51
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Fogarty AC, Potestio R, Kremer K. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties. J Chem Phys 2015; 142:195101. [DOI: 10.1063/1.4921347] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aoife C. Fogarty
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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52
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Abramov G, Morag O, Goldbourt A. Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:80-90. [PMID: 25797007 DOI: 10.1016/j.jmr.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/05/2015] [Accepted: 01/18/2015] [Indexed: 06/04/2023]
Abstract
Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.
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53
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Meirovitch E, Liang Z, Freed JH. Protein dynamics in the solid state from 2H NMR line shape analysis: a consistent perspective. J Phys Chem B 2015; 119:2857-68. [PMID: 25594631 DOI: 10.1021/jp511386b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Deuterium line shape analysis of CD3 groups has emerged as a particularly useful tool for studying microsecond-millisecond protein motions in the solid state. The models devised so far consist of several independently conceived simple jump-type motions. They are comprised of physical quantities encoded in their simplest form; improvements are only possible by adding yet another simple motion, thereby changing the model. The various treatments developed are case-specific; hence comparison among the different systems is not possible. Here we develop a new methodology for (2)H NMR line shape analysis free of these limitations. It is based on the microscopic-order-macroscopic-disorder (MOMD) approach. In MOMD motions are described by diffusion tensors, spatial restrictions by potentials/ordering tensors, and geometric features by relative tensor orientations. Jump-type motions are recovered in the limit of large orientational potentials. Model improvement is accomplished by monitoring the magnitude, symmetry, and orientation of the various tensors. The generality of MOMD makes possible comparison among different scenarios. CD3 line shapes from the Chicken Villin Headpiece Subdomain and the Streptomyces Subtilisin Inhibitor are used as experimental examples. All of these spectra are reproduced by using rhombic local potentials constrained for simplicity to be given by the L = 2 spherical harmonics, and by axial diffusion tensors. Potential strength and rhombicity are found to be ca. 2-3 k(B)T. The diffusion tensor is tilted at 120° from the C-CD3 axis. The perpendicular (parallel) correlation times for local motion are 0.1-1.0 ms (3.3-30 μs). Activation energies in the 1.1-8.0 kcal/mol range are estimated. Future prospects include extension to the (2)H relaxation limit, application to the (15)N and (13)C NMR nuclei, and accounting for collective motions and anisotropic media.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
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54
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Torchia DA. NMR studies of dynamic biomolecular conformational ensembles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 84-85:14-32. [PMID: 25669739 PMCID: PMC4325279 DOI: 10.1016/j.pnmrs.2014.11.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 11/19/2014] [Accepted: 11/19/2014] [Indexed: 05/06/2023]
Abstract
Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: "Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?" This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA.
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Affiliation(s)
- Dennis A Torchia
- National Institutes of Health (NIH), 5 Memorial Drive, Bethesda, MD 20892, USA.
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55
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Cobo MF, Reichert D, Saalwächter K, deAzevedo ER. A double-component Anderson-Weiss approach for describing NMR signals of mobile SIn units: application to constant-time DIPSHIFT experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 248:115-125. [PMID: 25442780 DOI: 10.1016/j.jmr.2014.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 09/11/2014] [Accepted: 09/15/2014] [Indexed: 06/04/2023]
Abstract
A composed Gaussian local field is proposed to describe the effect of molecular motions on NMR signals of SIn units (e.g., CHn or NHn), based upon the well-know Anderson-Weiss (AW) approximation. The approach is exemplified on constant-time recoupled dipolar chemical-shift correlation (tC-recDIPSHIFT) experiments, providing an analytical formula that can be used as a fitting function in studies of intermediate-regime motions. By comparison of analytical tC-recDIPSHIFT curves and dynamic spin dynamics simulations, we show that for heteronuclear spin pairs (SI system), the AW treatment assuming the usual Gaussian local field is accurate. However, the approximation fails for the case of SIn spin systems for motional rates higher than a few kHz. Based on earlier work of Terao et al., who proposed a decomposition of CHn dipolar powder patterns into to 2(n) spin-pair-type patterns, we propose an AW approach based upon a double-Gaussian local field. We derive an analytical formula for tC-recDIPSHIFT signals, and demonstrate its accuracy by comparison with simulations of several motional geometries and rates, and with experimental results for a model sample. The approach is not limited to the tC-recDIPSHIFT experiment and should be of general use in dipolar-coupling based experiments probing (partially) mobile SIn molecular moieties.
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Affiliation(s)
- Marcio Fernando Cobo
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, CEP, 13560-970 São Carlos, São Paulo, Brazil.
| | - Detlef Reichert
- Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle, Germany.
| | - Eduardo Ribeiro deAzevedo
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, CEP, 13560-970 São Carlos, São Paulo, Brazil.
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56
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Krushelnitsky A, Zinkevich T, Reif B, Saalwächter K. Slow motions in microcrystalline proteins as observed by MAS-dependent 15N rotating-frame NMR relaxation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 248:8-12. [PMID: 25282442 DOI: 10.1016/j.jmr.2014.09.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/04/2014] [Accepted: 09/09/2014] [Indexed: 05/14/2023]
Abstract
(15)N NMR relaxation rate R1ρ measurements reveal that a substantial fraction of residues in the microcrystalline chicken alpha-spectrin SH3 domain protein undergoes dynamics in the μs-ms timescale range. On the basis of a comparison of 2D site-resolved with 1D integrated (15)N spectral intensities, we demonstrate that the significant fraction of broad signals in the 2D spectrum exhibits the most pronounced slow mobility. We show that (15)N R1ρ's in proton-diluted protein samples are practically free from the coherent spin-spin contribution even at low MAS rates, and thus can be analysed quantitatively. Moderate MAS rates (10-30 kHz) can be more advantageous in comparison with the rates >50-60 kHz when slow dynamics are to be identified and quantified by means of R1ρ experiments.
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Affiliation(s)
- Alexey Krushelnitsky
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str.7, D-06120 Halle, Germany.
| | - Tatiana Zinkevich
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str.7, D-06120 Halle, Germany
| | - Bernd Reif
- Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Kay Saalwächter
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str.7, D-06120 Halle, Germany
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57
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Fechner P, Bleher O, Ewald M, Freudenberger K, Furin D, Hilbig U, Kolarov F, Krieg K, Leidner L, Markovic G, Proll G, Pröll F, Rau S, Riedt J, Schwarz B, Weber P, Widmaier J. Size does matter! Label-free detection of small molecule-protein interaction. Anal Bioanal Chem 2014; 406:4033-51. [PMID: 24817356 DOI: 10.1007/s00216-014-7834-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 11/28/2022]
Abstract
This review is focused on methods for detecting small molecules and, in particular, the characterisation of their interaction with natural proteins (e.g. receptors, ion channels). Because there are intrinsic advantages to using label-free methods over labelled methods (e.g. fluorescence, radioactivity), this review only covers label-free techniques. We briefly discuss available techniques and their advantages and disadvantages, especially as related to investigating the interaction between small molecules and proteins. The reviewed techniques include well-known and widely used standard analytical methods (e.g. HPLC-MS, NMR, calorimetry, and X-ray diffraction), newer and more specialised analytical methods (e.g. biosensors), biological systems (e.g. cell lines and animal models), and in-silico approaches.
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Affiliation(s)
- Peter Fechner
- Biametrics GmbH, Auf der Morgenstelle 18, 72076, Tübingen, Germany,
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58
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Palmer AG. Chemical exchange in biomacromolecules: past, present, and future. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:3-17. [PMID: 24656076 PMCID: PMC4049312 DOI: 10.1016/j.jmr.2014.01.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 05/08/2023]
Abstract
The perspective reviews quantitative investigations of chemical exchange phenomena in proteins and other biological macromolecules using NMR spectroscopy, particularly relaxation dispersion methods. The emphasis is on techniques and applications that quantify the populations, interconversion kinetics, and structural features of sparsely populated conformational states in equilibrium with a highly populated ground state. Applications to folding, molecular recognition, catalysis, and allostery by proteins and nucleic acids are highlighted.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States.
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59
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Good DB, Wang S, Ward ME, Struppe J, Brown LS, Lewandowski JR, Ladizhansky V. Conformational Dynamics of a Seven Transmembrane Helical Protein Anabaena Sensory Rhodopsin Probed by Solid-State NMR. J Am Chem Soc 2014; 136:2833-42. [DOI: 10.1021/ja411633w] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | - Jochem Struppe
- Bruker Biospin Ltd., Billerica, Massachusetts 01821, United States
| | | | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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60
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Hu W, Su Y, Zhou L, Pang A, Cai R, Ma X, Li S. Molecular dynamics of neutral polymer bonding agent (NPBA) as revealed by solid-state NMR spectroscopy. Molecules 2014; 19:1353-66. [PMID: 24451254 PMCID: PMC6270705 DOI: 10.3390/molecules19011353] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 01/03/2014] [Accepted: 01/16/2014] [Indexed: 12/04/2022] Open
Abstract
Neutral polymer bonding agent (NPBA) is one of the most promising polymeric materials, widely used in nitrate ester plasticized polyether (NEPE) propellant as bonding agent. The structure and dynamics of NPBA under different conditions of temperatures and sample processing are comprehensively investigated by solid state NMR (SSNMR). The results indicate that both the main chain and side chain of NPBA are quite rigid below its glass transition temperature (Tg). In contrast, above the Tg, the main chain remains relatively immobilized, while the side chains become highly flexible, which presumably weakens the interaction between bonding agent and the binder or oxidant fillers and in turn destabilizes the high modulus layer formed around the oxidant fillers. In addition, no obvious variation is found for the microstructure of NPBA upon aging treatment or soaking with acetone. These experimental results provide useful insights for understanding the structural properties of NPBA and its interaction with other constituents of solid composite propellants under different processing and working conditions.
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Affiliation(s)
- Wei Hu
- Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, China
| | - Yongchao Su
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China.
| | - Lei Zhou
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Aimin Pang
- Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, China.
| | - Rulin Cai
- Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, China
| | - Xingang Ma
- Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, China
| | - Shenhui Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China.
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61
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Loquet A, Habenstein B, Chevelkov V, Vasa SK, Giller K, Becker S, Lange A. Atomic Structure and Handedness of the Building Block of a Biological Assembly. J Am Chem Soc 2013; 135:19135-8. [DOI: 10.1021/ja411362q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Antoine Loquet
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Birgit Habenstein
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Veniamin Chevelkov
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Suresh Kumar Vasa
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Karin Giller
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
| | - Adam Lange
- Department
of NMR-based Structural
Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg
11, 37077 Göttingen, Germany
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