ArticleBiophysical journal2008
Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Attenuating dependence on structural data in computing protein energy landscapes.BMC bioinformatics · 2019Article
- Systematic Dissociation Pathway Searches Guided by Principal Component Modes.Journal of chemical theory and computation · 2017Article
- Understanding ligand-receptor non-covalent binding kinetics using molecular modeling.Frontiers in bioscience (Landmark edition) · 2017Review
- ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution.Journal of chemical theory and computation · 2016Article
- Article
- Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin.Scientific reports · 2015Article
- Features of large hinge-bending conformational transitions. Prediction of closed structure from open state.Biophysical journal · 2014Article
- Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.PLoS computational biology · 2014Article
- Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase.Biophysical journal · 2013Article
- Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.BMC structural biology · 2013Article
- Biomolecular dynamics: order-disorder transitions and energy landscapes.Reports on progress in physics. Physical Society (Great Britain) · 2012Article
- Towards the prediction of order parameters from molecular dynamics simulations in proteins.The Journal of chemical physics · 2012Article
- Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins.Protein science : a publication of the Protein Society · 2011Review
- On the functional significance of soft modes predicted by coarse-grained models for membrane proteins.The Journal of general physiology · 2010Article
- Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions.Biophysical journal · 2010Article
- Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.Journal of molecular biology · 2009Article
- Changes in electrostatic surface potential of Na+/K+-ATPase cytoplasmic headpiece induced by cytoplasmic ligand(s) binding.Biophysical journal · 2009Article
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3 authors.
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Abstract
Conformational transitions between open/closed or free/bound states in proteins possess functional importance. We propose a technique in which the collective modes obtained from an anisotropic network model (ANM) are used in conjunction with a Monte Carlo (MC) simulation approach, to investigate conformational transition pathways and pathway intermediates. The ANM-MC technique is applied to adenylate kinase (AK) and hemoglobin. The iterative method, in which normal modes are continuously updated during the simulation, proves successful in accomplishing the transition between open-closed conformations of AK and tense-relaxed forms of hemoglobin (C(alpha)-root mean square deviations between two end structures of 7.13 A and 3.55 A, respectively). Target conformations are reached by root mean-square deviations of 2.27 A and 1.90 A for AK and hemoglobin, respectively. The intermediate conformations overlap with crystal structures from the AK family within a 3.0-A root mean-square deviation. In the case of hemoglobin, the transition of tense-to-relaxed passes through the relaxed state. In both cases, the lowest-frequency modes are effective during transitions. The targeted Monte Carlo approach is used without the application of collective modes. Both the ANM-MC and targeted Monte Carlo techniques can explore sequences of events in transition pathways with an efficient yet realistic conformational search.
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