Detecting Allosteric Networks Using Molecular Dynamics Simulation

Bowerman, Samuel; Wereszczynski, Jeff

doi:10.1016/bs.mie.2016.05.027

Cited by 91 publications

(138 citation statements)

References 55 publications

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“…13 These identified allosteric effects are of particular interest in light of the wider scope of computational biophysics in deciphering protein allostery. 22−24 Besides this, and more importantly, the interplay between L2 and the nt -DNA strand—which has been here identified as a key element for the activation process—calls for novel mutagenesis and kinetic experiments, in an effort to structurally engineer Cas9 for achieving higher efficiency.…”

Section: Resultsmentioning

confidence: 95%

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

et al. 2016

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The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system recently emerged as a transformative genome-editing technology that is innovating basic bioscience and applied medicine and biotechnology. The endonuclease Cas9 associates with a guide RNA to match and cleave complementary sequences in double stranded DNA, forming an RNA:DNA hybrid and a displaced non-target DNA strand. Although extensive structural studies are ongoing, the conformational dynamics of Cas9 and its interplay with the nucleic acids during association and DNA cleavage are largely unclear. Here, by employing multi-microsecond time scale molecular dynamics, we reveal the conformational plasticity of Cas9 and identify key determinants that allow its large-scale conformational changes during nucleic acid binding and processing. We show how the “closure” of the protein, which accompanies nucleic acid binding, fundamentally relies on highly coupled and specific motions of the protein domains, collectively initiating the prominent conformational changes needed for nucleic acid association. We further reveal a key role of the non-target DNA during the process of activation of the nuclease HNH domain, showing how the nontarget DNA positioning triggers local conformational changes that favor the formation of a catalytically competent Cas9. Finally, a remarkable conformational plasticity is identified as an intrinsic property of the HNH domain, constituting a necessary element that allows for the HNH repositioning. These novel findings constitute a reference for future experimental studies aimed at a full characterization of the dynamic features of the CRISPR-Cas9 system, and—more importantly—call for novel structure engineering efforts that are of fundamental importance for the rational design of new genome-engineering applications.

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Section: Resultsmentioning

confidence: 95%

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

et al. 2016

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“…The potential utility of covariance analysis of MD simulations was described by McCammon and Harvey (McCAmmon & Harvey, 1987), and subsequent research comes from several laboratories (Harte et al, 1990;Harte, 1992;Hunenberger, Mark, & van Gunsteren, 1995;Ichiye, Olafson, Swaminathan & Karplus, 1986;Roy & Post, 2012). Insights into allostery from MD have been reported in a number of cases (Bowerman & Wereszczynski, 2016;Ho & Agard, 2009;Hertig, Latorraca & Dror, 2016;Ota & Agard, 2005;Sharp & Skinner, 2006). Pairwise coevolving amino acids have been used to identify structural and dynamical domains in proteins (Granata, Ponzoni, Micheletti, & Carneval, 2017;Ponzoni, Polles, Carnevale, & Micheletti, 2015).…”

Section: Introductionmentioning

confidence: 99%

Spectral analysis of molecular dynamics simulations on PDZ: MD sectors

Lakhani

Thayer

Black

et al. 2019

Journal of Biomolecular Structure and Dynamics

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The idea of protein "sectors" posits that sparse subsets of amino acid residues form cooperative networks that are key elements of protein stability, ligand binding, and allosterism. To date, protein sectors have been calculated by the statistical coupling analysis (SCA) method of Ranganathan and coworkers via the spectral analysis of conservation-weighted evolutionary covariance matrices obtained from a multiple sequence alignments of homologous families of proteins. SCA sectors, a knowledgebased protocol, have been indentified with functional properties and allosterism for a number of systems. In this study, we investigate the utility of the sector idea for the analysis of physics-based molecular dynamics (MD) trajectories of proteins. Our test case for this procedure is PSD95-PDZ3, one of the smallest proteins for which allosterism has been observed. It has served previously as a model system for a number of prediction algorithms, and is well characterized by X-ray crystallography, NMR spectroscopy and site specific mutagenisis. All-atom MD simulations were performed for a total of 500 nanoseconds using AMBER, and MD-calculated covariance matrices for the fluctuations of residue displacements and non-bonded interaction energies were subjected to spectral analysis in a manner analogous to that of SCA. The composition of MD sectors was compared with results from SCA, site specific mutagenesis, and allosterism. The concordance indicates that MD sectors are a viable protocol for analyzing MD trajectories and provide insight into the physical origin of the phenomenon.

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“…We adopted the concept of shortest path between nodes in weighted graph to get insights into internal pathways that are important for propagating allosteric signals [ 34 ]. The likely allosteric pathway between residues is calculated by the method which shows the propagation through networks of highly correlated neighbors [ 16 , 35 ]. With the graph of residue networks, we calculated and mapped out the potential allosteric pathways that were deemed important for energy propagation from residue mutation sites.…”

Section: Resultsmentioning

confidence: 99%

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations

Mei

Zhou

Zhu

et al. 2018

IJMS

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A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.

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Detecting Allosteric Networks Using Molecular Dynamics Simulation

Cited by 91 publications

References 55 publications

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

Spectral analysis of molecular dynamics simulations on PDZ: MD sectors

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations

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