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Dannenhoffer-Lafage T, Voth GA. Reactive Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2020; 16:2541-2549. [DOI: 10.1021/acs.jctc.9b01140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Thomas Dannenhoffer-Lafage
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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Sharp ME, Vázquez FX, Wagner JW, Dannenhoffer-Lafage T, Voth GA. Multiconfigurational Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2019; 15:3306-3315. [PMID: 30897328 PMCID: PMC6660024 DOI: 10.1021/acs.jctc.8b01133] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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Standard low resolution
coarse-grained modeling techniques have difficulty capturing multiple
configurations of protein systems. Here, we present a method for creating
accurate coarse-grained (CG) models with multiple configurations using
a linear combination of functions or “states”. Individual
CG models are created to capture the individual states, and the approximate
coupling between the two states is determined from an all-atom potential
of mean force. We show that the resulting multiconfiguration coarse-graining
(MCCG) method accurately captures the transition state as well as
the free energy between the two states. We have tested this method
on the folding of dodecaalanine, as well as the amphipathic helix
of endophilin.
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Affiliation(s)
- Morris E Sharp
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Francisco X Vázquez
- Department of Chemistry , St. John's University , Queens , New York 11439 , United States
| | - Jacob W Wagner
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Thomas Dannenhoffer-Lafage
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
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Knott M, Best RB. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model. J Chem Phys 2014; 140:175102. [PMID: 24811666 PMCID: PMC4032430 DOI: 10.1063/1.4873710] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/17/2014] [Indexed: 12/31/2022] Open
Abstract
Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.
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Affiliation(s)
- Michael Knott
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Robert B Best
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Bianchi C, Zangi R. Dual base-flipping of cytosines in a CpG dinucleotide sequence. Biophys Chem 2013; 187-188:14-22. [PMID: 24469333 DOI: 10.1016/j.bpc.2013.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 12/30/2022]
Abstract
Simultaneous flipped-out conformation of two neighboring bases on opposite strands of DNAs has been observed in several X-ray structures. It has also been detected for two cytosines on opposite strands in different contexts of CpG sites. In this paper, we study by MD simulations the dual base flipping of the two cytosines in hemi-methylated CpG site. We calculate the potential of mean force of flipping-out the unmethylated cytosine in three model systems. The first is for DNA bound to the regulatory protein UHRF1. In this case, the methyl-cytosine on the complementary strand is flipped-out into the binding pocket of the SRA domain of the protein. The other two systems are for unbound DNAs in which the methyl-cytosine is either intra-helical or extra-helical. We find that when the methyl-cytosine is flipped-out it is easier to flip-out the other (unmethylated) cytosine on the opposite strand by about 14-16kJ/mol. This lower penalty for dual-base flipping is observed for both the bound and unbound states of the DNA. Analyses of the hydrogen bond network and stacking interactions within the CpG site indicate that the lower penalty is due to stabilization of the dual-base flipped-out conformation via interactions involving the orphan guanines. The results presented in this paper suggest that the extra-helical conformation of the methyl-cytosine recognized by UHRF1 can facilitate the base-flipping process of the target cytosine to be methylated by Dnmt1.
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Affiliation(s)
- Caterina Bianchi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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Bianchi C, Zangi R. Base-Flipping Propensities of Unmethylated, Hemimethylated, and Fully Methylated CpG Sites. J Phys Chem B 2013; 117:2348-58. [DOI: 10.1021/jp312145b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Caterina Bianchi
- Department of Organic
Chemistry
I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic
Chemistry
I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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Dans PD, Pérez A, Faustino I, Lavery R, Orozco M. Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Res 2012; 40:10668-78. [PMID: 23012264 PMCID: PMC3510489 DOI: 10.1093/nar/gks884] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The traditional mesoscopic paradigm represents DNA as a series of base-pair steps whose energy response to equilibrium perturbations is elastic, with harmonic oscillations (defining local stiffness) around a single equilibrium conformation. In addition, base sequence effects are often analysed as a succession of independent XpY base-pair steps (i.e. a nearest-neighbour (NN) model with only 10 unique cases). Unfortunately, recent massive simulations carried out by the ABC consortium suggest that the real picture of DNA flexibility may be much more complex. The paradigm of DNA flexibility therefore needs to be revisited. In this article, we explore in detail one of the most obvious violations of the elastic NN model of flexibility: the bimodal distributions of some helical parameters. We perform here an in-depth statistical analysis of a very large set of MD trajectories and also of experimental structures, which lead to very solid evidence of bimodality. We then suggest ways to improve mesoscopic models to account for this deviation from the elastic regime.
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Affiliation(s)
- Pablo D Dans
- Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine, Parc Cientific de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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Abstract
It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global thermodynamic and kinetic picture of the binding landscape of DNA will become available in a few years. MD will become a crucial tool in areas such as biomolecular engineering and synthetic biology. MD has also been shown to be an excellent source of parameters for mesoscopic models of DNA flexibility. Such models can be refined through atomistic MD simulations on small duplexes and then applied to the study of entire chromosomes. Recent evidence suggests that MD-derived elastic models can successfully predict the position of regulatory regions in DNA and can help advance our understanding of nucleosome positioning and chromatin plasticity. If these results are confirmed, MD simulations can become the ultimate tool to decipher a physical code that can contribute to gene regulation. We are entering the golden age of MD simulations of DNA. Undoubtedly, the expectations are high, but the challenges are also enormous. These include the need for more accurate potential energy functionals and for longer and more complex simulations in more realistic systems. The joint research effort of several groups will be crucial for adapting the technique to the requirements of the coming decade.
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Affiliation(s)
- Alberto Pérez
- Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine Barcelona, Baldiri i Reixac 10, Barcelona 08028, Spain
| | - F. Javier Luque
- Department de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain
| | - Modesto Orozco
- Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine Barcelona, Baldiri i Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain, and Instituto Nacional de Bioinformàtica, Parc Científic de Barcelona, Baldiri i Reixac 10, Barcelona 08028, Spain
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Farah K, Müller-Plathe F, Böhm MC. Classical Reactive Molecular Dynamics Implementations: State of the Art. Chemphyschem 2012; 13:1127-51. [DOI: 10.1002/cphc.201100681] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Indexed: 11/09/2022]
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In Silico Strategies Toward Enzyme Function and Dynamics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [DOI: 10.1016/b978-0-12-398312-1.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Sutto L, Mereu I, Gervasio FL. A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions. J Chem Theory Comput 2011; 7:4208-17. [DOI: 10.1021/ct200547m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ludovico Sutto
- Spanish National Cancer Research Center (CNIO), Structural Biology and Biocomputing Programme, Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain
| | - Ilaria Mereu
- Spanish National Cancer Research Center (CNIO), Structural Biology and Biocomputing Programme, Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain
| | - Francesco Luigi Gervasio
- Spanish National Cancer Research Center (CNIO), Structural Biology and Biocomputing Programme, Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain
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