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Tzvetkova P, Sternberg U, Gloge T, Navarro-Vázquez A, Luy B. Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints. Chem Sci 2019; 10:8774-8791. [PMID: 31803450 PMCID: PMC6849632 DOI: 10.1039/c9sc01084j] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/19/2019] [Indexed: 12/27/2022] Open
Abstract
Residual dipolar couplings (RDCs) and other residual anisotropic NMR parameters provide valuable structural information of high quality and quantity, bringing detailed structural models of flexible molecules in solution in reach. The corresponding data interpretation so far is directly or indirectly based on the concept of a molecular alignment tensor, which, however, is ill-defined for flexible molecules. The concept is typically applied to a single or a small set of lowest energy structures, ignoring the effect of vibrational averaging. Here, we introduce an entirely different approach based on time averaged molecular dynamics with dipolar couplings as tensorial orientational restraints that can be used to solve structural problems in molecules of any size without the need of introducing an explicit molecular alignment tensor into the computation. RDC restraints are represented by their full 3D interaction tensor in the laboratory frame, for which pseudo forces are calculated using a secular dipolar Hamiltonian as the target. The resulting rotational averaging of each individual tensorial restraint leads to structural ensembles that best fulfil the experimental data. Using one-bond RDCs, the approach has been implemented in the force field procedures of the program COSMOS and extensively tested. A concise theoretical introduction, including the special treatment of force fields for stable and fast MD simulations, as well as applications regarding configurational analyses of small to medium-sized organic molecules with different degrees of flexibility, is given. The observed results are discussed in detail.
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Affiliation(s)
- Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Ulrich Sternberg
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Thomas Gloge
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Armando Navarro-Vázquez
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
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Di Pietro ME, Sternberg U, Luy B. Molecular Dynamics with Orientational Tensorial Constraints: A New Approach to Probe the Torsional Angle Distributions of Small Rotationally Flexible Molecules. J Phys Chem B 2019; 123:8480-8491. [PMID: 31502838 DOI: 10.1021/acs.jpcb.9b07008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The potential of residual dipolar couplings (RDCs) in conformational studies of small molecules is now widely recognized, but current theoretical approaches for their interpretation have several limitations and there is still the need for a general method to probe the torsional angle distributions applicable to any rotationally flexible molecule. Molecular dynamics simulations with RDC-based orientational tensorial constraints (MDOC), implemented in the software COSMOS, are presented here as a conceptually new strategy. For the cases of the fluorinated anti-inflammatory drug diflunisal and the disaccharide cellobiose, we demonstrate that MDOC simulations with one-bond RDCs as tensorial constraints unveil torsion distributions and allow the determination of relative configuration in the presence of rotational flexibility. The independence of the initial structure or any a priori assumption as well as the possibility to combine different experimental constraints represent features, which make the COSMOS software a promising tool for the investigation of torsional angle distributions of flexible molecules, regardless of their size and degree of freedom.
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Affiliation(s)
- Maria E Di Pietro
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Ulrich Sternberg
- COSMOS GbR , Jena 07743 , Germany.,Research Partner , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Burkhard Luy
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany.,Institute for Biological Interfaces 4-Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen 76021 , Germany
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Allison JR. Using simulation to interpret experimental data in terms of protein conformational ensembles. Curr Opin Struct Biol 2017; 43:79-87. [DOI: 10.1016/j.sbi.2016.11.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/15/2016] [Accepted: 11/21/2016] [Indexed: 01/03/2023]
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Salvi N, Salmon L, Blackledge M. Dynamic Descriptions of Highly Flexible Molecules from NMR Dipolar Couplings: Physical Basis and Limitations. J Am Chem Soc 2017; 139:5011-5014. [PMID: 28290683 DOI: 10.1021/jacs.7b01566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biomolecules that control physiological function by changing their conformation play key roles in biology and remain poorly characterized. NMR dipolar couplings (DCs) depend intrinsically on both molecular shape and structural fluctuations, thereby providing the enticing prospect of tracking these conformational changes at atomic detail. Although this dual dependence has until now severely complicated analysis of DCs from highly dynamic systems, general approaches have recently been proposed that simplify interpretation of experimental DCs, by entirely eliminating molecular alignment from the analysis. Using simple and intuitive simulation of target ensembles, we investigate the impact of such approaches on the resulting descriptions of the conformational energy landscape. We find that ensemble descriptions of highly flexible systems derived from DCs without explicit consideration of the alignment properties of the constituent conformations can be compromised and inaccurate, despite exhibiting high correlation with experimental measurement.
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Affiliation(s)
- Nicola Salvi
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes , Grenoble 38044, France
| | - Loïc Salmon
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes , Grenoble 38044, France
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes , Grenoble 38044, France
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Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M. Structure of a low-population binding intermediate in protein-RNA recognition. Proc Natl Acad Sci U S A 2016; 113:7171-6. [PMID: 27286828 PMCID: PMC4932932 DOI: 10.1073/pnas.1521349113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michael F Bardaro
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
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Venditti V, Egner TK, Clore GM. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering. Chem Rev 2016; 116:6305-22. [PMID: 26739383 PMCID: PMC5590664 DOI: 10.1021/acs.chemrev.5b00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Solving structures or structural ensembles of large macromolecular systems in solution poses a challenging problem. While NMR provides structural information at atomic resolution, increased spectral complexity, chemical shift overlap, and short transverse relaxation times (associated with slow tumbling) render application of the usual techniques that have been so successful for medium sized systems (<50 kDa) difficult. Solution X-ray scattering, on the other hand, is not limited by molecular weight but only provides low resolution structural information related to the overall shape and size of the system under investigation. Here we review how combining atomic resolution structures of smaller domains with sparse experimental data afforded by NMR residual dipolar couplings (which yield both orientational and shape information) and solution X-ray scattering data in rigid-body simulated annealing calculations provides a powerful approach for investigating the structural aspects of conformational dynamics in large multidomain proteins. The application of this hybrid methodology is illustrated for the 128 kDa dimer of bacterial Enzyme I which exists in a variety of open and closed states that are sampled at various points in the catalytic cycles, and for the capsid protein of the human immunodeficiency virus.
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Affiliation(s)
- Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Timothy K. Egner
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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Camilloni C, Vendruscolo M. Using Pseudocontact Shifts and Residual Dipolar Couplings as Exact NMR Restraints for the Determination of Protein Structural Ensembles. Biochemistry 2015; 54:7470-6. [DOI: 10.1021/acs.biochem.5b01138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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