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Saravanan V, Ahammed I, Bhattacharya A, Bhattacharya S. Uncovering allostery and regulation in SORCIN through molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:1812-1825. [PMID: 37098805 DOI: 10.1080/07391102.2023.2202772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/08/2023] [Indexed: 04/27/2023]
Abstract
Soluble resistance-related calcium-binding protein or Sorcin is an allosteric, calcium-binding Penta-EF hand (PEF) family protein implicated in multi-drug resistant cancers. Sorcin is known to bind chemotherapeutic molecules such as Doxorubicin. This study uses in-silico molecular dynamics simulations to explore the dynamics and allosteric behavior of Sorcin in the context of Ca2+ uptake and Doxorubicin binding. The results show that Ca2+ binding induces large, but reversible conformational changes in the Sorcin structure which manifest as rigid body reorientations that preserve the local secondary structure. A reciprocal allosteric handshake centered around the EF5 hand is found to be key in Sorcin dimer formation and stabilization. Binding of Doxorubicin results in rearrangement of allosteric communities which disrupts long-range allosteric information transfer from the N-terminal domain to the middle lobe. However, this binding does not result in secondary structure destabilization. Sorcin does not appear to have a distinct Ca2+ activated mode of Doxorubicin binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vinnarasi Saravanan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ijas Ahammed
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Akash Bhattacharya
- Visiting Assistant Professor of Physics, St. Mary's University, San Antonio, Texas, USA
| | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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2
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Wardenfelt S, Xiang X, Xie M, Yu L, Bruschweiler‐Li L, Brüschweiler R. Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle Assisted NMR Spin Relaxation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202007205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Stacey Wardenfelt
- Department of Chemistry and Biochemistry The Ohio State University 151 W. Woodruff Ave Columbus Ohio 43210 USA
| | - Xinyao Xiang
- Department of Chemistry and Biochemistry The Ohio State University 151 W. Woodruff Ave Columbus Ohio 43210 USA
| | - Mouzhe Xie
- Department of Chemistry and Biochemistry The Ohio State University 151 W. Woodruff Ave Columbus Ohio 43210 USA
| | - Lei Yu
- Department of Chemistry and Biochemistry The Ohio State University 151 W. Woodruff Ave Columbus Ohio 43210 USA
| | - Lei Bruschweiler‐Li
- Campus Chemical Instrument Center The Ohio State University 151 W. Woodruff Ave Columbus Ohio 43210 USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry The Ohio State University 151 W. Woodruff Ave Columbus Ohio 43210 USA
- Department of Biological Chemistry and Pharmacology The Ohio State University Columbus Ohio 43210 USA
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3
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Wardenfelt S, Xiang X, Xie M, Yu L, Bruschweiler-Li L, Brüschweiler R. Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle Assisted NMR Spin Relaxation. Angew Chem Int Ed Engl 2021; 60:148-152. [PMID: 32909358 DOI: 10.1002/anie.202007205] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 11/10/2022]
Abstract
The quantitative and comprehensive description of the internal dynamics of proteins is critical for understanding their function. Nanoparticle-assisted 15 N NMR spin relaxation spectroscopy is a new method for the observation of picosecond to microsecond dynamics of proteins when transiently interacting with the surface of the nanoparticles (NPs). The method is applied here to the protein ubiquitin in the presence of anionic and cationic silica NPs (SNPs) of different sizes. The backbone dynamics profiles are reproducible and strikingly similar to each other, indicating that specific protein-SNP interactions are unimportant. The dynamics profiles closely match the sub-nanosecond dynamics S2 values observed by model-free analysis of standard 15 N relaxation of ubiquitin in free solution, indicating that the bulk of the ubiquitin backbone dynamics in solution is confined to sub-nanosecond timescales and, hence, it is dynamically more restrained than previous NMR studies have suggested.
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Affiliation(s)
- Stacey Wardenfelt
- Department of Chemistry and Biochemistry, The Ohio State University, 151 W. Woodruff Ave, Columbus, Ohio, 43210, USA
| | - Xinyao Xiang
- Department of Chemistry and Biochemistry, The Ohio State University, 151 W. Woodruff Ave, Columbus, Ohio, 43210, USA
| | - Mouzhe Xie
- Department of Chemistry and Biochemistry, The Ohio State University, 151 W. Woodruff Ave, Columbus, Ohio, 43210, USA
| | - Lei Yu
- Department of Chemistry and Biochemistry, The Ohio State University, 151 W. Woodruff Ave, Columbus, Ohio, 43210, USA
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, 151 W. Woodruff Ave, Columbus, Ohio, 43210, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, 151 W. Woodruff Ave, Columbus, Ohio, 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, 43210, USA
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4
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de Brevern AG. Impact of protein dynamics on secondary structure prediction. Biochimie 2020; 179:14-22. [PMID: 32946990 DOI: 10.1016/j.biochi.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 02/08/2023]
Abstract
Protein 3D structures support their biological functions. As the number of protein structures is negligible in regards to the number of available protein sequences, prediction methodologies relying only on protein sequences are essential tools. In this field, protein secondary structure prediction (PSSPs) is a mature area, and is considered to have reached a plateau. Nonetheless, proteins are highly dynamical macromolecules, a property that could impact the PSSP methods. Indeed, in a previous study, the stability of local protein conformations was evaluated demonstrating that some regions easily changed to another type of secondary structure. The protein sequences of this dataset were used by PSSPs and their results compared to molecular dynamics to investigate their potential impact on the quality of the secondary structure prediction. Interestingly, a direct link is observed between the quality of the prediction and the stability of the assignment to the secondary structure state. The more stable a local protein conformation is, the better the prediction will be. The secondary structure assignment not taken from the crystallized structures but from the conformations observed during the dynamics slightly increase the quality of the secondary structure prediction. These results show that evaluation of PSSPs can be done differently, but also that the notion of dynamics can be included in development of PSSPs and other approaches such as de novo approaches.
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Affiliation(s)
- Alexandre G de Brevern
- Biologie Intégrée Du Globule Rouge UMR_S1134, Inserm, Université de Paris, Univ. de la Réunion, Univ. des Antilles, F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France; Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France; IBL, F-75015, Paris, France.
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5
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Golovin YI, Zhigachev AO, Efremova MV, Majouga AG, Kabanov AV, Klyachko NL. Ways and Methods for Controlling Biomolecular Structures Using Magnetic Nanoparticles Activated by an Alternating Magnetic Field. ACTA ACUST UNITED AC 2018. [DOI: 10.1134/s1995078018030072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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6
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Abstract
Many of the functions of biomacromolecules can be rationalized by the characterization of their conformational energy landscapes: the structures of the dominant states, transitions between states and motions within states. Nuclear magnetic resonance (NMR) spectroscopy is the technique of choice to study internal motions in proteins. The determination of motions on picosecond to nanosecond timescales requires the measurement of nuclear spin relaxation rates at multiple magnetic fields. High sensitivity and resolution are obtained only at high magnetic fields, so that, until recently, site-specific relaxation rates in biomolecules were only measured over a narrow range of high magnetic fields. This limitation was particularly striking for the quantification of motions on nanosecond timescales, close to the correlation time for overall rotational diffusion. High-resolution relaxometry is an emerging technique to investigate picosecond-nanosecond motions of proteins. This approach uses a high-field NMR spectrometer equipped with a sample shuttle device, which allows for the measurement of the relaxation rate constants at low magnetic fields, while preserving the sensitivity and resolution of a high-field NMR spectrometer. The combined analysis of high-resolution relaxometry and standard high-field relaxation data provides a more accurate description of the dynamics of proteins, in particular in the nanosecond range. The purpose of this chapter is to describe how to perform high-resolution relaxometry experiments and how to analyze the rates measured with this technique.
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7
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Hu R, Rodrigues JV, Pradeep Waduge J, Yamazaki H, Cressiot B, Chishti Y, Makowski L, Yu D, Shakhnovich E, Zhao Q, Wanunu M. Differential Enzyme Flexibility Probed Using Solid-State Nanopores. ACS NANO 2018; 12:4494-4502. [PMID: 29630824 PMCID: PMC9016714 DOI: 10.1021/acsnano.8b00734] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enzymes and motor proteins are dynamic macromolecules that coexist in a number of conformations of similar energies. Protein function is usually accompanied by a change in structure and flexibility, often induced upon binding to ligands. However, while measuring protein flexibility changes between active and resting states is of therapeutic significance, it remains a challenge. Recently, our group has demonstrated that breadth of signal amplitudes in measured electrical signatures as an ensemble of individual protein molecules is driven through solid-state nanopores and correlates with protein conformational dynamics. Here, we extend our study to resolve subtle flexibility variation in dihydrofolate reductase mutants from unlabeled single molecules in solution. We first demonstrate using a canonical protein system, adenylate kinase, that both size and flexibility changes can be observed upon binding to a substrate that locks the protein in a closed conformation. Next, we investigate the influence of voltage bias and pore geometry on the measured electrical pulse statistics during protein transport. Finally, using the optimal experimental conditions, we systematically study a series of wild-type and mutant dihydrofolate reductase proteins, finding a good correlation between nanopore-measured protein conformational dynamics and equilibrium bulk fluorescence probe measurements. Our results unequivocally demonstrate that nanopore-based measurements reliably probe conformational diversity in native protein ensembles.
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Affiliation(s)
- Rui Hu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - João V. Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - J Pradeep Waduge
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Hirohito Yamazaki
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yasmin Chishti
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Dapeng Yu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
- Corresponding Authors:.,
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Corresponding Authors:.,
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8
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Olivieri C, Subrahmanian MV, Xia Y, Kim J, Porcelli F, Veglia G. Simultaneous detection of intra- and inter-molecular paramagnetic relaxation enhancements in protein complexes. JOURNAL OF BIOMOLECULAR NMR 2018; 70:133-140. [PMID: 29396770 PMCID: PMC6029865 DOI: 10.1007/s10858-018-0165-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/19/2018] [Indexed: 05/16/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) measurements constitute a powerful approach for detecting both permanent and transient protein-protein interactions. Typical PRE experiments require an intrinsic or engineered paramagnetic site on one of the two interacting partners; while a second, diamagnetic binding partner is labeled with stable isotopes (15N or 13C). Multiple paramagnetic labeled centers or reversed labeling schemes are often necessary to obtain sufficient distance restraints to model protein-protein complexes, making this approach time consuming and expensive. Here, we show a new strategy that combines a modified pulse sequence (1HN-Γ2-CCLS) with an asymmetric labeling scheme to enable the detection of both intra- and inter-molecular PREs simultaneously using only one sample preparation. We applied this strategy to the non-covalent dimer of ubiquitin. Our method confirmed the previously identified binding interface for the transient di-ubiquitin complex, and at the same time, unveiled the internal structural dynamics rearrangements of ubiquitin upon interaction. In addition to reducing the cost of sample preparation and speed up PRE measurements, by detecting the intra-molecular PRE this new strategy will make it possible to measure and calibrate inter-molecular distances more accurately for both symmetric and asymmetric protein-protein complexes.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- DIBAF - University of Tuscia - Largo dell'Università, Blocco D, 01100, Viterbo, Italy
| | - Manu Veliparambil Subrahmanian
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
| | - Youlin Xia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jonggul Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- Department of Chemistry, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
| | - Fernando Porcelli
- DIBAF - University of Tuscia - Largo dell'Università, Blocco D, 01100, Viterbo, Italy
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA.
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9
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Rabbani S, Fiege B, Eris D, Silbermann M, Jakob RP, Navarra G, Maier T, Ernst B. Conformational switch of the bacterial adhesin FimH in the absence of the regulatory domain: Engineering a minimalistic allosteric system. J Biol Chem 2018; 293:1835-1849. [PMID: 29180452 PMCID: PMC5798311 DOI: 10.1074/jbc.m117.802942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/23/2017] [Indexed: 11/06/2022] Open
Abstract
For many biological processes such as ligand binding, enzymatic catalysis, or protein folding, allosteric regulation of protein conformation and dynamics is fundamentally important. One example is the bacterial adhesin FimH, where the C-terminal pilin domain exerts negative allosteric control over binding of the N-terminal lectin domain to mannosylated ligands on host cells. When the lectin and pilin domains are separated under shear stress, the FimH-ligand interaction switches in a so-called catch-bond mechanism from the low- to high-affinity state. So far, it has been assumed that the pilin domain is essential for the allosteric propagation within the lectin domain that would otherwise be conformationally rigid. To test this hypothesis, we generated mutants of the isolated FimH lectin domain and characterized their thermodynamic, kinetic, and structural properties using isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance, and X-ray techniques. Intriguingly, some of the mutants mimicked the conformational and kinetic behaviors of the full-length protein and, even in absence of the pilin domain, conducted the cross-talk between allosteric sites and the mannoside-binding pocket. Thus, these mutants represent a minimalistic allosteric system of FimH, useful for further mechanistic studies and antagonist design.
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Affiliation(s)
- Said Rabbani
- From the Department of Pharmaceutical Sciences, Pharmacenter of the University of Basel, Klingelbergstrasse 50 and
| | - Brigitte Fiege
- From the Department of Pharmaceutical Sciences, Pharmacenter of the University of Basel, Klingelbergstrasse 50 and
| | - Deniz Eris
- From the Department of Pharmaceutical Sciences, Pharmacenter of the University of Basel, Klingelbergstrasse 50 and
| | - Marleen Silbermann
- From the Department of Pharmaceutical Sciences, Pharmacenter of the University of Basel, Klingelbergstrasse 50 and
| | - Roman Peter Jakob
- the Department Biozentrum, Focal Area Structural Biology, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Giulio Navarra
- From the Department of Pharmaceutical Sciences, Pharmacenter of the University of Basel, Klingelbergstrasse 50 and
| | - Timm Maier
- the Department Biozentrum, Focal Area Structural Biology, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Beat Ernst
- From the Department of Pharmaceutical Sciences, Pharmacenter of the University of Basel, Klingelbergstrasse 50 and
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10
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Narayanan C, Bafna K, Roux LD, Agarwal PK, Doucet N. Applications of NMR and computational methodologies to study protein dynamics. Arch Biochem Biophys 2017; 628:71-80. [PMID: 28483383 DOI: 10.1016/j.abb.2017.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023]
Abstract
Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes.
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Affiliation(s)
- Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada
| | - Khushboo Bafna
- Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Louise D Roux
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada
| | - Pratul K Agarwal
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA; Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada; PROTEO, The Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada; GRASP, The Groupe de Recherche Axé sur la Structure des Protéines, 3649 Promenade Sir William Osler, McGill University, Montréal, QC H3G 0B1, Canada.
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11
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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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12
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Cole CA, Mukhopadhyay R, Omar H, Hennig M, Valafar H. Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings. J Chem Theory Comput 2016; 12:1408-22. [PMID: 26984680 DOI: 10.1021/acs.jctc.5b01091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Residual dipolar couplings (RDCs) acquired by nuclear magnetic resonance (NMR) spectroscopy are an indispensable source of information in investigation of molecular structures and dynamics. Here, we present a comprehensive strategy for structure calculation and reconstruction of discrete-state dynamics from RDC data that is based on the singular value decomposition (SVD) method of order tensor estimation. In addition to structure determination, we provide a mechanism of producing an ensemble of conformations for the dynamical regions of a protein from RDC data. The developed methodology has been tested on simulated RDC data with ±1 Hz of error from an 83 residue α protein (PDB ID 1A1Z ) and a 213 residue α/β protein DGCR8 (PDB ID 2YT4 ). In nearly all instances, our method reproduced the structure of the protein including the conformational ensemble to within less than 2 Å. On the basis of our investigations, arc motions with more than 30° of rotation are identified as internal dynamics and are reconstructed with sufficient accuracy. Furthermore, states with relative occupancies above 20% are consistently recognized and reconstructed successfully. Arc motions with a magnitude of 15° or relative occupancy of less than 10% are consistently unrecognizable as dynamical regions within the context of ±1 Hz of error.
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Affiliation(s)
- Casey A Cole
- Department of Computer Science & Engineering, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Rishi Mukhopadhyay
- Department of Computer Science & Engineering, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Hanin Omar
- Department of Computer Science & Engineering, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Mirko Hennig
- Nutrition Research Institute, University of North Carolina at Chapel Hill , Kannapolis, North Carolina 27514, United States
| | - Homayoun Valafar
- Department of Computer Science & Engineering, University of South Carolina , Columbia, South Carolina 29208, United States
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13
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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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14
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Hung YF, Schwarten M, Schünke S, Thiagarajan-Rosenkranz P, Hoffmann S, Sklan EH, Willbold D, Koenig BW. Dengue virus NS4A cytoplasmic domain binding to liposomes is sensitive to membrane curvature. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1119-26. [DOI: 10.1016/j.bbamem.2015.01.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 12/23/2014] [Accepted: 01/21/2015] [Indexed: 11/17/2022]
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15
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Kragelj J, Blackledge M, Jensen MR. Ensemble Calculation for Intrinsically Disordered Proteins Using NMR Parameters. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:123-47. [PMID: 26387101 DOI: 10.1007/978-3-319-20164-1_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intrinsically disordered proteins (IDPs) perform their function despite their lack of well-defined tertiary structure. Residual structure has been observed in IDPs, commonly described as transient/dynamic or expressed in terms of fractional populations. In order to understand how the protein primary sequence dictates the dynamic and structural properties of IDPs and in general to understand how IDPs function, atomic-level descriptions are needed. Nuclear magnetic resonance spectroscopy provides information about local and long-range structure in IDPs at amino acid specific resolution and can be used in combination with ensemble descriptions to represent the dynamic nature of IDPs. In this chapter we describe sample-and-select approaches for ensemble modelling of local structural propensities in IDPs with specific emphasis on validation of these ensembles.
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Affiliation(s)
- Jaka Kragelj
- IBS, University Grenoble Alpes, 38044, Grenoble, France.,IBS, CNRS, 38044, Grenoble, France.,IBS, CEA, 38044, Grenoble, France
| | - Martin Blackledge
- IBS, University Grenoble Alpes, 38044, Grenoble, France.,IBS, CNRS, 38044, Grenoble, France.,IBS, CEA, 38044, Grenoble, France
| | - Malene Ringkjøbing Jensen
- IBS, University Grenoble Alpes, 38044, Grenoble, France. .,IBS, CNRS, 38044, Grenoble, France. .,IBS, CEA, 38044, Grenoble, France.
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Montalvao R, Camilloni C, De Simone A, Vendruscolo M. New opportunities for tensor-free calculations of residual dipolar couplings for the study of protein dynamics. JOURNAL OF BIOMOLECULAR NMR 2014; 58:233-238. [PMID: 24477919 DOI: 10.1007/s10858-013-9801-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/05/2013] [Indexed: 06/03/2023]
Abstract
Residual dipolar couplings (RDCs) can provide exquisitely detailed information about the structure and dynamics of proteins. It is challenging, however, to extract such information from RDC measurements in conformationally heterogeneous states of proteins because of the complex relationship between RDCs and protein structures. To obtain new insights into this problem, we discuss methods of calculating the RDCs that do not require the definition of an alignment tensor. These methods can help in particular in the search of effective ways to use RDCs to characterise disordered or partially disordered states of proteins.
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Affiliation(s)
- Rinaldo Montalvao
- São Carlos Institute of Physics, University of São Paulo, São Carlos, CEP 13566-590, Brazil
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17
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Vögeli B, Orts J, Strotz D, Chi C, Minges M, Wälti MA, Güntert P, Riek R. Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:53-59. [PMID: 24656080 DOI: 10.1016/j.jmr.2013.11.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
| | - Julien Orts
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Celestine Chi
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Martina Minges
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Graduate School of Science, Tokyo Metropolitan University, Hachioji, 192-0397 Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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18
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Charlier C, Khan SN, Marquardsen T, Pelupessy P, Reiss V, Sakellariou D, Bodenhausen G, Engelke F, Ferrage F. Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry. J Am Chem Soc 2013; 135:18665-72. [PMID: 24228712 PMCID: PMC3865798 DOI: 10.1021/ja409820g] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Understanding
the molecular determinants underlying protein function
requires the characterization of both structure and dynamics at atomic
resolution. Nuclear relaxation rates allow a precise characterization
of protein dynamics at the Larmor frequencies of spins. This usually
limits the sampling of motions to a narrow range of frequencies corresponding
to high magnetic fields. At lower fields one cannot achieve sufficient
sensitivity and resolution in NMR. Here, we use a fast shuttle device
where the polarization builds up and the signals are detected at high
field, while longitudinal relaxation takes place at low fields 0.5
< B0 < 14.1 T. The sample is propelled
over a distance up to 50 cm by a blowgun-like system in about 50 ms.
The analysis of nitrogen-15 relaxation in the protein ubiquitin over
such a wide range of magnetic fields offers unprecedented insights
into molecular dynamics. Some key regions of the protein feature structural
fluctuations on nanosecond time scales, which have so far been overlooked
in high-field relaxation studies. Nanosecond motions in proteins may
have been underestimated by traditional high-field approaches, and
slower supra-τc motions that have no effect on relaxation
may have been overestimated. High-resolution relaxometry thus opens
the way to a quantitative characterization of nanosecond motions in
proteins.
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Affiliation(s)
- Cyril Charlier
- Laboratoire des Biomolécules, Département de Chimie, UMR 7203 CNRS-UPMC-ENS, Ecole Normale Supérieure , 24 Rue Lhomond, 75231 Paris Cedex 05, France
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19
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Schmidt C, Irausquin SJ, Valafar H. Advances in the REDCAT software package. BMC Bioinformatics 2013; 14:302. [PMID: 24098943 PMCID: PMC3840585 DOI: 10.1186/1471-2105-14-302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/13/2013] [Indexed: 12/24/2022] Open
Abstract
Background Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation. Results We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions. Conclusions The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development.
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Affiliation(s)
- Chris Schmidt
- Department of Computer Science & Engineering, University of South Carolina, Columbia, SC 29208, USA.
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20
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Revealing the properties of plant defensins through dynamics. Molecules 2013; 18:11311-26. [PMID: 24064452 PMCID: PMC6270066 DOI: 10.3390/molecules180911311] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/07/2013] [Accepted: 09/10/2013] [Indexed: 12/11/2022] Open
Abstract
Defensins are potent, ancient natural antibiotics that are present in organisms ranging from lower organisms to humans. Although the structures of several defensins have been well characterized, the dynamics of only a few have been studied. This review discusses the diverse dynamics of two plant defensins for which the structure and dynamics have been characterized, both in the free state and in the presence of target membranes. Multiple motions are observed in loops and in secondary structure elements and may be related to twisting or breathing of the α-helix and β-sheet. This complex behavior is altered in the presence of an interface and is responsive to the presence of the putative target. The stages of membrane recognition and disruption can be mapped over a large time scale range, demonstrating that defensins in solution exist as an ensemble of different conformations, a subset of which is selected upon membrane binding. Therefore, studies on the dynamics have revealed that defensins interact with membranes through a mechanism of conformational selection.
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21
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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22
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Mahajan S, de Brevern AG, Offmann B, Srinivasan N. Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure. J Biomol Struct Dyn 2013; 32:751-8. [PMID: 23730714 DOI: 10.1080/07391102.2013.789989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a-p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and β-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.
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Affiliation(s)
- Swapnil Mahajan
- a Faculté des Sciences et Technologies, Université de La Réunion , F-97715 Saint Denis Messag Cedex 09, La Réunion , France
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23
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Guerry P, Mollica L, Blackledge M. Mapping Protein Conformational Energy Landscapes Using NMR and Molecular Simulation. Chemphyschem 2013; 14:3046-58. [DOI: 10.1002/cphc.201300377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Indexed: 02/06/2023]
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24
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Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM. A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed. J Am Chem Soc 2013; 135:5457-66. [PMID: 23473378 DOI: 10.1021/ja400920w] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to modulate alignment and measure multiple independent sets of NMR residual dipolar couplings (RDCs) has made it possible to characterize internal motions in proteins at atomic resolution and with time scale sensitivity ranging from picoseconds up to milliseconds. The application of such methods to the study of RNA dynamics, however, remains fundamentally limited by the inability to modulate alignment and by strong couplings between internal and overall motions that complicate the quantitative interpretation of RDCs. Here, we address this problem by showing that RNA alignment can be generally modulated, in a controlled manner, by variable elongation of A-form helices and that the information contained within the measured RDCs can be extracted even in the presence of strong couplings between motions and overall alignment via structure-based prediction of alignment. Using this approach, four RDC data sets, and a broad conformational pool obtained from a 8.2 μs molecular dynamics simulation, we successfully construct and validate an atomic resolution ensemble of human immunodeficiency virus type I transactivation response element RNA. This ensemble reveals local motions in and around the bulge involving changes in stacking and hydrogen-bonding interactions, which are undetectable by traditional spin relaxation and drive global changes in interhelical orientation. This new approach broadens the scope of using RDCs in characterizing the dynamics of nucleic acids.
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Affiliation(s)
- Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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25
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NMR as a tool to identify and characterize protein folding intermediates. Arch Biochem Biophys 2013; 531:90-9. [DOI: 10.1016/j.abb.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/20/2022]
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26
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Guerry P, Salmon L, Mollica L, Ortega Roldan JL, Markwick P, van Nuland NAJ, McCammon JA, Blackledge M. Mapping the Population of Protein Conformational Energy Sub-States from NMR Dipolar Couplings. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Guerry P, Salmon L, Mollica L, Ortega Roldan J, Markwick P, van Nuland NAJ, McCammon JA, Blackledge M. Mapping the Population of Protein Conformational Energy Sub‐States from NMR Dipolar Couplings. Angew Chem Int Ed Engl 2013; 52:3181-5. [DOI: 10.1002/anie.201209669] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Paul Guerry
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean‐Pierre Ebel, CNRS‐CEA‐UJF UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)
| | - Loïc Salmon
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean‐Pierre Ebel, CNRS‐CEA‐UJF UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)
| | - Luca Mollica
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean‐Pierre Ebel, CNRS‐CEA‐UJF UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)
| | | | - Phineus Markwick
- Department of Chemistry and Biochemistry UCSD San Diego CA, Howard Hughes Medical Institute, San Diego Supercomputer Center, La Jolla CA (USA)
| | | | - J. Andrew McCammon
- Department of Chemistry and Biochemistry UCSD San Diego CA, Howard Hughes Medical Institute, San Diego Supercomputer Center, La Jolla CA (USA)
| | - Martin Blackledge
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean‐Pierre Ebel, CNRS‐CEA‐UJF UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)
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28
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Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PRL, Komives EA. The dynamic structure of thrombin in solution. Biophys J 2012; 103:79-88. [PMID: 22828334 DOI: 10.1016/j.bpj.2012.05.047] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/04/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022] Open
Abstract
The backbone dynamics of human α-thrombin inhibited at the active site serine were analyzed using R(1), R(2), and heteronuclear NOE experiments, variable temperature TROSY 2D [(1)H-(15)N] correlation spectra, and R(ex) measurements. The N-terminus of the heavy chain, which is formed upon zymogen activation and inserts into the protein core, is highly ordered, as is much of the double beta-barrel core. Some of the surface loops, by contrast, remain very dynamic with order parameters as low as 0.5 indicating significant motions on the ps-ns timescale. Regions of the protein that were thought to be dynamic in the zymogen and to become rigid upon activation, in particular the γ-loop, the 180s loop, and the Na(+) binding site have order parameters below 0.8. Significant R(ex) was observed in most of the γ-loop, in regions proximal to the light chain, and in the β-sheet core. Accelerated molecular dynamics simulations yielded a molecular ensemble consistent with measured residual dipolar couplings that revealed dynamic motions up to milliseconds. Several regions, including the light chain and two proximal loops, did not appear highly dynamic on the ps-ns timescale, but had significant motions on slower timescales.
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Affiliation(s)
- Brian Fuglestad
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA
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29
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Canales A, Jiménez-Barbero J, Martín-Pastor M. Review: Use of residual dipolar couplings to determine the structure of carbohydrates. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S80-S85. [PMID: 23280664 DOI: 10.1002/mrc.3888] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 09/08/2012] [Accepted: 09/20/2012] [Indexed: 05/28/2023]
Abstract
Solution nuclear magnetic resonance spectroscopy is especially useful in the carbohydrate field. The measurement of residual dipolar couplings provides long-range structural information, a valuable complement for the structural study of carbohydrates either in its free form or in the bound state to proteins. They permit to deduce the geometry and the flexibility of the glycosidic linkages, which have a major influence on the conformation of carbohydrates and their overall shape. This article reviews the current application of the residual dipolar couplings methodology to carbohydrates.
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Affiliation(s)
- A Canales
- Department Organic Chemistry, Universidad Complutense de Madrid, Madrid, Spain
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30
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Montalvao RW, De Simone A, Vendruscolo M. Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2012; 53:281-292. [PMID: 22729708 DOI: 10.1007/s10858-012-9644-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 05/19/2012] [Indexed: 05/27/2023]
Abstract
Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.
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Affiliation(s)
- Rinaldo W Montalvao
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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31
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Steiner D, Allison JR, Eichenberger AP, van Gunsteren WF. On the calculation of ³Jαβ-coupling constants for side chains in proteins. JOURNAL OF BIOMOLECULAR NMR 2012; 53:223-246. [PMID: 22714630 DOI: 10.1007/s10858-012-9634-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 05/01/2012] [Indexed: 06/01/2023]
Abstract
Structural knowledge about proteins is mainly derived from values of observables, measurable in NMR spectroscopic or X-ray diffraction experiments, i.e. absorbed or scattered intensities, through theoretically derived relationships between structural quantities such as atom positions or torsional angles on the one hand and observable quantities such as squared structure factor amplitudes, NOE intensities or (3) J-coupling constants on the other. The standardly used relation connecting (3) J-couplings to torsional angles is the Karplus relation, which is used in protein structure refinement as well as in the evaluation of simulated properties of proteins. The accuracy of the simple and generalised Karplus relations is investigated using side-chain structural and (3) J (αβ)-coupling data for three different proteins, Plastocyanin, Lysozyme, and FKBP, for which such data are available. The results show that the widely used Karplus relations are only a rough estimate for the relation between (3) J (αβ)-couplings and the corresponding χ(1)-angle in proteins.
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Affiliation(s)
- Denise Steiner
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
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32
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An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:579-95. [PMID: 22706892 DOI: 10.1007/s00249-012-0824-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 04/27/2012] [Accepted: 05/10/2012] [Indexed: 10/28/2022]
Abstract
Deriving structural information about a protein from NMR experimental data is still a non-trivial challenge to computational biochemistry. This is because of the low ratio of the number of independent observables to the number of molecular degrees of freedom, the approximations involved in the different relationships between particular observable quantities and molecular conformation, and the averaged character of the experimental data. For example, protein (3)J-coupling data are seldom used for structure refinement because of the multiple-valuedness and limited accuracy of the Karplus relationship linking a (3)J-coupling to a torsional angle. Moreover, sampling of the large conformational space is still problematic. Using the 99-residue protein plastocyanin as an example we investigated whether use of a thermodynamically calibrated force field, inclusion of solvent degrees of freedom, and application of adaptive local-elevation sampling that accounts for conformational averaging produces a more realistic representation of the ensemble of protein conformations than standard single-structure refinement in a non-explicit solvent using restraints that do not account for averaging and are partly based on non-observed data. Yielding better agreement with observed experimental data, the protein conformational ensemble is less restricted than when using standard single-structure refinement techniques, which are likely to yield a picture of the protein which is too rigid.
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33
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Meirovitch E, Lee D, Walter KFA, Griesinger C. Standard tensorial analysis of local ordering in proteins from residual dipolar couplings. J Phys Chem B 2012; 116:6106-17. [PMID: 22512459 DOI: 10.1021/jp301451v] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Residual dipolar couplings (RDCs) in proteins arise from independent external medium-related and internal protein-related ordering of the spin-bearing probe. Griesinger et al. developed a method for treating RDCs in proteins. The global ordering is given in the standard manner by a rank 2 tensor specified in a known molecular frame, MF. The local ordering is described by the spherical harmonic ensemble averages, <Y(2m)(θ, φ)>, m = 0, ±1, ±2, also given in MF. From these quantities, a method we call mf-RDC derives the squared generalized order parameter (S(rdc)(2)), the amplitude (direction) of the anisotropic disorder, η (Φ′), and an approximation, (N−H)(eff), to the average probe orientation, i.e., to the local director. (N−H)(eff) is determined through a frame transformation where <Y(20)> is maximized. Φ′ is associated with a subsequent frame transformation where <Y(22) + Y(2−2)> is maximized. The mf-RDC method was applied previously to N−H and C−C(methyl) sites in ubiquitin. In this study, we convert the respective <Y(2m)(θ, φ)>'s into a Saupe tensor, which is diagonalized. This is the standard procedure. It yields the eigenvalues, S(xx), S(yy), and S(zz), and the Principal Axis System (PAS) of the rank 2 local ordering tensor, S(l). S(rdc)(2), η, and Φ′ can be recast as S(xx), S(yy), and S(zz). The mf-RDC frame transformations are not the same as the conventional Wigner rotation. The standard tensorial analysis provides new information. The contribution of local ordering rhombicity to S(rdc)(2) is evaluated. For the α-helix of ubiquitin, the main local ordering axis is assigned as C(i−1)(α) − C(i)(α); for the methyl sites, it is associated with the C−C(methyl) axis, as in mf-RDC. Ordering strength correlates with methyl type. The strength (rhombicity) of S(l) associated with picosecond−nanosecond local motions is reduced moderately (substantially) by nanosecond−millisecond local motions. A scheme for analyzing experimental RDCs based on the standard tensorial perspective, which allows for arbitrary orientation of the local director in the protein and of the PAS of S(l) in the probe, is formulated.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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34
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Salmon L, Pierce L, Grimm A, Ortega Roldan JL, Mollica L, Jensen MR, van Nuland N, Markwick PRL, McCammon JA, Blackledge M. Multi-Timescale Conformational Dynamics of the SH3 Domain of CD2-Associated Protein using NMR Spectroscopy and Accelerated Molecular Dynamics. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Salmon L, Pierce L, Grimm A, Ortega Roldan JL, Mollica L, Jensen MR, van Nuland N, Markwick PRL, McCammon JA, Blackledge M. Multi-timescale conformational dynamics of the SH3 domain of CD2-associated protein using NMR spectroscopy and accelerated molecular dynamics. Angew Chem Int Ed Engl 2012; 51:6103-6. [PMID: 22565613 PMCID: PMC3541011 DOI: 10.1002/anie.201202026] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Loïc Salmon
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CNRS-CEA-UJF, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble Cedex, France
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36
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Salvi N, Ulzega S, Ferrage F, Bodenhausen G. Time Scales of Slow Motions in Ubiquitin Explored by Heteronuclear Double Resonance. J Am Chem Soc 2012; 134:2481-4. [DOI: 10.1021/ja210238g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Nicola Salvi
- Ecole Polytechnique Fédérale de Lausanne, Institut des Sciences
et Ingénierie Chimiques, BCH, 1015 Lausanne, Switzerland
| | - Simone Ulzega
- Ecole Polytechnique Fédérale de Lausanne, Institut des Sciences
et Ingénierie Chimiques, BCH, 1015 Lausanne, Switzerland
| | - Fabien Ferrage
- Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75231
Paris Cedex 05, France
- Université Pierre et Marie Curie, Paris, France
- UMR 7203 Laboratoire des Biomolécules CNRS-UPMC-ENS, Paris, France
| | - Geoffrey Bodenhausen
- Ecole Polytechnique Fédérale de Lausanne, Institut des Sciences
et Ingénierie Chimiques, BCH, 1015 Lausanne, Switzerland
- Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75231
Paris Cedex 05, France
- Université Pierre et Marie Curie, Paris, France
- UMR 7203 Laboratoire des Biomolécules CNRS-UPMC-ENS, Paris, France
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37
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Synergistic applications of MD and NMR for the study of biological systems. J Biomed Biotechnol 2012; 2012:254208. [PMID: 22319241 PMCID: PMC3272818 DOI: 10.1155/2012/254208] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 10/19/2011] [Indexed: 12/22/2022] Open
Abstract
Modern biological sciences are becoming more and more multidisciplinary. At the same time, theoretical and computational approaches gain in reliability and their field of application widens. In this short paper, we discuss recent advances in the areas of solution nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations that were made possible by the combination of both methods, that is, through their synergistic use. We present the main NMR observables and parameters that can be computed from simulations, and how they are used in a variety of complementary applications, including dynamics studies, model-free analysis, force field validation, and structural studies.
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38
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Marcos E, Mestres P, Crehuet R. Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results. Biophys J 2011; 101:2782-9. [PMID: 22261067 PMCID: PMC3297780 DOI: 10.1016/j.bpj.2011.09.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/20/2011] [Accepted: 09/23/2011] [Indexed: 10/14/2022] Open
Abstract
The dynamical basis underlying the increased thermal stability of thermophilic proteins remains uncertain. Here, we challenge the new paradigm established by neutron scattering experiments in solution, in which the adaptation of thermophilic proteins to high temperatures lies in the lower sensitivity of their flexibility to temperature changes. By means of a combination of molecular dynamics and Brownian dynamics simulations, we report a reinterpretation of those experiments and show evidence that under crowding conditions, such as in vivo, thermophilic and homolog mesophilic proteins have diffusional properties with different thermal behavior.
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Affiliation(s)
| | | | - Ramon Crehuet
- Department of Biological Chemistry and Molecular Modeling, Institute of Advanced Chemistry of Catalonia (IQAC – CSIC), Barcelona, Spain
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39
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Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1339-55. [PMID: 22089251 PMCID: PMC3222826 DOI: 10.1007/s00249-011-0754-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Revised: 09/06/2011] [Accepted: 09/14/2011] [Indexed: 10/31/2022]
Abstract
We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery. We introduce currently available methods for generating ensembles of biomolecules and illustrate their application with relevant examples from the literature. We show how, for binding, conformational ensembles provide a way of distinguishing the competing models of induced fit and conformational selection. For allostery we review the classic models and show how conformational ensembles can play a role in unravelling the intricate pathways of communication that enable allostery to occur. Finally, we discuss the limitations of conformational ensembles and highlight some potential applications for the future.
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40
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De Simone A, Montalvao RW, Vendruscolo M. Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings. J Chem Theory Comput 2011; 7:4189-4195. [PMID: 22180735 PMCID: PMC3236604 DOI: 10.1021/ct200361b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 01/05/2023]
Abstract
In order to carry out their functions, proteins often undergo significant conformational fluctuations that enable them to interact with their partners. The accurate characterization of these motions is key in order to understand the mechanisms by which macromolecular recognition events take place. Nuclear magnetic resonance spectroscopy offers a variety of powerful methods to achieve this result. We discuss a method of using residual dipolar couplings as replica-averaged restraints in molecular dynamics simulations to determine large amplitude motions of proteins, including those involved in the conformational equilibria that are established through interconversions between different states. By applying this method to ribonuclease A, we show that it enables one to characterize the ample fluctuations in interdomain orientations expected to play an important functional role.
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41
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Abstract
Dynamic communication between atoms within folded proteins is potentially important for function, but its measurement has been a challenge. Now, a combined NMR and modelling study provides insights on the presence and strengths of such correlations.
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42
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Jensen MR, Ortega-Roldan JL, Salmon L, van Nuland N, Blackledge M. Characterizing weak protein-protein complexes by NMR residual dipolar couplings. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1371-81. [PMID: 21710303 DOI: 10.1007/s00249-011-0720-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Revised: 05/27/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
Abstract
Protein-protein interactions occur with a wide range of affinities from tight complexes characterized by femtomolar dissociation constants to weak, and more transient, complexes of millimolar affinity. Many of the weak and transiently formed protein-protein complexes have escaped characterization due to the difficulties in obtaining experimental parameters that report on the complexes alone without contributions from the unbound, free proteins. Here, we review recent developments for characterizing the structures of weak protein-protein complexes using nuclear magnetic resonance spectroscopy with special emphasis on the utility of residual dipolar couplings.
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Affiliation(s)
- Malene Ringkjøbing Jensen
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
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