1
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Orioli S, Larsen AH, Bottaro S, Lindorff-Larsen K. How to learn from inconsistencies: Integrating molecular simulations with experimental data. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:123-176. [PMID: 32145944 DOI: 10.1016/bs.pmbts.2019.12.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modeling tool to interpret experimental measurements, and to use experimental data to refine our biophysical models. Thus, explicit integration and synergy between molecular simulations and experiments is fundamental for furthering our understanding of biological processes. This is especially true in the case where discrepancies between measured and simulated observables emerge. In this chapter, we provide an overview of some of the core ideas behind methods that were developed to improve the consistency between experimental information and numerical predictions. We distinguish between situations where experiments are used to refine our understanding and models of specific systems, and situations where experiments are used more generally to refine transferable models. We discuss different philosophies and attempt to unify them in a single framework. Until now, such integration between experiments and simulations have mostly been applied to equilibrium data, and we discuss more recent developments aimed to analyze time-dependent or time-resolved data.
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Affiliation(s)
- Simone Orioli
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Haahr Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Atomistic Simulations Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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2
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Abstract
Bayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem.
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3
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Köfinger J, Stelzl LS, Reuter K, Allande C, Reichel K, Hummer G. Efficient Ensemble Refinement by Reweighting. J Chem Theory Comput 2019; 15:3390-3401. [PMID: 30939006 PMCID: PMC6727217 DOI: 10.1021/acs.jctc.8b01231] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Indexed: 01/24/2023]
Abstract
Ensemble refinement produces structural ensembles of flexible and dynamic biomolecules by integrating experimental data and molecular simulations. Here we present two efficient numerical methods to solve the computationally challenging maximum-entropy problem arising from a Bayesian formulation of ensemble refinement. Recasting the resulting constrained weight optimization problem into an unconstrained form enables the use of gradient-based algorithms. In two complementary formulations that differ in their dimensionality, we optimize either the log-weights directly or the generalized forces appearing in the explicit analytical form of the solution. We first demonstrate the robustness, accuracy, and efficiency of the two methods using synthetic data. We then use NMR J-couplings to reweight an all-atom molecular dynamics simulation ensemble of the disordered peptide Ala-5 simulated with the AMBER99SB*-ildn-q force field. After reweighting, we find a consistent increase in the population of the polyproline-II conformations and a decrease of α-helical-like conformations. Ensemble refinement makes it possible to infer detailed structural models for biomolecules exhibiting significant dynamics, such as intrinsically disordered proteins, by combining input from experiment and simulation in a balanced manner.
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Affiliation(s)
- Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße
3, 60438 Frankfurt
am Main, Germany
| | - Lukas S. Stelzl
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße
3, 60438 Frankfurt
am Main, Germany
| | - Klaus Reuter
- Max Planck Computing and
Data Facility, Gießenbachstr. 2, 85748 Garching, Germany
| | - César Allande
- Max Planck Computing and
Data Facility, Gießenbachstr. 2, 85748 Garching, Germany
| | - Katrin Reichel
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße
3, 60438 Frankfurt
am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße
3, 60438 Frankfurt
am Main, Germany
- Institute for Biophysics, Goethe University, 60438 Frankfurt
am Main, Germany
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4
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Reichel K, Stelzl LS, Köfinger J, Hummer G. Precision DEER Distances from Spin-Label Ensemble Refinement. J Phys Chem Lett 2018; 9:5748-5752. [PMID: 30212206 DOI: 10.1021/acs.jpclett.8b02439] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Double electron-electron resonance (DEER) experiments probe nanometer-scale distances in spin-labeled proteins and nucleic acids. Rotamer libraries of the covalently attached spin-labels help reduce position uncertainties. Here we show that rotamer reweighting is essential for precision distance measurements, making it possible to resolve Ångstrom-scale domain motions. We analyze extensive DEER measurements on the three N-terminal polypeptide transport-associated (POTRA) domains of the outer membrane protein Omp85. Using the "Bayesian inference of ensembles" maximum-entropy method, we extract rotamer weights from the DEER measurements. Small weight changes suffice to eliminate otherwise significant discrepancies between experiments and model and unmask 1-3 Å domain motions relative to the crystal structure. Rotamer-weight refinement is a simple yet powerful tool for precision distance measurements that should be broadly applicable to label-based measurements including DEER, paramagnetic relaxation enhancement, and fluorescence resonance energy transfer (FRET).
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Affiliation(s)
- Katrin Reichel
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
- Institute of Biophysics , Goethe University , Max-von-Laue-Straße 9 , 60438 Frankfurt am Main , Germany
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5
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Vögeli B, Vugmeyster L. Distance-independent Cross-correlated Relaxation and Isotropic Chemical Shift Modulation in Protein Dynamics Studies. Chemphyschem 2018; 20:178-196. [PMID: 30110510 DOI: 10.1002/cphc.201800602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 01/09/2023]
Abstract
Cross-correlated relaxation (CCR) in multiple-quantum coherences differs from other relaxation phenomena in its theoretical ability to be mediated across an infinite distance. The two interfering relaxation mechanisms may be dipolar interactions, chemical shift anisotropies, chemical shift modulations or quadrupolar interactions. These properties make multiple-quantum CCR an attractive probe for structure and dynamics of biomacromolecules not accessible from other measurements. Here, we review the use of multiple-quantum CCR measurements in dynamics studies of proteins. We compile a list of all experiments proposed for CCR rate measurements, provide an overview of the theory with a focus on protein dynamics, and present applications to various protein systems.
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Affiliation(s)
- Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, 12801 East 17th Avenue, Aurora, CO, 80045, United States
| | - Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, 1201 Laurimer Street Denver, CO, 80204, United States
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6
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Papaleo E, Camilloni C, Teilum K, Vendruscolo M, Lindorff-Larsen K. Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs. PeerJ 2018; 6:e5125. [PMID: 30013831 PMCID: PMC6035720 DOI: 10.7717/peerj.5125] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/08/2018] [Indexed: 01/24/2023] Open
Abstract
Many proteins display complex dynamical properties that are often intimately linked to their biological functions. As the native state of a protein is best described as an ensemble of conformations, it is important to be able to generate models of native state ensembles with high accuracy. Due to limitations in sampling efficiency and force field accuracy it is, however, challenging to obtain accurate ensembles of protein conformations by the use of molecular simulations alone. Here we show that dynamic ensemble refinement, which combines an accurate atomistic force field with commonly available nuclear magnetic resonance (NMR) chemical shifts and NOEs, can provide a detailed and accurate description of the conformational ensemble of the native state of a highly dynamic protein. As both NOEs and chemical shifts are averaged on timescales up to milliseconds, the resulting ensembles reflect the structural heterogeneity that goes beyond that probed, e.g., by NMR relaxation order parameters. We selected the small protein domain NCBD as object of our study since this protein, which has been characterized experimentally in substantial detail, displays a rich and complex dynamical behaviour. In particular, the protein has been described as having a molten-globule like structure, but with a relatively rigid core. Our approach allowed us to describe the conformational dynamics of NCBD in solution, and to probe the structural heterogeneity resulting from both short- and long-timescale dynamics by the calculation of order parameters on different time scales. These results illustrate the usefulness of our approach since they show that NCBD is rather rigid on the nanosecond timescale, but interconverts within a broader ensemble on longer timescales, thus enabling the derivation of a coherent set of conclusions from various NMR experiments on this protein, which could otherwise appear in contradiction with each other.
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Affiliation(s)
- Elena Papaleo
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Current affiliation: Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Current affiliation: Department of Biosciences, University of Milano, Milano, Italy
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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7
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Matsunaga Y, Sugita Y. Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning. eLife 2018; 7:32668. [PMID: 29723137 PMCID: PMC5933924 DOI: 10.7554/elife.32668] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide time-series data, such as donor-acceptor distances, whereas the latter give atomistic information, although this information is often biased by model parameters. Here, we devise a machine-learning method to combine the complementary information from the two approaches and construct a consistent model of conformational dynamics. It is applied to the folding dynamics of the formin-binding protein WW domain. MD simulations over 400 μs led to an initial Markov state model (MSM), which was then "refined" using single-molecule Förster resonance energy transfer (FRET) data through hidden Markov modeling. The refined or data-assimilated MSM reproduces the FRET data and features hairpin one in the transition-state ensemble, consistent with mutation experiments. The folding pathway in the data-assimilated MSM suggests interplay between hydrophobic contacts and turn formation. Our method provides a general framework for investigating conformational transitions in other proteins.
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Affiliation(s)
- Yasuhiro Matsunaga
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.,JST PRESTO, Kawaguchi, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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8
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Sabo TM, Gapsys V, Walter KFA, Fenwick RB, Becker S, Salvatella X, de Groot BL, Lee D, Griesinger C. Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 2018; 138-139:85-92. [PMID: 29656081 DOI: 10.1016/j.ymeth.2018.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/02/2018] [Accepted: 04/10/2018] [Indexed: 11/30/2022] Open
Abstract
Dipole-dipole cross-correlated relaxation (CCR) between two spin pairs is rich with macromolecular structural and dynamic information on inter-nuclear bond vectors. Measurement of short range dipolar CCR rates has been demonstrated for a variety of inter-nuclear vector spin pairs in proteins and nucleic acids, where the multiple quantum coherence necessary for observing the CCR rate is created by through-bond scalar coupling. In principle, CCR rates can be measured for any pair of inter-nuclear vectors where coherence can be generated between one spin of each spin pair, regardless of both the distance between the two spin pairs and the distance of the two spins forming the multiple quantum coherence. In practice, however, long range CCR (lrCCR) rates are challenging to measure due to difficulties in linking spatially distant spin pairs. By utilizing through-space relaxation allowed coherence transfer (RACT), we have developed a new method for the measurement of lrCCR rates involving CαHα bonds on opposing anti-parallel β-strands. The resulting lrCCR rates are straightforward to interpret since only the angle between the two vectors modulates the strength of the interference effect. We applied our lrCCR measurement to the third immunoglobulin-binding domain of the streptococcal protein G (GB3) and utilize published NMR ensembles and static NMR/X-ray structures to highlight the relationship between the lrCCR rates and the CαHα-CαHα inter-bond angle and bond mobility. Furthermore, we employ the lrCCR rates to guide the selection of sub-ensembles from the published NMR ensembles for enhancing the structural and dynamic interpretation of the data. We foresee this methodology for measuring lrCCR rates as improving the generation of structural ensembles by providing highly accurate details concerning the orientation of CαHα bonds on opposing anti-parallel β-strands.
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Affiliation(s)
- T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
| | - Vytautas Gapsys
- Department for Computational Biomolecular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Korvin F A Walter
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - R Bryn Fenwick
- Department of Integrative Structural and Computational Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Stefan Becker
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis AvanÅats (ICREA), Barcelona, Spain
| | - Bert L de Groot
- Department for Computational Biomolecular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
| | - Christian Griesinger
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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9
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Fenwick RB, Vögeli B. Detection of Correlated Protein Backbone and Side-Chain Angle Fluctuations. Chembiochem 2017; 18:2016-2021. [PMID: 28771902 DOI: 10.1002/cbic.201700312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Indexed: 11/09/2022]
Abstract
NMR methods for the characterization of local protein motions have attained a high level of sophistication. Measurement of the synchronization between those motions, however, poses a serious challenge. Such correlated motions are one of the underlying mechanisms for the propagation of local changes to remote sites and as such for information transfer. Here, we demonstrate the experimental detection of the synchronization of motion over an intermediate range. To that purpose, we designed pulse sequences for the measurement of cross-correlated relaxation between the backbone HN -N and side-chain Hβ -Cβ dipoles in Ile, Thr, and Val in the protein GB3. These bonds are related through two and three intervening dihedral angles. We show that the correlated motions inherent in a structural ensemble obtained from a large and diverse array of NMR probes are in excellent agreement with our measurements.
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Affiliation(s)
- R Bryn Fenwick
- The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, Research Center 1 South, Room 9103, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO, 80045, USA
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10
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Combining experimental and simulation data of molecular processes via augmented Markov models. Proc Natl Acad Sci U S A 2017; 114:8265-8270. [PMID: 28716931 DOI: 10.1073/pnas.1704803114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.
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11
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The Exact Nuclear Overhauser Enhancement: Recent Advances. Molecules 2017; 22:molecules22071176. [PMID: 28708092 PMCID: PMC6152122 DOI: 10.3390/molecules22071176] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 02/04/2023] Open
Abstract
Although often depicted as rigid structures, proteins are highly dynamic systems, whose motions are essential to their functions. Despite this, it is difficult to investigate protein dynamics due to the rapid timescale at which they sample their conformational space, leading most NMR-determined structures to represent only an averaged snapshot of the dynamic picture. While NMR relaxation measurements can help to determine local dynamics, it is difficult to detect translational or concerted motion, and only recently have significant advances been made to make it possible to acquire a more holistic representation of the dynamics and structural landscapes of proteins. Here, we briefly revisit our most recent progress in the theory and use of exact nuclear Overhauser enhancements (eNOEs) for the calculation of structural ensembles that describe their conformational space. New developments are primarily targeted at increasing the number and improving the quality of extracted eNOE distance restraints, such that the multi-state structure calculation can be applied to proteins of higher molecular weights. We then review the implications of the exact NOE to the protein dynamics and function of cyclophilin A and the WW domain of Pin1, and finally discuss our current research and future directions.
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12
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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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13
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Vögeli B. Cross-correlated relaxation rates between protein backbone H-X dipolar interactions. JOURNAL OF BIOMOLECULAR NMR 2017; 67:211-232. [PMID: 28286915 DOI: 10.1007/s10858-017-0098-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 02/19/2017] [Indexed: 06/06/2023]
Abstract
The relaxation interference between dipole-dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive HN-N and Hα-Cα dipole-dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates. All rates were obtained from at least two different pulse sequences, of which the yet unpublished ones are presented. Detailed comparisons between the different methods and corrections for unwanted pathways demonstrate that the averaged CCR rates are highly accurate and precise with errors of 1.5-3% of the entire value ranges.
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Affiliation(s)
- Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Research Center 1 South, Room 9103, 12801 East 17th Avenue, Aurora, CO, 80045, USA.
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14
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Antonov LD, Olsson S, Boomsma W, Hamelryck T. Bayesian inference of protein ensembles from SAXS data. Phys Chem Chem Phys 2017; 18:5832-8. [PMID: 26548662 DOI: 10.1039/c5cp04886a] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The inherent flexibility of intrinsically disordered proteins (IDPs) and multi-domain proteins with intrinsically disordered regions (IDRs) presents challenges to structural analysis. These macromolecules need to be represented by an ensemble of conformations, rather than a single structure. Small-angle X-ray scattering (SAXS) experiments capture ensemble-averaged data for the set of conformations. We present a Bayesian approach to ensemble inference from SAXS data, called Bayesian ensemble SAXS (BE-SAXS). We address two issues with existing methods: the use of a finite ensemble of structures to represent the underlying distribution, and the selection of that ensemble as a subset of an initial pool of structures. This is achieved through the formulation of a Bayesian posterior of the conformational space. BE-SAXS modifies a structural prior distribution in accordance with the experimental data. It uses multi-step expectation maximization, with alternating rounds of Markov-chain Monte Carlo simulation and empirical Bayes optimization. We demonstrate the method by employing it to obtain a conformational ensemble of the antitoxin PaaA2 and comparing the results to a published ensemble.
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Affiliation(s)
- L D Antonov
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - S Olsson
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland and Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - W Boomsma
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - T Hamelryck
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
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15
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Olsson S, Noé F. Mechanistic Models of Chemical Exchange Induced Relaxation in Protein NMR. J Am Chem Soc 2016; 139:200-210. [DOI: 10.1021/jacs.6b09460] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Simon Olsson
- Computational Molecular
Biology,
FB Mathematik und Informatik, Freie Universität Berlin, Berlin 14195, Germany
| | - Frank Noé
- Computational Molecular
Biology,
FB Mathematik und Informatik, Freie Universität Berlin, Berlin 14195, Germany
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16
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Vögeli B, Olsson S, Güntert P, Riek R. The Exact NOE as an Alternative in Ensemble Structure Determination. Biophys J 2016; 110:113-26. [PMID: 26745415 DOI: 10.1016/j.bpj.2015.11.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 10/22/2022] Open
Abstract
The structure-function paradigm is increasingly replaced by the structure-dynamics-function paradigm. All protein activity is steered by the interplay between enthalpy and entropy. Conformational dynamics serves as a proxy of conformational entropy. Therefore, it is essential to study not only the average conformation but also the spatial sampling of a protein on all timescales. To this purpose, we have established a protocol for determining multiple-state ensembles of proteins based on exact nuclear Overhauser effects (eNOEs). We have recently extended our previously reported eNOE data set for the protein GB3 by a very large set of backbone and side-chain residual dipolar couplings and three-bond J couplings. Here, we demonstrate that at least four structural states are required to represent the complete data set by dissecting the contributions to the CYANA target function, which quantifies restraint violations in structure calculation. We present a four-state ensemble of GB3, which largely preserves the characteristics obtained from eNOEs only. Due to the abundance of the input data, the ensemble and χ(1) angles in particular are well suited for cross-validation of the input data and comparison to x-ray structures. Principal component analysis is used to automatically identify and validate relevant states of the ensembles. Overall, our findings suggest that eNOEs are a valuable alternative to traditional NMR probes in spatial elucidation of proteins.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland.
| | - Simon Olsson
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland; Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Frankfurt am Main, Germany; Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
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17
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Hummer G, Köfinger J. Bayesian ensemble refinement by replica simulations and reweighting. J Chem Phys 2016; 143:243150. [PMID: 26723635 DOI: 10.1063/1.4937786] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.
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Affiliation(s)
- Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
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18
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Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. Finding Our Way in the Dark Proteome. J Am Chem Soc 2016; 138:9730-42. [PMID: 27387657 PMCID: PMC5051545 DOI: 10.1021/jacs.6b06543] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. We envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.
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Affiliation(s)
- Asmit Bhowmick
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - David H. Brookes
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037
| | - Julie D. Forman-Kay
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Daniel Gunter
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| | | | - Gregory L. Hura
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - David E. Wemmer
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Peter E. Wright
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
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19
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The Dynamic Basis for Signal Propagation in Human Pin1-WW. Structure 2016; 24:1464-75. [PMID: 27499442 DOI: 10.1016/j.str.2016.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/11/2016] [Accepted: 06/14/2016] [Indexed: 12/23/2022]
Abstract
Allostery is the structural manifestation of information transduction in biomolecules. Its hallmark is conformational change induced by perturbations at a distal site. An increasing body of evidence demonstrates the presence of allostery in very flexible and even disordered proteins, encouraging a thermodynamic description of this phenomenon. Still, resolving such processes at atomic resolution is difficult. Here we establish a protocol to determine atomistic thermodynamic models of such systems using high-resolution solution state nuclear magnetic resonance data and extensive molecular simulations. Using this methodology, we study information transduction in the WW domain of a key cell-cycle regulator Pin1. Pin1 binds promiscuously to phospho-Ser/Thr-Pro motifs, however, disparate structural and dynamic responses have been reported upon binding different ligands. Our model consists of two topologically distinct states whose relative population may be specifically skewed by an incoming ligand. This model provides a canonical basis for the understanding of multi-functionality in Pin1.
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20
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Fenwick RB, Schwieters CD, Vögeli B. Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions. J Am Chem Soc 2016; 138:8412-21. [PMID: 27331619 PMCID: PMC5055379 DOI: 10.1021/jacs.6b01447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synchronization of native state motions as they transition between microstates influences catalysis kinetics, mediates allosteric interactions, and reduces the conformational entropy of proteins. However, it has proven difficult to describe native microstates because they are usually minimally frustrated and may interconvert on the micro- to millisecond time scale. Direct observation of concerted equilibrium fluctuations would therefore be an important tool for describing protein native states. Here we propose a strategy that relates NMR cross-correlated relaxation (CCR) rates between dipolar interactions to residual dipolar couplings (RDCs) of individual consecutive H(N)-N and H(α)-C(α) bonds, which act as a proxy for the peptide planes and the side chains, respectively. Using Xplor-NIH ensemble structure calculations restrained with the RDC and CCR data, we observe collective motions on time scales slower than nanoseconds in the backbone for GB3. To directly access the correlations from CCR, we develop a structure-free data analysis. The resulting dynamic correlation map is consistent with the ensemble-restrained simulations and reveals a complex network. In general, we find that the bond motions are on average slightly correlated and that the local environment dominates many observations. Despite this, some patterns are typical over entire secondary structure elements. In the β-sheet, nearly all bonds are weakly correlated, and there is an approximately binary alternation in correlation intensity corresponding to the solvent exposure/shielding alternation of the side chains. For α-helices, there is also a weak correlation in the H(N)-N bonds. The degree of correlation involving H(α)-C(α) bonds is directly affected by side-chain fluctuations, whereas loops show complex and nonuniform behavior.
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Affiliation(s)
- R. Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Spain
- The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Building 12A Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - Beat Vögeli
- Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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21
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Abstract
Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation:https://bitbucket.org/mjamroz/flexscore Contact:dkihara@purdue.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michal Jamroz
- Department of Chemistry, University of Warsaw, Warsaw, 02-093, Poland
| | - Andrzej Kolinski
- Department of Chemistry, University of Warsaw, Warsaw, 02-093, Poland
| | - Daisuke Kihara
- Department of Biological Sciences Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
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22
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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23
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Tian P, Lindorff-Larsen K, Boomsma W, Jensen MH, Otzen DE. A Monte Carlo Study of the Early Steps of Functional Amyloid Formation. PLoS One 2016; 11:e0146096. [PMID: 26745180 PMCID: PMC4706413 DOI: 10.1371/journal.pone.0146096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/14/2015] [Indexed: 11/18/2022] Open
Abstract
In addition to their well-known roles in neurodegenerative diseases and amyloidoses, amyloid structures also assume important functional roles in the cell. Although functional amyloid shares many physiochemical properties with its pathogenic counterpart, it is evolutionarily optimized to avoid cytotoxicity. This makes it an interesting study case for aggregation phenomenon in general. One of the most well-known examples of a functional amyloid, E. coli curli, is an essential component in the formation of bacterial biofilm, and is primarily formed by aggregates of the protein CsgA. Previous studies have shown that the minor sequence variations observed in the five different subrepeats (R1-R5), which comprise the CsgA primary sequence, have a substantial influence on their individual aggregation propensities. Using a recently described diffusion-optimized enhanced sampling approach for Monte Carlo simulations, we here investigate the equilibrium properties of the monomeric and dimeric states of these subrepeats, to probe whether structural properties observed in these early stage oligomers are decisive for the characteristics of the resulting aggregate. We show that the dimerization propensities of these peptides have strong correlations with their propensity for amyloid formation, and provide structural insights into the inter- and intramolecular contacts that appear to be essential in this process.
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Affiliation(s)
- Pengfei Tian
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.,Linderstrøm-Lang Centre for Protein Science and Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science and Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Linderstrøm-Lang Centre for Protein Science and Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Mogens Høgh Jensen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Centre for Insoluble Protein Structures (inSPIN), Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
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24
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Salmon L, Blackledge M. Investigating protein conformational energy landscapes and atomic resolution dynamics from NMR dipolar couplings: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:126601. [PMID: 26517337 DOI: 10.1088/0034-4885/78/12/126601] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nuclear magnetic resonance spectroscopy is exquisitely sensitive to protein dynamics. In particular inter-nuclear dipolar couplings, that become measurable in solution when the protein is dissolved in a dilute liquid crystalline solution, report on all conformations sampled up to millisecond timescales. As such they provide the opportunity to describe the Boltzmann distribution present in solution at atomic resolution, and thereby to map the conformational energy landscape in unprecedented detail. The development of analytical methods and approaches based on numerical simulation and their application to numerous biologically important systems is presented.
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Affiliation(s)
- Loïc Salmon
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France. CEA, DSV, IBS, F-38027 Grenoble, France. CNRS, IBS, F-38027 Grenoble, France
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25
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Li F, Grishaev A, Ying J, Bax A. Side Chain Conformational Distributions of a Small Protein Derived from Model-Free Analysis of a Large Set of Residual Dipolar Couplings. J Am Chem Soc 2015; 137:14798-811. [PMID: 26523828 PMCID: PMC4665082 DOI: 10.1021/jacs.5b10072] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Accurate
quantitative measurement of structural dispersion in proteins
remains a prime challenge to both X-ray crystallography and NMR spectroscopy.
Here we use a model-free approach based on measurement of many residual
dipolar couplings (RDCs) in differentially orienting aqueous liquid
crystalline solutions to obtain the side chain χ1 distribution sampled by each residue in solution. Applied to the
small well-ordered model protein GB3, our approach reveals that the
RDC data are compatible with a single narrow distribution of side
chain χ1 angles for only about 40% of the residues.
For more than half of the residues, populations greater than 10% for
a second rotamer are observed, and four residues require sampling
of three rotameric states to fit the RDC data. In virtually all cases,
sampled χ1 values are found to center closely around
ideal g–, g+ and t rotameric angles, even though no rotamer
restraint is used when deriving the sampled angles. The root-mean-square
difference between experimental 3JHαHβ couplings and those predicted by the Haasnoot-parametrized, motion-adjusted
Karplus equation reduces from 2.05 to 0.75 Hz when using the new rotamer
analysis instead of the 1.1-Å X-ray structure as input for the
dihedral angles. A comparison between observed and predicted 3JHαHβ values suggests that the root-mean-square
amplitude of χ1 angle fluctuations within a given
rotamer well is ca. 20°. The quantitatively defined side chain
rotamer equilibria obtained from our study set new benchmarks for
evaluating improved molecular dynamics force fields, and also will
enable further development of quantitative relations between side
chain chemical shift and structure.
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Affiliation(s)
- Fang Li
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Alexander Grishaev
- National Institute of Standards and Technology , Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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26
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Vögeli B, Olsson S, Riek R, Güntert P. Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics. J Struct Biol 2015. [DOI: 10.1016/j.jsb.2015.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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27
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Olsson S, Cavalli A. Quantification of Entropy-Loss in Replica-Averaged Modeling. J Chem Theory Comput 2015; 11:3973-7. [DOI: 10.1021/acs.jctc.5b00579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Simon Olsson
- Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Ticino, Switzerland
- Laboratory
of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Zürich, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Ticino, Switzerland
- Department
of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom
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28
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Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. Protein flexibility in the light of structural alphabets. Front Mol Biosci 2015; 2:20. [PMID: 26075209 PMCID: PMC4445325 DOI: 10.3389/fmolb.2015.00020] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/30/2015] [Indexed: 01/01/2023] Open
Abstract
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.
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Affiliation(s)
- Pierrick Craveur
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Agnel P Joseph
- Rutherford Appleton Laboratory, Science and Technology Facilities Council Didcot, UK
| | - Jeremy Esque
- Institut National de la Santé et de la Recherche Médicale U964,7 UMR Centre National de la Recherche Scientifique 7104, IGBMC, Université de Strasbourg Illkirch, France
| | - Tarun J Narwani
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Floriane Noël
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Nicolas Shinada
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Matthieu Goguet
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Sylvain Leonard
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Pierre Poulain
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Ets Poulain Pointe-Noire, Congo
| | - Olivier Bertrand
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Guilhem Faure
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD, USA
| | - Joseph Rebehmed
- Centre National de la Recherche Scientifique UMR7590, Sorbonne Universités, Université Pierre et Marie Curie - MNHN - IRD - IUC Paris, France
| | | | - Lakshmipuram S Swapna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto Toronto, ON, Canada
| | - Ramachandra M Bhaskara
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Department of Theoretical Biophysics, Max Planck Institute of Biophysics Frankfurt, Germany
| | - Jonathan Barnoud
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Laboratoire de Physique, École Normale Supérieure de Lyon, Université de Lyon, Centre National de la Recherche Scientifique UMR 5672 Lyon, France
| | - Stéphane Téletchéa
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Faculté des Sciences et Techniques, Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines, Centre National de la Recherche Scientifique UMR 6286, Université Nantes Nantes, France
| | - Vincent Jallu
- Platelet Unit, Institut National de la Transfusion Sanguine Paris, France
| | - Jiri Cerny
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Catherine Etchebest
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | | | - Jean-Christophe Gelly
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Alexandre G de Brevern
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
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29
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Olsson S, Ekonomiuk D, Sgrignani J, Cavalli A. Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings. J Am Chem Soc 2015; 137:6270-8. [PMID: 25895902 DOI: 10.1021/jacs.5b01289] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are important probes in structural biology, but their analysis is often complicated by the determination of an alignment tensor or its associated assumptions. We here apply the maximum entropy principle to derive a tensor-free formalism which allows for direct, dynamic analysis of RDCs and holds the classic tensor formalism as a special case. Specifically, the framework enables us to robustly analyze data regardless of whether a clear separation of internal and overall dynamics is possible. Such a separation is often difficult in the core subjects of current structural biology, which include multidomain and intrinsically disordered proteins as well as nucleic acids. We demonstrate the method is tractable and self-consistent and generalizes to data sets comprised of observations from multiple different alignment conditions.
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Affiliation(s)
- Simon Olsson
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland.,‡Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Dariusz Ekonomiuk
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Andrea Cavalli
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland.,§Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom
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30
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Chi CN, Strotz D, Riek R, Vögeli B. Extending the eNOE data set of large proteins by evaluation of NOEs with unresolved diagonals. JOURNAL OF BIOMOLECULAR NMR 2015; 62:63-69. [PMID: 25749872 DOI: 10.1007/s10858-015-9917-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
The representation of a protein's spatial sampling at atomic resolution is fundamental for understanding its function. NMR has been established as the best-suited technique toward this goal for small proteins. However, the accessible information content rapidly deteriorates with increasing protein size. We have recently demonstrated that for small proteins distance restraints with an accuracy smaller than 0.1 Å can be obtained by replacing traditional semi-quantitative Nuclear Overhauser Effects (NOEs) with exact NOEs (eNOE). The high quality of the data allowed us to calculate structural ensembles of the small model protein GB3 consisting of multiple rather than a single state. The analysis has been limited to small proteins because NOEs of spins with unresolved diagonal peaks cannot be used. Here we propose a simple approach to translate such NOEs into correct upper distance restraints, which opens access to larger biomolecules. We demonstrate that for 16 kDa cyclophilin A the collection of such restraints extends the original 1254 eNOEs to 3471.
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Affiliation(s)
- Celestine N Chi
- Laboratory of Physical Chemistry, Vladimir-Prelog Weg 2, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093, Zurich, Switzerland
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31
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Schröder GF. Hybrid methods for macromolecular structure determination: experiment with expectations. Curr Opin Struct Biol 2015; 31:20-7. [DOI: 10.1016/j.sbi.2015.02.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/22/2015] [Accepted: 02/26/2015] [Indexed: 12/15/2022]
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32
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Hansen N, Heller F, Schmid N, van Gunsteren WF. Time-averaged order parameter restraints in molecular dynamics simulations. JOURNAL OF BIOMOLECULAR NMR 2014; 60:169-187. [PMID: 25312596 DOI: 10.1007/s10858-014-9866-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/25/2014] [Indexed: 06/04/2023]
Abstract
A method is described that allows experimental S(2) order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N-H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution.
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Affiliation(s)
- Niels Hansen
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland,
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33
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Sanchez-Martinez M, Crehuet R. Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings. Phys Chem Chem Phys 2014; 16:26030-9. [DOI: 10.1039/c4cp03114h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present a method based on the maximum entropy principle that can re-weight an ensemble of protein structures based on data from residual dipolar couplings (RDCs).
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Affiliation(s)
| | - R. Crehuet
- Institute of Advanced Chemistry of Catalunya (IQAC)
- CSIC
- Spain
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