1
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Jung JE, Ewing MA, Valentine SJ, Clemmer DE. Structural Insights into Linkage-Specific Ubiquitin Chains Using Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:982-991. [PMID: 38597281 DOI: 10.1021/jasms.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The structural characterization and differentiation of four types of oligoubiquitin conjugates [linear (Met1)-, Lys11-, Lys48-, Lys63-linked di-, tri-, and tetraubiquitin chains] using ion mobility mass spectrometry are reported. A comparison of collision cross sections for the same linkage of di-, tri-, and tetraubiquitin chains shows differences in conformational elongation for higher charge states due to the interplay of linkage-derived structure and Coulombic repulsion. For di- and triubiquitin chains, this elongation results in a single narrow feature representing an elongated conformation type for multiple higher charge state species. In contrast, higher charge state tetraubiquitin species do not form a single conformer type as readily. A comparison of different linkages in tetraubiquitin chains reveals greater similarity in conformation type at lower charge states; with increasing charge state, the four linkage types diverge in the relative proportions of elongated conformer types with Met1- ≥ Lys11- > Lys63- > Lys48-linkage. These differences in conformational trends could be discussed with respect to biological functions of linkage-specific polyubiquitinated proteins.
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Affiliation(s)
- Ji Eun Jung
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Forensic Chemistry Division, National Forensic Service, Wonju 26460, Korea
| | - Michael A Ewing
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Roche Infomatics, F. Hoffman-La Roche AG, Basel, CH 4070, Switzerland
| | - Stephen J Valentine
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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2
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Gama Lima Costa R, Fushman D. Reweighting methods for elucidation of conformation ensembles of proteins. Curr Opin Struct Biol 2022; 77:102470. [PMID: 36183447 PMCID: PMC9771963 DOI: 10.1016/j.sbi.2022.102470] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/24/2022]
Abstract
Proteins are inherently dynamic macromolecules that exist in equilibrium among multiple conformational states, and motions of protein backbone and side chains are fundamental to biological function. The ability to characterize the conformational landscape is particularly important for intrinsically disordered proteins, multidomain proteins, and weakly bound complexes, where single-structure representations are inadequate. As the focus of structural biology shifts from relatively rigid macromolecules toward larger and more complex systems and molecular assemblies, there is a need for structural approaches that can paint a more realistic picture of such conformationally heterogeneous systems. Here, we review reweighting methods for elucidation of structural ensembles based on experimental data, with the focus on applications to multidomain proteins.
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Affiliation(s)
- Raquel Gama Lima Costa
- Chemical Physics Program, Institute for Physical Sciences and Technology, University of Maryland, College Park, 20742, MD, USA.
| | - David Fushman
- Chemical Physics Program, Institute for Physical Sciences and Technology, University of Maryland, College Park, 20742, MD, USA; Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, 20742, MD, USA.
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3
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High-Resolution Conformational Analysis of RGDechi-Derived Peptides Based on a Combination of NMR Spectroscopy and MD Simulations. Int J Mol Sci 2022; 23:ijms231911039. [PMID: 36232339 PMCID: PMC9569650 DOI: 10.3390/ijms231911039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
The crucial role of integrin in pathological processes such as tumor progression and metastasis formation has inspired intense efforts to design novel pharmaceutical agents modulating integrin functions in order to provide new tools for potential therapies. In the past decade, we have investigated the biological proprieties of the chimeric peptide RGDechi, containing a cyclic RGD motif linked to an echistatin C-terminal fragment, able to specifically recognize αvβ3 without cross reacting with αvβ5 and αIIbβ3 integrin. Additionally, we have demonstrated using two RGDechi-derived peptides, called RGDechi1-14 and ψRGDechi, that chemical modifications introduced in the C-terminal part of the peptide alter or abolish the binding to the αvβ3 integrin. Here, to shed light on the structural and dynamical determinants involved in the integrin recognition mechanism, we investigate the effects of the chemical modifications by exploring the conformational space sampled by RGDechi1-14 and ψRGDechi using an integrated natural-abundance NMR/MD approach. Our data demonstrate that the flexibility of the RGD-containing cycle is driven by the echistatin C-terminal region of the RGDechi peptide through a coupling mechanism between the N- and C-terminal regions.
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4
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Born A, Henen MA, Nichols PJ, Vögeli B. On the use of residual dipolar couplings in multi-state structure calculation of two-domain proteins. MAGNETIC RESONANCE LETTERS 2022; 2:61-68. [PMID: 35734611 PMCID: PMC9210859 DOI: 10.1016/j.mrl.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Residual dipolar couplings (RDCs) are powerful nuclear magnetic resonance (NMR) probes for the structure calculation of biomacromolecules. Typically, an alignment tensor that defines the orientation of the entire molecule relative to the magnetic field is determined either before refinement of individual bond vectors or simultaneously with this refinement. For single-domain proteins this approach works well since all bond vectors can be described within the same coordinate frame, which is given by the alignment tensor. However, novel approaches are sought after for systems where no universal alignment tensor can be used. Here, we present an approach that can be applied to two-domain proteins that enables the calculation of multiple states within each domain as well as with respect to the relative positions of the two domains.
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Affiliation(s)
- Alexandra Born
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
| | - Morkos A. Henen
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Parker J. Nichols
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
| | - Beat Vögeli
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
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5
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Abyzov A, Blackledge M, Zweckstetter M. Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry. Chem Rev 2022; 122:6719-6748. [PMID: 35179885 PMCID: PMC8949871 DOI: 10.1021/acs.chemrev.1c00774] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Motions in biomolecules
are critical for biochemical reactions.
In cells, many biochemical reactions are executed inside of biomolecular
condensates formed by ultradynamic intrinsically disordered proteins.
A deep understanding of the conformational dynamics of intrinsically
disordered proteins in biomolecular condensates is therefore of utmost
importance but is complicated by diverse obstacles. Here we review
emerging data on the motions of intrinsically disordered proteins
inside of liquidlike condensates. We discuss how liquid–liquid
phase separation modulates internal motions across a wide range of
time and length scales. We further highlight the importance of intermolecular
interactions that not only drive liquid–liquid phase separation
but appear as key determinants for changes in biomolecular motions
and the aging of condensates in human diseases. The review provides
a framework for future studies to reveal the conformational dynamics
of intrinsically disordered proteins in the regulation of biomolecular
condensate chemistry.
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Affiliation(s)
- Anton Abyzov
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Martin Blackledge
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble, France.,CEA, DSV, IBS, 38044 Grenoble, France.,CNRS, IBS, 38044 Grenoble, France
| | - Markus Zweckstetter
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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6
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Born A, Soetbeer J, Breitgoff F, Henen MA, Sgourakis N, Polyhach Y, Nichols PJ, Strotz D, Jeschke G, Vögeli B. Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance. J Am Chem Soc 2021; 143:16055-16067. [PMID: 34579531 DOI: 10.1021/jacs.1c06289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States.,Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nikolaos Sgourakis
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Dean Strotz
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
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7
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Gaalswyk K, Liu Z, Vogel HJ, MacCallum JL. An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling. Front Mol Biosci 2021; 8:676268. [PMID: 34476238 PMCID: PMC8407082 DOI: 10.3389/fmolb.2021.676268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Paramagnetic nuclear magnetic resonance (NMR) methods have emerged as powerful tools for structure determination of large, sparsely protonated proteins. However traditional applications face several challenges, including a need for large datasets to offset the sparsity of restraints, the difficulty in accounting for the conformational heterogeneity of the spin-label, and noisy experimental data. Here we propose an integrative approach to structure determination combining sparse paramagnetic NMR with physical modelling to infer approximate protein structural ensembles. We use calmodulin in complex with the smooth muscle myosin light chain kinase peptide as a model system. Despite acquiring data from samples labeled only at the backbone amide positions, we are able to produce an ensemble with an average RMSD of ∼2.8 Å from a reference X-ray crystal structure. Our approach requires only backbone chemical shifts and measurements of the paramagnetic relaxation enhancement and residual dipolar couplings that can be obtained from sparsely labeled samples.
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Affiliation(s)
- Kari Gaalswyk
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
| | - Zhihong Liu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Hans J. Vogel
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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8
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Rogers JM, Nawatha M, Lemma B, Vamisetti GB, Livneh I, Barash U, Vlodavsky I, Ciechanover A, Fushman D, Suga H, Brik A. In vivo modulation of ubiquitin chains by N-methylated non-proteinogenic cyclic peptides. RSC Chem Biol 2020; 2:513-522. [PMID: 34179781 PMCID: PMC8232551 DOI: 10.1039/d0cb00179a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cancer and other disease states can change the landscape of proteins post-translationally tagged with ubiquitin (Ub) chains. Molecules capable of modulating Ub chains are potential therapeutic agents, but their discovery represents a significant challenge. Recently, it was shown that de novo cyclic peptides, selected from trillion-member random libraries, are capable of binding particular Ub chains. However, these peptides were overwhelmingly proteinogenic, so the prospect of in vivo activity was uncertain. Here, we report the discovery of small, non-proteinogenic cyclic peptides, rich in non-canonical features like N-methylation, which can tightly and specifically bind Lys48-linked Ub chains. These peptides engage three Lys48-linked Ub units simultaneously, block the action of deubiquitinases and the proteasome, induce apoptosis in vitro, and attenuate tumor growth in vivo. This highlights the potential of non-proteinogenic cyclic peptide screening to rapidly find in vivo-active leads, and the targeting of ubiquitin chains as a promising anti-cancer mechanism of action.
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Affiliation(s)
- Joseph M Rogers
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Mickal Nawatha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Betsegaw Lemma
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Ganga B Vamisetti
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Ido Livneh
- The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Uri Barash
- The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Israel Vlodavsky
- The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Aaron Ciechanover
- The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
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9
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Lu X, Ebelle DL, Matsuo H, Walters KJ. An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure. Structure 2020; 28:495-506.e3. [PMID: 32160516 DOI: 10.1016/j.str.2020.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/06/2020] [Accepted: 02/26/2020] [Indexed: 12/24/2022]
Abstract
Rpn13/Adrm1 is recruited to the proteasome by PSMD1/Rpn2, where it serves as a substrate receptor that binds preferentially to K48-linked ubiquitin chains, an established signal for protein proteolysis. Here, we use NMR to solve the structure of hRpn13 Pru:hRpn2 (940-953):K48-diubiquitin. Surprisingly, hRpn2-bound hRpn13 selects a dynamic, extended conformation of K48-diubiquitin that is unique from previously determined structures. NMR experiments on free K48-diubiquitin demonstrate the presence of the reported "closed" conformation observed by crystallography, but also this more extended state, in which the hRpn13-binding surface is exposed. This extended K48-diubiquitin conformation is defined by interactions between L73 from G76-linked (distal) ubiquitin and a Y59-centered surface of K48-linked (proximal) ubiquitin. Furthermore, hRpn13 exchanges between the two ubiquitins within 100 ms, although prefers the proximal ubiquitin due to interactions with the K48 linker region. Altogether, these data lead to a revised model of how ubiquitinated substrates interact with the proteasome.
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Affiliation(s)
- Xiuxiu Lu
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Danielle L Ebelle
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hiroshi Matsuo
- Basic Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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10
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Abstract
Large scale functional motions of molecules are studied experimentally using numerous molecular and biophysics techniques, the data from which are subsequently interpreted using diverse models of Brownian molecular dynamics. To unify all rotational physics techniques and motional models, the frame order tensor - a universal statistical mechanics theory based on the rotational ordering of rigid body frames - is herein formulated. The frame ordering is the fundamental physics that governs how motions modulate rotational molecular physics and it defines the properties and maximum information content encoded in the observable physics. Using the tensor to link residual dipolar couplings and pseudo-contact shifts, two distinct information-rich and atomic-level biophysical measurements from the field of nuclear magnetic resonance spectroscopy, to a number of basic mechanical joint models, a highly dynamic state of calmodulin (CaM) bound to a target peptide in a tightly closed conformation was observed. Intra- and inter-domain motions reveal the CaM complex to be entropically primed for peptide release.
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11
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Avanzini F, Moro GJ. Quantum Stochastic Trajectories: The Fokker-Planck-Bohm Equation Driven by the Reduced Density Matrix. J Phys Chem A 2018; 122:2751-2763. [PMID: 29466006 DOI: 10.1021/acs.jpca.7b11943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The quantum molecular trajectory is the deterministic trajectory, arising from the Bohm theory, that describes the instantaneous positions of the nuclei of molecules by assuring the agreement with the predictions of quantum mechanics. Therefore, it provides the suitable framework for representing the geometry and the motions of molecules without neglecting their quantum nature. However, the quantum molecular trajectory is extremely demanding from the computational point of view, and this strongly limits its applications. To overcome such a drawback, we derive a stochastic representation of the quantum molecular trajectory, through projection operator techniques, for the degrees of freedom of an open quantum system. The resulting Fokker-Planck operator is parametrically dependent upon the reduced density matrix of the open system. Because of the pilot role played by the reduced density matrix, this stochastic approach is able to represent accurately the main features of the open system motions both at equilibrium and out of equilibrium with the environment. To verify this procedure, the predictions of the stochastic and deterministic representation are compared for a model system of six interacting harmonic oscillators, where one oscillator is taken as the open quantum system of interest. The undeniable advantage of the stochastic approach is that of providing a simplified and self-contained representation of the dynamics of the open system coordinates. Furthermore, it can be employed to study the out of equilibrium dynamics and the relaxation of quantum molecular motions during photoinduced processes, like photoinduced conformational changes and proton transfers.
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Affiliation(s)
- Francesco Avanzini
- Dipartimento di Scienze Chimiche , Università di Padova , via Marzolo 1 , 35131 Padova , Italy
| | - Giorgio J Moro
- Dipartimento di Scienze Chimiche , Università di Padova , via Marzolo 1 , 35131 Padova , Italy
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12
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Avanzini F, Moro GJ. Quantum stochastic trajectories: the Smoluchowski-Bohm equation. Phys Chem Chem Phys 2018; 20:165-179. [PMID: 29181466 DOI: 10.1039/c7cp06071h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular systems are quantum systems, but the complete characterization of molecular motions within a fully quantum framework might appear to be an unfeasible task because it would require that the actual nuclear positions are established at any time. One would like to use a quantum molecular trajectory that defines the instantaneous nuclear positions and satisfies the predictions of quantum mechanics in terms of its statistical properties. Even though it can be proven that the single Bohm trajectory provides a representation of the quantum molecular trajectory, this solves the issue only on a theoretical ground: exact solutions of the Schrödinger-Bohm dynamical system are extremely computationally demanding. Therefore, we derive a stochastic equation of Smoluchowski type from the Schrödinger-Bohm dynamics, through projection operator techniques, in order to characterize the molecular motions of open quantum systems. The main quantum features of the motions emerge from the equilibrium distribution, i.e., the wave function's squared modulus integrated on the environment degrees of freedom. Furthermore, we verify the accuracy of the stochastic equation by comparing its predictions with those of the deterministic dynamics for a model system of six interacting harmonic oscillators. The indisputable advantage of this full quantum mechanical approach is that of representing the molecular dynamics, which controls important phenomena like vibrational relaxation, conformational transitions and activated processes, in a self consistent way and at the low computational cost of solving simple stochastic equations.
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Affiliation(s)
- Francesco Avanzini
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova, Italy.
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13
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Ceccon A, Tugarinov V, Boughton AJ, Fushman D, Clore GM. Probing the Binding Modes of a Multidomain Protein to Lipid-based Nanoparticles by Relaxation-based NMR. J Phys Chem Lett 2017; 8:2535-2540. [PMID: 28530812 PMCID: PMC5576874 DOI: 10.1021/acs.jpclett.7b01019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The interactions of two model multidomain proteins-covalently linked diubiquitins, Ub2-with lipid-based nanoparticles have been quantitatively probed by the measurements of NMR lifetime line broadening, ΔR2. By combined analysis of ΔR2 profiles arising from interactions with liposomes of varying sizes, an approach recently developed for the characterization of interactions of monoubiquitin with liposomes, we determine how the parameters of exchange (liposome binding) and dynamics of each individual domain of Ub2 on the surface of liposomes change when the domains are covalently attached to one another by a flexible linker. Two different covalent linkages were used: K63-linked and K48-linked Ub2. The possibility of three distinct modes of binding of Ub2 to liposomes requires the introduction of simple but important modifications to the strategy of analysis originally developed for monoubiquitin.
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Corresponding Authors: G.M.C.: ., V.T.:
| | - Andrew J. Boughton
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742-4454, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742-4454, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Corresponding Authors: G.M.C.: ., V.T.:
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14
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Andrałojć W, Ravera E, Salmon L, Parigi G, Al-Hashimi HM, Luchinat C. Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations. Phys Chem Chem Phys 2017; 18:5743-52. [PMID: 26360616 DOI: 10.1039/c5cp03993b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Detecting conformational heterogeneity in biological macromolecules is a key for the understanding of their biological function. We here provide a comparison between two independent approaches to assess conformational heterogeneity: molecular dynamics simulations, performed without inclusion of any experimental data, and maximum occurrence (MaxOcc) distribution over the topologically available conformational space. The latter only reflects the extent of the averaging and identifies regions which are most compliant with the experimentally measured NMR Residual Dipolar Couplings (RDCs). The analysis was performed for the HIV-1 TAR RNA, consisting of two helical domains connected by a flexible bulge junction, for which four sets of RDCs were available as well as an 8.2 μs all-atom molecular dynamics simulation. A sample and select approach was previously applied to extract from the molecular dynamics trajectory conformational ensembles in agreement with the four sets of RDCs. The MaxOcc analysis performed here identifies the most likely sampled region in the conformational space of the system which, strikingly, overlaps well with the structures independently sampled in the molecular dynamics calculations and even better with the RDC selected ensemble.
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Affiliation(s)
- Witold Andrałojć
- Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.
| | - Enrico Ravera
- Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Loïc Salmon
- Department of Molecular, Cellular and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Giacomo Parigi
- Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Department of Chemistry, Duke University School of Medicine, 307 Research Drive, Durham, North Carolina 27710, USA
| | - Claudio Luchinat
- Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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15
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Ravera E, Sgheri L, Parigi G, Luchinat C. A critical assessment of methods to recover information from averaged data. Phys Chem Chem Phys 2017; 18:5686-701. [PMID: 26565805 DOI: 10.1039/c5cp04077a] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Conformational heterogeneity is key to the function of many biomacromolecules, but only a few groups have tried to characterize it until recently. Now, thanks to the increased throughput of experimental data and the increased computational power, the problem of the characterization of protein structural variability has become more and more popular. Several groups have devoted their efforts in trying to create quantitative, reliable and accurate protocols for extracting such information from averaged data. We analyze here different approaches, discussing strengths and weaknesses of each. All approaches can roughly be clustered into two groups: those satisfying the maximum entropy principle and those recovering ensembles composed of a restricted number of molecular conformations. In the first case, the solution focuses on the features that are common to all the infinite solutions satisfying the experimental data; in the second case, the reconstructed ensemble shows the conformational regions where a large probability can be placed. The upper limits for conformational probabilities (MaxOcc) can also be calculated. We also give an overview of the mainstream experimental observables, with considerations on the assumptions underlying their usage.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo, Sezione di Firenze, CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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16
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Delaforge E, Milles S, Huang JR, Bouvier D, Jensen MR, Sattler M, Hart DJ, Blackledge M. Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions. Front Mol Biosci 2016; 3:54. [PMID: 27679800 PMCID: PMC5020063 DOI: 10.3389/fmolb.2016.00054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/30/2016] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.
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Affiliation(s)
- Elise Delaforge
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Sigrid Milles
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Jie-Rong Huang
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Denis Bouvier
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum MünchenNeuherberg, Germany; Center for Integrated Protein Science Munich at Biomolecular NMR, Technische Universität MünchenGarching, Germany
| | - Darren J Hart
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
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17
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Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity. Int J Mol Sci 2016; 17:ijms17081305. [PMID: 27517921 PMCID: PMC5000702 DOI: 10.3390/ijms17081305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/13/2023] Open
Abstract
Spider aciniform (wrapping) silk is a remarkable fibrillar biomaterial with outstanding mechanical properties. It is a modular protein consisting, in Argiope trifasciata, of a core repetitive domain of 200 amino acid units (W units). In solution, the W units comprise a globular folded core, with five α-helices, and disordered tails that are linked to form a ~63-residue intrinsically disordered linker in concatemers. Herein, we present nuclear magnetic resonance (NMR) spectroscopy-based 15N spin relaxation analysis, allowing characterization of backbone dynamics as a function of residue on the ps–ns timescale in the context of the single W unit (W1) and the two unit concatemer (W2). Unambiguous mapping of backbone dynamics throughout W2 was made possible by segmental NMR active isotope-enrichment through split intein-mediated trans-splicing. Spectral density mapping for W1 and W2 reveals a striking disparity in dynamics between the folded core and the disordered linker and tail regions. These data are also consistent with rotational diffusion behaviour where each globular domain tumbles almost independently of its neighbour. At a localized level, helix 5 exhibits elevated high frequency dynamics relative to the proximal helix 4, supporting a model of fibrillogenesis where this helix unfolds as part of the transition to a mixed α-helix/β-sheet fibre.
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18
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Khan SN, Charlier C, Augustyniak R, Salvi N, Déjean V, Bodenhausen G, Lequin O, Pelupessy P, Ferrage F. Distribution of Pico- and Nanosecond Motions in Disordered Proteins from Nuclear Spin Relaxation. Biophys J 2016; 109:988-99. [PMID: 26331256 PMCID: PMC4564687 DOI: 10.1016/j.bpj.2015.06.069] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered proteins and intrinsically disordered regions (IDRs) are ubiquitous in the eukaryotic proteome. The description and understanding of their conformational properties require the development of new experimental, computational, and theoretical approaches. Here, we use nuclear spin relaxation to investigate the distribution of timescales of motions in an IDR from picoseconds to nanoseconds. Nitrogen-15 relaxation rates have been measured at five magnetic fields, ranging from 9.4 to 23.5 T (400-1000 MHz for protons). This exceptional wealth of data allowed us to map the spectral density function for the motions of backbone NH pairs in the partially disordered transcription factor Engrailed at 11 different frequencies. We introduce an approach called interpretation of motions by a projection onto an array of correlation times (IMPACT), which focuses on an array of six correlation times with intervals that are equidistant on a logarithmic scale between 21 ps and 21 ns. The distribution of motions in Engrailed varies smoothly along the protein sequence and is multimodal for most residues, with a prevalence of motions around 1 ns in the IDR. We show that IMPACT often provides better quantitative agreement with experimental data than conventional model-free or extended model-free analyses with two or three correlation times. We introduce a graphical representation that offers a convenient platform for a qualitative discussion of dynamics. Even when relaxation data are only acquired at three magnetic fields that are readily accessible, the IMPACT analysis gives a satisfactory characterization of spectral density functions, thus opening the way to a broad use of this approach.
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Affiliation(s)
- Shahid N Khan
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Cyril Charlier
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Rafal Augustyniak
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Nicola Salvi
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, BCH, Lausanne, Switzerland
| | - Victoire Déjean
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Geoffrey Bodenhausen
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France; Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, BCH, Lausanne, Switzerland
| | - Olivier Lequin
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Philippe Pelupessy
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Fabien Ferrage
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France.
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19
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Liu W, Zhang J, Fan JS, Tria G, Grüber G, Yang D. A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein. Biophys J 2016; 110:1943-56. [PMID: 27166803 PMCID: PMC4939551 DOI: 10.1016/j.bpj.2016.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 04/05/2016] [Accepted: 04/05/2016] [Indexed: 10/21/2022] Open
Abstract
Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein.
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Affiliation(s)
- Wei Liu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jingfeng Zhang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Giancarlo Tria
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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20
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Carlon A, Ravera E, Hennig J, Parigi G, Sattler M, Luchinat C. Improved Accuracy from Joint X-ray and NMR Refinement of a Protein-RNA Complex Structure. J Am Chem Soc 2016; 138:1601-10. [PMID: 26761154 DOI: 10.1021/jacs.5b11598] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Integrated experimental approaches play an increasingly important role in structural biology, taking advantage of the complementary information provided by different techniques. In particular, the combination of NMR data with X-ray diffraction patterns may provide accurate and precise information about local conformations not available from average-resolution X-ray structures alone. Here, we refined the structure of a ternary protein-protein-RNA complex comprising three domains, Sxl and Unr, bound to a single-stranded region derived in the msl2 mRNA. The joint X-ray and NMR refinement reveals that-despite the poor quality of the fit found for the original structural model-the NMR data can be largely accommodated within the uncertainty in the atom positioning (structural noise) from the primary X-ray data and that the overall domain arrangements and binding interfaces are preserved on passing from the crystalline state to the solution. The refinement highlights local conformational differences, which provide additional information on specific features of the structure. For example, conformational dynamics and heterogeneity observed at the interface between the CSD1 and the Sxl protein components in the ternary complex are revealed by the combination of NMR and crystallographic data. The joint refinement protocol offers unique opportunities to detect structural differences arising from various experimental conditions and reveals static or dynamic differences in the conformation of the biomolecule between the solution and the crystals.
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Affiliation(s)
- Azzurra Carlon
- Magnetic Resonance Center "CERM" and Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Consortium (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Enrico Ravera
- Magnetic Resonance Center "CERM" and Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Consortium (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Janosch Hennig
- Center for Integrated Protein Science Munich (CIPSM) at Department Chemie, Technische Universität München , 85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , 85764 Neuherberg, Germany
| | - Giacomo Parigi
- Magnetic Resonance Center "CERM" and Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Consortium (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Michael Sattler
- Center for Integrated Protein Science Munich (CIPSM) at Department Chemie, Technische Universität München , 85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , 85764 Neuherberg, Germany
| | - Claudio Luchinat
- Magnetic Resonance Center "CERM" and Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Consortium (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Firenze, Italy
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21
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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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22
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Andrałojć W, Berlin K, Fushman D, Luchinat C, Parigi G, Ravera E, Sgheri L. Information content of long-range NMR data for the characterization of conformational heterogeneity. JOURNAL OF BIOMOLECULAR NMR 2015; 62:353-71. [PMID: 26044033 PMCID: PMC4782772 DOI: 10.1007/s10858-015-9951-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/25/2015] [Indexed: 05/16/2023]
Abstract
Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.
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Affiliation(s)
- Witold Andrałojć
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Konstantin Berlin
- Department of Chemistry and Biochemistry, Center for Biomolecular
Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular
Structure and Organization, University of Maryland, College Park, MD 20742, USA
- Corresponding authors: David Fushman, ,
Claudio Luchinat,
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Corresponding authors: David Fushman, ,
Claudio Luchinat,
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo, Sezione di Firenze,
CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
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23
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Zanzoni S, Ceccon A, Assfalg M, Singh RK, Fushman D, D'Onofrio M. Polyhydroxylated [60]fullerene binds specifically to functional recognition sites on a monomeric and a dimeric ubiquitin. NANOSCALE 2015; 7:7197-205. [PMID: 25811293 PMCID: PMC4443925 DOI: 10.1039/c5nr00539f] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which NPs interact with biomolecules. NPs associating with proteins may interfere with protein-protein interactions and affect cellular communication pathways, however the impact of NPs on biomolecular recognition remains poorly characterized. In this respect, particularly relevant is the study of NP-induced functional perturbations of proteins implicated in the regulation of key biochemical pathways. Ubiquitin (Ub) is a prototypical protein post-translational modifier playing a central role in numerous essential biological processes. To contribute to the understanding of the interactions between this universally distributed biomacromolecule and NPs, we investigated the adsorption of polyhydroxylated [60]fullerene on monomeric Ub and on a minimal polyubiquitin chain in vitro at atomic resolution. Site-resolved chemical shift and intensity perturbations of Ub's NMR signals, together with (15)N spin relaxation rate changes, exchange saturation transfer effects, and fluorescence quenching data were consistent with the reversible formation of soluble aggregates incorporating fullerenol clusters. The specific interaction epitopes were identified, coincident with functional recognition sites in a monomeric and lysine48-linked dimeric Ub. Fullerenol appeared to target the open state of the dynamic structure of a dimeric Ub according to a conformational selection mechanism. Importantly, the protein-NP association prevented the enzyme-catalyzed synthesis of polyubiquitin chains. Our findings provide an experiment-based insight into protein/fullerenol recognition, with implications in functional biomolecular communication, including regulatory protein turnover, and for the opportunity of therapeutic intervention in Ub-dependent cellular pathways.
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Affiliation(s)
- Serena Zanzoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy.
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24
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Ryabov Y. Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra. Proteins 2015; 83:1571-81. [PMID: 25900685 DOI: 10.1002/prot.24814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/23/2015] [Accepted: 04/05/2015] [Indexed: 11/08/2022]
Abstract
In this work, we formulate a closed-form solution of the model of a semirigid molecule for the case of fluctuating and reorienting molecular electric dipole moment. We illustrate with numeric calculations the impact of protein domain motions on dielectric spectra using the example of the 128 kDa protein dimer of Enzyme I. We demonstrate that the most drastic effect occurs for situations when the characteristic time of protein domain dynamics is comparable to the time of overall molecular rotational diffusion. We suggest that protein domain motions could be a possible explanation for the high-frequency contribution that accompanies the major relaxation dispersion peak in the dielectric spectra of protein aqueous solutions. We propose that the presented computational methodology could be used for the simultaneous analysis of dielectric spectroscopy and nuclear magnetic resonance data. Proteins 2015; 83:1571-1581. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Yaroslav Ryabov
- BC Portal Inc., 260 Congressional Ln. #204, Rockville, Maryland, 20852
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25
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Berlin K, Castañeda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. J Am Chem Soc 2014; 135:16595-609. [PMID: 24093873 DOI: 10.1021/ja4083717] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Structural analysis of proteins and nucleic acids is complicated by their inherent flexibility, conferred, for example, by linkers between their contiguous domains. Therefore, the macromolecule needs to be represented by an ensemble of conformations instead of a single conformation. Determining this ensemble is challenging because the experimental data are a convoluted average of contributions from multiple conformations. As the number of the ensemble degrees of freedom generally greatly exceeds the number of independent observables, directly deconvolving experimental data into a representative ensemble is an ill-posed problem. Recent developments in sparse approximations and compressive sensing have demonstrated that useful information can be recovered from underdetermined (ill-posed) systems of linear equations by using sparsity regularization. Inspired by these advances, we designed the Sparse Ensemble Selection (SES) method for recovering multiple conformations from a limited number of observations. SES is more general and accurate than previously published minimum-ensemble methods, and we use it to obtain representative conformational ensembles of Lys48-linked diubiquitin, characterized by the residual dipolar coupling data measured at several pH conditions. These representative ensembles are validated against NMR chemical shift perturbation data and compared to maximum-entropy results. The SES method reproduced and quantified the previously observed pH dependence of the major conformation of Lys48-linked diubiquitin, and revealed lesser-populated conformations that are preorganized for binding known diubiquitin receptors, thus providing insights into possible mechanisms of receptor recognition by polyubiquitin. SES is applicable to any experimental observables that can be expressed as a weighted linear combination of data for individual states.
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26
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Russo L, Palmieri M, Caso JV, D'Abrosca G, Diana D, Malgieri G, Baglivo I, Isernia C, Pedone PV, Fattorusso R. Towards understanding the molecular recognition process in prokaryotic zinc-finger domain. Eur J Med Chem 2014; 91:100-8. [PMID: 25240418 DOI: 10.1016/j.ejmech.2014.09.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Abstract
Eukaryotic Cys2His2 zinc finger domain is one of the most common and important structural motifs involved in protein-DNA interaction. The recognition motif is characterized by the tetrahedral coordination of a zinc ion by conserved cysteine and histidine residues. We have characterized the prokaryotic Cys2His2 zinc finger motif, included in the DNA binding region (Ros87) of Ros protein from Agrobacterium tumefaciens, demonstrating that, although possessing a similar zinc coordination sphere, this domain presents significant differences from its eukaryotic counterpart. Furthermore, basic residues flanking the zinc binding region on either side have been demonstrated, by Electrophoretic Mobility Shift Assay (EMSA) experiments, to be essential for Ros DNA binding. In spite of this wealth of knowledge, the structural details of the mechanism through which the prokaryotic zinc fingers recognize their target genes are still unclear. Here, to gain insights into the molecular DNA recognition process of prokaryotic zinc finger domains we applied a strategy in which we performed molecular docking studies using a combination of Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations data. The results demonstrate that the MD ensemble provides a reasonable picture of Ros87 backbone dynamics in solution. The Ros87-DNA model indicates that the interaction involves the first two residue of the first α-helix, and several residues located in the basic regions flanking the zinc finger domain. Interestingly, the prokaryotic zinc finger domain, mainly with the C-terminal tail that is wrapped around the DNA, binds a more extended recognition site than the eukaryotic counterpart. Our analysis demonstrates that the introduction of the protein flexibility in docking studies can improve, in terms of accuracy, the quality of the obtained models and could be particularly useful for protein showing high conformational heterogeneity as well as for computational drug design applications.
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Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Jolanda Valentina Caso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Donatella Diana
- Institute of Biostructures and Bioimaging -CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.
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27
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Andrałojć W, Luchinat C, Parigi G, Ravera E. Exploring regions of conformational space occupied by two-domain proteins. J Phys Chem B 2014; 118:10576-87. [PMID: 25144917 DOI: 10.1021/jp504820w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The presence of heterogeneity in the interdomain arrangement of several biomolecules is required for their function. Here we present a method to obtain crucial clues to distinguish between different kinds of protein conformational distributions based on experimental NMR data. The method explores subregions of the conformational space and provides both upper and lower bounds of probability for the system to be in each subregion.
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Affiliation(s)
- Witold Andrałojć
- Center for Magnetic Resonance, University of Florence , Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
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28
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Mechanisms of generating polyubiquitin chains of different topology. Cells 2014; 3:674-89. [PMID: 24987835 PMCID: PMC4197637 DOI: 10.3390/cells3030674] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/11/2014] [Accepted: 06/19/2014] [Indexed: 01/02/2023] Open
Abstract
Ubiquitination is an important post-translational process involving attachment of the ubiquitin molecule to lysine residue/s on a substrate protein or on another ubiquitin molecule, leading to the formation of protein mono-, multi- or polyubiquitination. Protein ubiquitination requires a cascade of three enzymes, where the interplay between different ubiquitin-conjugating and ubiquitin-ligase enzymes generates diverse ubiquitinated proteins topologies. Structurally diverse ubiquitin conjugates are recognized by specific proteins with ubiquitin-binding domains (UBDs) to target the substrate proteins of different pathways. The mechanism/s for generating the different ubiquitinated proteins topologies is not well understood. Here, we will discuss our current understanding of the mechanisms underpinning the generation of mono- or polyubiquitinated substrates. In addition, we will discuss how linkage-specific polyubiquitin chains through lysines-11, -48 or -63 are formed to target proteins to different fates by binding specific UBD proteins.
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29
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Wang Y, Tang C, Wang E, Wang J. PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape. PLoS Comput Biol 2014; 10:e1003691. [PMID: 24992446 PMCID: PMC4081019 DOI: 10.1371/journal.pcbi.1003691] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/12/2014] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China
| | - Chun Tang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China
- College of Physics, Jilin University, Changchun, Jilin, P.R. China
- Department of Chemistry, Physics and Applied Mathematics, State University of New York at Stony Brook, Stony Brook, New York, United States of America
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30
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Huang JR, Warner LR, Sanchez C, Gabel F, Madl T, Mackereth CD, Sattler M, Blackledge M. Transient electrostatic interactions dominate the conformational equilibrium sampled by multidomain splicing factor U2AF65: a combined NMR and SAXS study. J Am Chem Soc 2014; 136:7068-76. [PMID: 24734879 DOI: 10.1021/ja502030n] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Multidomain proteins containing intrinsically disordered linkers exhibit large-scale dynamic modes that play key roles in a multitude of molecular recognition and signaling processes. Here, we determine the conformational space sampled by the multidomain splicing factor U2AF65 using complementary nuclear magnetic resonance spectroscopy and small-angle scattering data. Available degrees of conformational freedom are initially stochastically sampled and experimental data then used to delineate the potential energy landscape in terms of statistical probability. The spatial distribution of U2AF65 conformations is found to be highly anisotropic, comprising significantly populated interdomain contacts that appear to be electrostatic in origin. This hypothesis is supported by the reduction of signature PREs reporting on expected interfaces with increasing salt concentration. The described spatial distribution reveals the complete spectrum of the unbound forms of U2AF65 that coexist with the small percentage of a preformed RNA-bound domain arrangement required for polypyrimidine-tract recognition by conformational selection. More generally, the proposed approach to describing conformational equilibria of multidomain proteins can be further combined with other experimental data that are sensitive to domain dynamics.
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Affiliation(s)
- Jie-rong Huang
- University Grenoble Alpes, ‡CNRS, and §CEA, Protein Dynamics and Flexibility, Institut de Biologie Structurale , 38000 Grenoble, France
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31
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Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:958-67. [PMID: 24699641 PMCID: PMC4306559 DOI: 10.1107/s1399004713034160] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/18/2013] [Indexed: 11/12/2022]
Abstract
The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.
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Affiliation(s)
- Mauro Rinaldelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Vito Calderone
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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32
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Bouvier B. Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations. Phys Chem Chem Phys 2014; 16:48-60. [DOI: 10.1039/c3cp52436a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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33
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Maciejewski M, Barlow PN, Tjandra N. Decoding the components of dynamics in three-domain proteins. J Comput Chem 2013; 35:518-25. [PMID: 24323885 DOI: 10.1002/jcc.23510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/07/2013] [Accepted: 11/24/2013] [Indexed: 01/05/2023]
Abstract
In this study, we examine the feasibility and limitations of describing the motional behavior of three-domain proteins in which the domains are linearly connected. In addition to attempting the determination of the internal and overall reorientational correlation times, we investigate the existence of correlations in the motions between the three domains. Since in linearly arranged three-domain proteins, there are typically no experimental data that can directly report on motional correlation between the first and the third domain, we address this question by dynamics simulations. Two limiting cases occur: (1) for weak repulsive potentials and (2) when strong repulsive potentials are applied between sequential domains. The motions of the terminal domains become correlated in the case of strong interdomain repulsive potentials when these potentials do not allow the angle between the sequential domains to be smaller than about 60°. Using the model-free (MF) and extended MF formalisms of Lipari and Szabo, we find that the motional behavior can be separated into two components; the first component represents the concerted overall motion of the three domains, and the second describes the independent component of the motion of each individual domain. We find that this division of the motional behavior of the protein is maintained only when their timescales are distinct and can be made when the angles between sequential domains remain between 60° and 160°. In this work, we identify and quantify interdomain motional correlations.
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Affiliation(s)
- Mateusz Maciejewski
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts, 02139
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34
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Berlin K, Longhini A, Dayie TK, Fushman D. Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface. JOURNAL OF BIOMOLECULAR NMR 2013; 57:333-352. [PMID: 24170368 PMCID: PMC3939081 DOI: 10.1007/s10858-013-9791-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/11/2013] [Indexed: 05/28/2023]
Abstract
To facilitate rigorous analysis of molecular motions in proteins, DNA, and RNA, we present a new version of ROTDIF, a program for determining the overall rotational diffusion tensor from single- or multiple-field nuclear magnetic resonance relaxation data. We introduce four major features that expand the program's versatility and usability. The first feature is the ability to analyze, separately or together, (13)C and/or (15)N relaxation data collected at a single or multiple fields. A significant improvement in the accuracy compared to direct analysis of R2/R1 ratios, especially critical for analysis of (13)C relaxation data, is achieved by subtracting high-frequency contributions to relaxation rates. The second new feature is an improved method for computing the rotational diffusion tensor in the presence of biased errors, such as large conformational exchange contributions, that significantly enhances the accuracy of the computation. The third new feature is the integration of the domain alignment and docking module for relaxation-based structure determination of multi-domain systems. Finally, to improve accessibility to all the program features, we introduced a graphical user interface that simplifies and speeds up the analysis of the data. Written in Java, the new ROTDIF can run on virtually any computer platform. In addition, the new ROTDIF achieves an order of magnitude speedup over the previous version by implementing a more efficient deterministic minimization algorithm. We not only demonstrate the improvement in accuracy and speed of the new algorithm for synthetic and experimental (13)C and (15)N relaxation data for several proteins and nucleic acids, but also show that careful analysis required especially for characterizing RNA dynamics allowed us to uncover subtle conformational changes in RNA as a function of temperature that were opaque to previous analysis.
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Affiliation(s)
- Konstantin Berlin
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
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35
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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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36
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Russo L, Maestre-Martinez M, Wolff S, Becker S, Griesinger C. Interdomain dynamics explored by paramagnetic NMR. J Am Chem Soc 2013; 135:17111-20. [PMID: 24111622 DOI: 10.1021/ja408143f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An ensemble-based approach is presented to explore the conformational space sampled by a multidomain protein showing moderate interdomain dynamics in terms of translational and rotational motions. The strategy was applied on a complex of calmodulin (CaM) with the IQ-recognition motif from the voltage-gated calcium channel Ca(v)1.2 (IQ), which adopts three different interdomain orientations in the crystal. The N60D mutant of calmodulin was used to collect pseudocontact shifts and paramagnetically induced residual dipolar couplings for six different lanthanide ions. Then, starting from the crystal structure, pools of conformations were generated by free MD. We found the three crystal conformations in solution, but four additional MD-derived conformations had to be included into the ensemble to fulfill all the paramagnetic data and cross-validate optimally against unused paramagnetic data. Alternative approaches led to similar ensembles. Our "ensemble" approach is a simple and efficient tool to probe and describe the interdomain dynamics and represents a general method that can be used to provide a proper ensemble description of multidomain proteins.
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Affiliation(s)
- Luigi Russo
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 37077 Göttingen, Germany
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37
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Rezaei-Ghaleh N, Klama F, Munari F, Zweckstetter M. Vorhersage der Rotationskorrelationszeit in dynamischen Mehrdomänenproteinen und supramolekularen Komplexen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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38
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Fragai M, Luchinat C, Parigi G, Ravera E. Conformational freedom of metalloproteins revealed by paramagnetism-assisted NMR. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Cerofolini L, Fields GB, Fragai M, Geraldes CFGC, Luchinat C, Parigi G, Ravera E, Svergun DI, Teixeira JMC. Examination of matrix metalloproteinase-1 in solution: a preference for the pre-collagenolysis state. J Biol Chem 2013; 288:30659-30671. [PMID: 24025334 DOI: 10.1074/jbc.m113.477240] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalysis of collagen degradation by matrix metalloproteinase 1 (MMP-1) has been proposed to critically rely on flexibility between the catalytic (CAT) and hemopexin-like (HPX) domains. A rigorous assessment of the most readily accessed conformations in solution is required to explain the onset of substrate recognition and collagenolysis. The present study utilized paramagnetic NMR spectroscopy and small angle x-ray scattering (SAXS) to calculate the maximum occurrence (MO) of MMP-1 conformations. The MMP-1 conformations with large MO values (up to 47%) are restricted into a relatively small conformational region. All conformations with high MO values differ largely from the closed MMP-1 structures obtained by x-ray crystallography. The MO of the latter is ~20%, which represents the upper limit for the presence of this conformation in the ensemble sampled by the protein in solution. In all the high MO conformations, the CAT and HPX domains are not in tight contact, and the residues of the HPX domain reported to be responsible for the binding to the collagen triple-helix are solvent exposed. Thus, overall analysis of the highest MO conformations indicated that MMP-1 in solution was poised to interact with collagen and then could readily proceed along the steps of collagenolysis.
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Affiliation(s)
| | - Gregg B Fields
- the Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987,.
| | - Marco Fragai
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Carlos F G C Geraldes
- the Center for Neuroscience and Cell Biology and; the Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, P.O. Box 3046, 3001-401 Coimbra, Portugal, and
| | - Claudio Luchinat
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy,.
| | - Giacomo Parigi
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Dmitri I Svergun
- the EMBL, c/o DESY, Notkestrasse 85, Geb. 25 A, 22603 Hamburg, Germany
| | - João M C Teixeira
- From the CERM and; the Center for Neuroscience and Cell Biology and; the Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, P.O. Box 3046, 3001-401 Coimbra, Portugal, and
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40
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Rezaei-Ghaleh N, Klama F, Munari F, Zweckstetter M. Predicting the Rotational Tumbling of Dynamic Multidomain Proteins and Supramolecular Complexes. Angew Chem Int Ed Engl 2013; 52:11410-4. [DOI: 10.1002/anie.201305094] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Indexed: 01/10/2023]
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41
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Chen K, Tjandra N. Determining interdomain structure and dynamics of a retroviral capsid protein in the presence of oligomerization: implication for structural transition in capsid assembly. Biochemistry 2013; 52:5365-71. [PMID: 23906107 DOI: 10.1021/bi400592d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Capsid (CA) proteins from all retroviruses, including HIV-1, are structurally homologous dual-domain helical proteins. They form a capsid lattice composed of unitary symmetric CA hexamers. X-ray crystallography has shown that within each hexamer a monomeric CA adopts a single conformation, where most helices are parallel to the symmetry axis. In solution, large differences in averaged NMR spin relaxation rates for the two domains were observed, suggesting they are dynamically independent. One relevant question for the capsid assembly remains: whether the interdomain conformer within a hexamer unit needs to be induced or pre-exists within the conformational space of a monomeric CA. The latter seems more consistent with the relaxation data. However, possible CA protein oligomerization and the structure of each domain will affect relaxation measurements and data interpretation. This study, using CA proteins from equine infectious anemia virus (EIAV) as an example, demonstrates a linear extrapolation approach to obtain backbone (15)N spin relaxation time ratios T1/T2 for a monomeric EIAV-CA in the presence of oligomerization equilibrium. The interdomain motion turns out to be limited. The large difference in the domain averaged <T1/T2> for a CA monomer is a consequence of the orthogonal distributions of helices in the two domains. The new monomeric interdomain conformation in solution is significantly different from that in CA hexamer. Therefore, if capsid assembly follows a nucleation-propagation process, the interdomain conformational change might be a key step during the nucleation, as the configuration in hexagonal assembly is never formed by diffusion of its two domains in solution.
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Affiliation(s)
- Kang Chen
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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42
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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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43
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Uversky VN. Hypothesis: The unfolding power of protein dielectricity. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25725. [PMID: 28516018 PMCID: PMC5424796 DOI: 10.4161/idp.25725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 07/02/2013] [Accepted: 07/11/2013] [Indexed: 01/25/2023]
Abstract
A hypothesis is proposed on a potential role of protein dielectricity as an unfolding factor in protein-protein interactions. It is suggested that large protein complexes and aggregation seeds can unfold target proteins by virtue of their effect on the dielectric properties of water at the protein-solvent interface. Here, similar to the effect of membrane surfaces, protein surface can cause decrease in the local dielectric constant of solvent and thereby induce structural changes in a target protein approaching this surface. Some potential implementations of this hypothetical mechanism are also discussed.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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44
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Xia J, Deng NJ, Levy RM. NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B 2013; 117:6625-34. [PMID: 23638941 DOI: 10.1021/jp400797y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calculating NMR relaxation effects for proteins with dynamics on multiple time scales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report, we have built Markov state models from multiple MD trajectories and used the resulting MSM to capture the very fast internal motions of the protein within a free energy basin on a time scale up to hundreds of picoseconds and the more than 3 orders of magnitude slower conformational exchange between macrostates. To interpret the relaxation data, we derive new equations using the model-free framework which includes two slowly exchanging macrostates, each of which also exhibits fast local motions. Using simulations of HIV-1 protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the NMR relaxation data.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA
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45
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Soss SE, Klevit RE, Chazin WJ. Activation of UbcH5c~Ub is the result of a shift in interdomain motions of the conjugate bound to U-box E3 ligase E4B. Biochemistry 2013; 52:2991-9. [PMID: 23550736 DOI: 10.1021/bi3015949] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Post-translational modification of proteins with ubiquitin is mediated by dynamic multienzyme machinery (E1, E2, and E3). E3 ubiquitin ligases play a key role acting as both scaffolds to bring reactants together and activators to catalyze ubiquitin (Ub) transfer from E2~Ub conjugates to substrates. Our recent studies provided insights into the mechanism of the activation event; binding of an E3 to an E2~Ub conjugate was found to affect the motions of E2~Ub and allosterically stimulate Ub transfer. This proposed mechanism implies that the dynamics of the conjugate, which has been shown to occupy a wide range of E2~Ub orientations, will be altered significantly upon binding of E3. To directly assess the effect of E3 binding on E2~Ub dynamics, we undertook an in-depth comparative analysis of (15)N nuclear magnetic resonance relaxation of UbcH5c~Ub in the absence and presence of the E3 ligase, E4B. Challenges encountered in deciphering interdomain motions for this ternary complex are discussed along with the limitations of the current approaches. Notably, although a reduction in interdomain dynamics of UbcH5c~Ub is observed upon binding to E4B, Ub retains an extensive degree of flexibility. These results provide strong support for our dynamic model of a significant orientational bias of Ub toward a more closed conformation in the E3/E2~Ub complex.
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Affiliation(s)
- Sarah E Soss
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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Nakasone MA, Livnat-Levanon N, Glickman MH, Cohen RE, Fushman D. Mixed-linkage ubiquitin chains send mixed messages. Structure 2013; 21:727-40. [PMID: 23562397 DOI: 10.1016/j.str.2013.02.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/14/2013] [Accepted: 02/17/2013] [Indexed: 02/02/2023]
Abstract
Research on ubiquitin (Ub) signaling has focused primarily on homogeneously linked polyUb. Although polyUb containing different linkages within the same chain exist, their structures and signaling properties are unknown. These mixed-linkage chains could be unbranched (i.e., no more than one lysine or methionine linkage per Ub) or branched. Here, we examined the structure, dynamics, receptor selectivity, and disassembly of branched and unbranched tri-Ub containing both K48 and K63 linkages. Each linkage was virtually indistinguishable from its counterpart in homogeneously linked polyUb. Linkage-selective receptors from hHR23A and Rap80 preferentially bound to the K48 or K63 linkages in the branched trimer. Linkage-selective deubiquitinases specifically cleaved their cognate Ub-Ub linkages in mixed-linkage chains, and the 26S proteasome recognized and processed branched tri-Ub. We conclude that mixed-linkage chains retain the distinctive signaling properties of their K48 and K63 components and that these multiple signals can be recognized by multiple linkage-specific receptors. Finally, we propose a new, comprehensive notation for Ub and Ub-like polymers.
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Affiliation(s)
- Mark A Nakasone
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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Abstract
Diflavin reductases are essential proteins capable of splitting the two-electron flux from reduced pyridine nucleotides to a variety of one electron acceptors. The primary sequence of diflavin reductases shows a conserved domain organization harboring two catalytic domains bound to the FAD and FMN flavins sandwiched by one or several non-catalytic domains. The catalytic domains are analogous to existing globular proteins: the FMN domain is analogous to flavodoxins while the FAD domain resembles ferredoxin reductases. The first structural determination of one member of the diflavin reductases family raised some questions about the architecture of the enzyme during catalysis: both FMN and FAD were in perfect position for interflavin transfers but the steric hindrance of the FAD domain rapidly prompted more complex hypotheses on the possible mechanisms for the electron transfer from FMN to external acceptors. Hypotheses of domain reorganization during catalysis in the context of the different members of this family were given by many groups during the past twenty years. This review will address the recent advances in various structural approaches that have highlighted specific dynamic features of diflavin reductases.
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Affiliation(s)
- Louise Aigrain
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK; E-Mail:
| | - Fataneh Fatemi
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Centre de Recherche de Gif, 1 Av. de la Terrasse, 91198 Gif-sur-Yvette Cedex, France; E-Mails: (F.F.); (O.F.); (E.L.)
| | - Oriane Frances
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Centre de Recherche de Gif, 1 Av. de la Terrasse, 91198 Gif-sur-Yvette Cedex, France; E-Mails: (F.F.); (O.F.); (E.L.)
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Centre de Recherche de Gif, 1 Av. de la Terrasse, 91198 Gif-sur-Yvette Cedex, France; E-Mails: (F.F.); (O.F.); (E.L.)
| | - Gilles Truan
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-567048813; Fax: +33-567048814
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Bertini I, Ferella L, Luchinat C, Parigi G, Petoukhov MV, Ravera E, Rosato A, Svergun DI. MaxOcc: a web portal for maximum occurrence analysis. JOURNAL OF BIOMOLECULAR NMR 2012; 53:271-280. [PMID: 22639196 DOI: 10.1007/s10858-012-9638-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 05/16/2012] [Indexed: 06/01/2023]
Abstract
The MaxOcc web portal is presented for the characterization of the conformational heterogeneity of two-domain proteins, through the calculation of the Maximum Occurrence that each protein conformation can have in agreement with experimental data. Whatever the real ensemble of conformations sampled by a protein, the weight of any conformation cannot exceed the calculated corresponding Maximum Occurrence value. The present portal allows users to compute these values using any combination of restraints like pseudocontact shifts, paramagnetism-based residual dipolar couplings, paramagnetic relaxation enhancements and small angle X-ray scattering profiles, given the 3D structure of the two domains as input. MaxOcc is embedded within the NMR grid services of the WeNMR project and is available via the WeNMR gateway at http://py-enmr.cerm.unifi.it/access/index/maxocc . It can be used freely upon registration to the grid with a digital certificate.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy.
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Bertini I, Luchinat C, Nagulapalli M, Parigi G, Ravera E. Paramagnetic relaxation enhancement for the characterization of the conformational heterogeneity in two-domain proteins. Phys Chem Chem Phys 2012; 14:9149-56. [PMID: 22622816 DOI: 10.1039/c2cp40139h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multidomain proteins are often composed of rigid domains that can reorient in solution more or less freely. Calmodulin (CaM) is a two domain protein which can experience a large degree of conformational freedom thanks to a mobile linker connecting the N-terminal and C-terminal domains of the protein. The maximum occurrences (MOs) of the possible protein conformations have been analyzed using the paramagnetic relaxation enhancements (PREs) induced by a gadolinium(III) ion together with the paramagnetic pseudocontact shift and residual dipolar coupling restraints measured in the presence of terbium(III), thulium(III) or dysprosium(III) ions. The results suggest that the PREs provide complementary information useful for improving the description of the conformational heterogeneity of the protein. The data, acquired at 298 K and at 278 K, suggest that compact conformations are disfavoured by decreasing the temperature.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.
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Ryabov Y, Clore GM, Schwieters CD. Coupling between internal dynamics and rotational diffusion in the presence of exchange between discrete molecular conformations. J Chem Phys 2012; 136:034108. [PMID: 22280745 DOI: 10.1063/1.3675602] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We present a general formalism for the computation of orientation correlation functions involving a molecular system undergoing rotational diffusion in the presence of transitions between discrete conformational states. In this formalism, there are no proscriptions on the time scales of conformational rearrangement relative to that for rotational diffusion, and the rotational diffusion tensors of the different states can be completely arbitrary. Although closed-form results are limited to the frequency domain, this is generally useful for many spectroscopic observables as the result allows the computation of the spectral density function. We specialize the results for the computation of the frequency-domain correlation function associated with the NMR relaxation.
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Affiliation(s)
- Yaroslav Ryabov
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, Maryland 20892-5624, USA
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