosteric communication, and molecular mechanics, as well as in further classification and refinement of electron microscopy based structures.

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Building-block approach for determining low-frequency normal modes of macromolecules

Cited by 446 publications

References 38 publications

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

Normal mode analysis of macromolecular systems with the mobile block Hessian method

Conformational dynamics of supramolecular protein assemblies

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