1
|
Bhattacharya S, Varney KM, Dahmane T, Johnson BA, Weber DJ, Palmer AG. Deuterium spin relaxation of fractionally deuterated ribonuclease H using paired 475 and 950 MHz NMR spectrometers. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00443-w. [PMID: 38856928 DOI: 10.1007/s10858-024-00443-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/27/2024] [Indexed: 06/11/2024]
Abstract
Deuterium (2H) spin relaxation of 13CH2D methyl groups has been widely applied to investigate picosecond-to-nanosecond conformational dynamics in proteins by solution-state NMR spectroscopy. The B0 dependence of the 2H spin relaxation rates is represented by a linear relationship between the spectral density function at three discrete frequencies J(0), J(ωD) and J(2ωD). In this study, the linear relation between 2H relaxation rates at B0 fields separated by a factor of two and the interpolation of rates at intermediate frequencies are combined for a more robust approach for spectral density mapping. The general usefulness of the approach is demonstrated on a fractionally deuterated (55%) and alternate 13C-12C labeled sample of E. coli RNase H. Deuterium relaxation rate constants (R1, R1ρ, RQ, RAP) were measured for 57 well-resolved 13CH2D moieties in RNase H at 1H frequencies of 475 MHz, 500 MHz, 900 MHz, and 950 MHz. The spectral density mapping of the 475/950 MHz data combination was performed independently and jointly to validate the expected relationship between data recorded at B0 fields separated by a factor of two. The final analysis was performed by jointly analyzing 475/950 MHz rates with 700 MHz rates interpolated from 500/900 MHz data to yield six J(ωD) values for each methyl peak. The J(ω) profile for each peak was fit to the original (τM, Sf2, τf) or extended model-free function (τM, Sf2, Ss2, τf, τs) to obtain optimized dynamic parameters.
Collapse
Affiliation(s)
| | - Kristen M Varney
- University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA
| | - Tassadite Dahmane
- New York Structural Biology Center, 89 Convent Ave, New York, NY, 10027, USA
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - David J Weber
- University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA
| | - Arthur G Palmer
- New York Structural Biology Center, 89 Convent Ave, New York, NY, 10027, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY, 10032, USA.
| |
Collapse
|
2
|
Zumpfe K, Berbon M, Habenstein B, Loquet A, Smith AA. Analytical Framework to Understand the Origins of Methyl Side-Chain Dynamics in Protein Assemblies. J Am Chem Soc 2024; 146:8164-8178. [PMID: 38476076 PMCID: PMC10979401 DOI: 10.1021/jacs.3c12620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Side-chain motions play an important role in understanding protein structure, dynamics, protein-protein, and protein-ligand interactions. However, our understanding of protein side-chain dynamics is currently limited by the lack of analytical tools. Here, we present a novel analytical framework employing experimental nuclear magnetic resonance (NMR) relaxation measurements at atomic resolution combined with molecular dynamics (MD) simulation to characterize with a high level of detail the methyl side-chain dynamics in insoluble protein assemblies, using amyloid fibrils formed by the prion HET-s. We use MD simulation to interpret experimental results, where rotameric hops, including methyl group rotation and χ1/χ2 rotations, cannot be completely described with a single correlation time but rather sample a broad distribution of correlation times, resulting from continuously changing local structure in the fibril. Backbone motion similarly samples a broad range of correlation times, from ∼100 ps to μs, although resulting from mostly different dynamic processes; nonetheless, we find that the backbone is not fully decoupled from the side-chain motion, where changes in side-chain dynamics influence backbone motion and vice versa. While the complexity of side-chain motion in protein assemblies makes it very challenging to obtain perfect agreement between experiment and simulation, our analytical framework improves the interpretation of experimental dynamics measurements for complex protein assemblies.
Collapse
Affiliation(s)
- Kai Zumpfe
- Institute
for Medical Physics and Biophysics, Leipzig
University, Härtelstraße
16-18, 04107 Leipzig, Germany
| | - Mélanie Berbon
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Birgit Habenstein
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Antoine Loquet
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Albert A. Smith
- Institute
for Medical Physics and Biophysics, Leipzig
University, Härtelstraße
16-18, 04107 Leipzig, Germany
| |
Collapse
|
3
|
Vugmeyster L, Ostrovsky D, Rodgers A, Gwin K, Smirnov SL, McKnight CJ, Fu R. Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR. Chemphyschem 2024; 25:e202300565. [PMID: 38175858 PMCID: PMC10922872 DOI: 10.1002/cphc.202300565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/01/2023] [Indexed: 01/06/2024]
Abstract
Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Kirsten Gwin
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, WA 98225
| | - C. James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL USA 32310
| |
Collapse
|
4
|
Gunaga SS, Bryce DL. Modulation of Rotational Dynamics in Halogen-Bonded Cocrystalline Solids. J Am Chem Soc 2023; 145:19005-19017. [PMID: 37586107 DOI: 10.1021/jacs.3c06343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Dynamic processes are responsible for the functionality of a range of materials, biomolecules, and catalysts. We report a detailed systematic study of the modulation of methyl rotational dynamics via the direct and the indirect influence of noncovalent halogen bonds. For this purpose, a novel series of cocrystalline architectures featuring halogen bonds (XB) to tetramethylpyrazine (TMP) is designed and prepared using gas-phase, solution, and solid-state mechanochemical methods. Single-crystal X-ray diffraction reveals the capacity of molecular bromine as well as weak chloro-XB donors to act as robust directional structure-directing elements. Methyl rotational barriers (Ea) measured using variable-temperature deuterium solid-state NMR range from 3.75 ± 0.04 kJ mol-1 in 1,3,5-trichloro-2,4,6-trifluorobenzene·TMP to 7.08 ± 0.15 kJ mol-1 in 1,4-dichlorotetrafluorobenzene·TMP. Ea data for a larger series of TMP cocrystals featuring chloro-, bromo-, and iodo-XB donors are shown to be governed by a combination of steric and electronic factors. The average number of carbon-carbon close contacts to the methyl group is found to be a key steric metric capable of rationalizing the observed trends within each of the Cl, Br, and I series. Differences between each series are accounted for by considering the strength of the σ-hole on the XB donor. One possible route to modulating dynamics is therefore via designer cocrystals of variable stoichiometry, maintaining the core chemical features of interest between a given donor and acceptor while simultaneously modifying the number of carbon close contacts affecting dynamics. These principles may provide design opportunities to modulate more complex geared or cascade dynamics involving larger functional groups.
Collapse
Affiliation(s)
- Shubha S Gunaga
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5 Canada
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5 Canada
| |
Collapse
|
5
|
Tatman BP, Franks WT, Brown SP, Lewandowski JR. Nuclear spin diffusion under fast magic-angle spinning in solid-state NMR. J Chem Phys 2023; 158:2890210. [PMID: 37171196 DOI: 10.1063/5.0142201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Solid-state nuclear spin diffusion is the coherent and reversible process through which spin order is transferred via dipolar couplings. With the recent increases in magic-angle spinning (MAS) frequencies and magnetic fields becoming routinely applied in solid-state nuclear magnetic resonance, understanding how the increased 1H resolution obtained affects spin diffusion is necessary for interpretation of several common experiments. To investigate the coherent contributions to spin diffusion with fast MAS, we have developed a low-order correlation in Liouville space model based on the work of Dumez et al. (J. Chem. Phys. 33, 224501, 2010). Specifically, we introduce a new method for basis set selection, which accounts for the resonance-offset dependence at fast MAS. Furthermore, we consider the necessity of including chemical shift, both isotropic and anisotropic, in the modeling of spin diffusion. Using this model, we explore how different experimental factors change the nature of spin diffusion. Then, we show case studies to exemplify the issues that arise in using spin diffusion techniques at fast spinning. We show that the efficiency of polarization transfer via spin diffusion occurring within a deuterated and 100% back-exchanged protein sample at 60 kHz MAS is almost entirely dependent on resonance offset. We additionally identify temperature-dependent magnetization transfer in beta-aspartyl L-alanine, which could be explained by the influence of an incoherent relaxation-based nuclear Overhauser effect.
Collapse
Affiliation(s)
- Ben P Tatman
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
6
|
Unravelling the Adaptation Mechanisms to High Pressure in Proteins. Int J Mol Sci 2022; 23:ijms23158469. [PMID: 35955607 PMCID: PMC9369236 DOI: 10.3390/ijms23158469] [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: 07/06/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/06/2023] Open
Abstract
Life is thought to have appeared in the depth of the sea under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high-pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here, we show the molecular bases of these mechanisms through a joint structural and dynamical study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein–water dynamics and the elimination of cavities in the protein core. This is achieved by rearranging the charged residues on the protein surface and using bulkier hydrophobic residues in the core. These findings will be the starting point in the search for a complete genomic model explaining high-pressure adaptation.
Collapse
|
7
|
Šimėnas M, Klose D, Ptak M, Aidas K, Mączka M, Banys J, Pöppl A, Jeschke G. Magnetic excitation and readout of methyl group tunnel coherence. SCIENCE ADVANCES 2020; 6:eaba1517. [PMID: 32494689 PMCID: PMC7195165 DOI: 10.1126/sciadv.aba1517] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/04/2020] [Indexed: 05/07/2023]
Abstract
Methyl groups are ubiquitous in synthetic materials and biomolecules. At sufficiently low temperature, they behave as quantum rotors and populate only the rotational ground state. In a symmetric potential, the three localized substates are degenerate and become mixed by the tunnel overlap to delocalized states separated by the tunnel splitting ν t . Although ν t can be inferred by several techniques, coherent superposition of the tunnel-split states and direct measurement of ν t have proven elusive. Here, we show that a nearby electron spin provides a handle on the tunnel transition, allowing for its excitation and readout. Unlike existing dynamical nuclear polarization techniques, our experiment transfers polarization from the electron spin to methyl proton spins with an efficiency that is independent of the magnetic field and does not rely on an unusually large tunnel splitting. Our results also demonstrate control of quantum states despite the lack of an associated transition dipole moment.
Collapse
Affiliation(s)
- M. Šimėnas
- Faculty of Physics, Vilnius University, Sauletekio av. 9, 10222 Vilnius, Lithuania
| | - D. Klose
- ETH-Zürich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - M. Ptak
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box-1410, PL-50-950 Wrocław 2, Poland
| | - K. Aidas
- Faculty of Physics, Vilnius University, Sauletekio av. 9, 10222 Vilnius, Lithuania
| | - M. Mączka
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box-1410, PL-50-950 Wrocław 2, Poland
| | - J. Banys
- Faculty of Physics, Vilnius University, Sauletekio av. 9, 10222 Vilnius, Lithuania
| | - A. Pöppl
- Felix Bloch Institute for Solid State Physics, Leipzig University, Linnéstr. 5, 04103 Leipzig, Germany
| | - G. Jeschke
- ETH-Zürich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
- Corresponding author.
| |
Collapse
|
8
|
Hoffmann F, Mulder FAA, Schäfer LV. Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers. J Chem Phys 2020; 152:084102. [DOI: 10.1063/1.5135379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Falk Hoffmann
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| |
Collapse
|
9
|
Smith CA, Mazur A, Rout AK, Becker S, Lee D, de Groot BL, Griesinger C. Enhancing NMR derived ensembles with kinetics on multiple timescales. JOURNAL OF BIOMOLECULAR NMR 2020; 74:27-43. [PMID: 31838619 PMCID: PMC7015964 DOI: 10.1007/s10858-019-00288-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/11/2019] [Indexed: 05/14/2023]
Abstract
Nuclear magnetic resonance (NMR) has the unique advantage of elucidating the structure and dynamics of biomolecules in solution at physiological temperatures, where they are in constant movement on timescales from picoseconds to milliseconds. Such motions have been shown to be critical for enzyme catalysis, allosteric regulation, and molecular recognition. With NMR being particularly sensitive to these timescales, detailed information about the kinetics can be acquired. However, nearly all methods of NMR-based biomolecular structure determination neglect kinetics, which introduces a large approximation to the underlying physics, limiting both structural resolution and the ability to accurately determine molecular flexibility. Here we present the Kinetic Ensemble approach that uses a hierarchy of interconversion rates between a set of ensemble members to rigorously calculate Nuclear Overhauser Effect (NOE) intensities. It can be used to simultaneously refine both temporal and structural coordinates. By generalizing ideas from the extended model free approach, the method can analyze the amplitudes and kinetics of motions anywhere along the backbone or side chains. Furthermore, analysis of a large set of crystal structures suggests that NOE data contains a surprising amount of high-resolution information that is better modeled using our approach. The Kinetic Ensemble approach provides the means to unify numerous types of experiments under a single quantitative framework and more fully characterize and exploit kinetically distinct protein states. While we apply the approach here to the protein ubiquitin and cross validate it with previously derived datasets, the approach can be applied to any protein for which NOE data is available.
Collapse
Affiliation(s)
- Colin A Smith
- Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
- Department of Chemistry, Wesleyan University, Middletown, USA.
| | - Adam Mazur
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Biozentrum, University of Basel, Basel, Switzerland
| | - Ashok K Rout
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Donghan Lee
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
- James Graham Brown Cancer Center, University of Louisville, Louisville, USA.
| | - Bert L de Groot
- Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Christian Griesinger
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| |
Collapse
|
10
|
Emani PS, Yimer YY, Davidowski SK, Gebhart RN, Ferreira HE, Kuprov I, Pfaendtner J, Drobny GP. Combining Molecular and Spin Dynamics Simulations with Solid-State NMR: A Case Study of Amphiphilic Lysine-Leucine Repeat Peptide Aggregates. J Phys Chem B 2019; 123:10915-10929. [PMID: 31769684 DOI: 10.1021/acs.jpcb.9b09245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interpreting dynamics in solid-state molecular systems requires characterization of the potentially heterogeneous environmental contexts of molecules. In particular, the analysis of solid-state nuclear magnetic resonance (ssNMR) data to elucidate molecular dynamics (MD) involves modeling the restriction to overall tumbling by neighbors, as well as the concentrations of water and buffer. In this exploration of the factors that influence motion, we utilize atomistic MD trajectories of peptide aggregates with varying hydration to mimic an amorphous solid-state environment and predict ssNMR relaxation rates. We also account for spin diffusion in multiply spin-labeled (up to 19 nuclei) residues, with several models of dipolar-coupling networks. The framework serves as a general approach to determine essential spin couplings affecting relaxation, benchmark MD force fields, and reveal the hydration dependence of dynamics in a crowded environment. We demonstrate the methodology on a previously characterized amphiphilic 14-residue lysine-leucine repeat peptide, LKα14 (Ac-LKKLLKLLKKLLKL-c), which has an α-helical secondary structure and putatively forms leucine-burying tetramers in the solid state. We measure the R1 relaxation rates of uniformly 13C-labeled and site-specific 2H-labeled leucines in the hydrophobic core of LKα14 at multiple hydration levels. Studies of 9 and 18 tetramer bundles reveal the following: (a) for the incoherent component of 13C relaxation, the nearest-neighbor spin interactions dominate, while the 1H-1H interactions have minimal impact; (b) the AMBER ff14SB dihedral barriers for the leucine Cγ-Cδ bond ("methyl rotation barriers") must be lowered by a factor of 0.7 to better match the 2H data; (c) proton-driven spin diffusion explains some of the discrepancy between experimental and simulated rates for the Cβ and Cα nuclei; and (d) 13C relaxation rates are mostly underestimated in the MD simulations at all hydrations, and the discrepancies identify likely motions missing in the 50 ns MD trajectories.
Collapse
Affiliation(s)
- Prashant S Emani
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Yeneneh Y Yimer
- Department of Chemical Engineering , University of Washington , 105 Benson Hall, Box 351750 , Seattle , Washington 98195-1750 , United States
| | - Stephen K Davidowski
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Rachel N Gebhart
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Helen E Ferreira
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Ilya Kuprov
- Department of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , U.K
| | - Jim Pfaendtner
- Department of Chemical Engineering , University of Washington , 105 Benson Hall, Box 351750 , Seattle , Washington 98195-1750 , United States
| | - Gary P Drobny
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| |
Collapse
|
11
|
Exploring Protein Structures by DNP-Enhanced Methyl Solid-State NMR Spectroscopy. J Am Chem Soc 2019; 141:19888-19901. [DOI: 10.1021/jacs.9b11195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
12
|
Phan VC, Fry EA, Zilm KW. Accounting for the temperature dependence of 13C spin-lattice relaxation of methyl groups in the glycyl-alanyl-leucine model system under MAS with spin diffusion. JOURNAL OF BIOMOLECULAR NMR 2019; 73:411-421. [PMID: 31407207 PMCID: PMC6817761 DOI: 10.1007/s10858-019-00261-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/19/2019] [Indexed: 06/10/2023]
Abstract
The difficulties in quantitatively modeling the temperature dependence of spin-lattice relaxation in a model isotope-enriched peptide are explored as a prelude to obtaining dynamics parameters for motions in proteins from such measurements. The degree to which this can be handled by adding spin diffusion to a bath in standard rate matrix relaxation theory is studied using a small tri-peptide model system, glycyl-alanyl-leucine (GAL). We observe in this molecule that the relaxation of backbone carbons CO and Cα is not dominated by local fluctuations of the 13C-1H dipolar couplings, but rather by 13C-13C spin diffusion to nearby methyl relaxation sinks. A treatment of the methyl relaxation itself, which ignores 13C-13C spin diffusion effects back to the otherwise slowly relaxing bath, provides poor agreement between theory and experimental data obtained for the temperature dependence of the methyl relaxation rates. Closed form approximate spectral densities and relaxation rates for a methyl group during magic angle spinning are obtained to compute the needed transition rates. These average computed rates, in conjunction with an extended form of the Solomon equations, are found to adequately model the temperature dependence of the methyl relaxation rates when spin diffusion is included. The barrier to rotation for the alanine methyl in GAL is determined to be 3.5 kcal mol-1.
Collapse
Affiliation(s)
- Van C Phan
- Natural Science Department, Hostos Community College, 500 Grand Concourse, The Bronx, NY, 10451, USA
| | - Elizabeth A Fry
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
| | - Kurt W Zilm
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
| |
Collapse
|
13
|
Tavagnacco L, Chiessi E, Zanatta M, Orecchini A, Zaccarelli E. Water-Polymer Coupling Induces a Dynamical Transition in Microgels. J Phys Chem Lett 2019; 10:870-876. [PMID: 30735054 PMCID: PMC6416711 DOI: 10.1021/acs.jpclett.9b00190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
Collapse
Affiliation(s)
- Letizia Tavagnacco
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| | - Ester Chiessi
- Department
of Chemical Sciences and Technologies, University
of Rome Tor Vergata, Via della Ricerca Scientica I, 00133 Rome, Italy
| | - Marco Zanatta
- Department
of Computer Science, University of Verona, Strada Le Grazie 15, 37138 Verona, Italy
| | - Andrea Orecchini
- Department
of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM
c/o Department of Physics and Geology, University
of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| |
Collapse
|
14
|
Liu Z, Yang C, Huang J, Ciampalini G, Li J, García Sakai V, Tyagi M, O'Neill H, Zhang Q, Capaccioli S, Ngai KL, Hong L. Direct Experimental Characterization of Contributions from Self-Motion of Hydrogen and from Interatomic Motion of Heavy Atoms to Protein Anharmonicity. J Phys Chem B 2018; 122:9956-9961. [PMID: 30295486 DOI: 10.1021/acs.jpcb.8b09355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One fundamental challenge in biophysics is to understand the connection between protein dynamics and its function. Part of the difficulty arises from the fact that proteins often present local atomic motions and collective dynamics on the same time scales, and challenge the experimental identification and quantification of different dynamic modes. Here, by taking lyophilized proteins as the example, we combined deuteration technique and neutron scattering to separate and characterize the self-motion of hydrogen and the collective interatomic motion of heavy atoms (C, O, N) in proteins on the pico-to-nanosecond time scales. We found that hydrogen atoms present an instrument-resolution-dependent onset for anharmonic motions, which can be ascribed to the thermal activation of local side-group motions. However, the protein heavy atoms exhibit an instrument-resolution-independent anharmonicity around 200 K, which results from unfreezing of the relaxation of the protein structures on the laboratory equilibrium time (100-1000 s), softening of the entire bio-macromolecules.
Collapse
Affiliation(s)
| | | | | | - Gaia Ciampalini
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
| | | | - Victoria García Sakai
- ISIS Neutron and Muon Facility , Rutherford Appleton Laboratory, Science & Technology Facilities Council , Didcot OX11 0QX , United Kingdom
| | - Madhusudan Tyagi
- National Institute of Standards and Technology (NIST) , NIST Center for Neutron Research , Gaithersburg , Maryland 20899 , United States.,Department of Materials Science and Engineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Hugh O'Neill
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37931 , United States
| | - Qiu Zhang
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37931 , United States
| | - Simone Capaccioli
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
| | - K L Ngai
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
| | | |
Collapse
|
15
|
Cousin SF, Kadeřávek P, Bolik-Coulon N, Gu Y, Charlier C, Carlier L, Bruschweiler-Li L, Marquardsen T, Tyburn JM, Brüschweiler R, Ferrage F. Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations. J Am Chem Soc 2018; 140:13456-13465. [DOI: 10.1021/jacs.8b09107] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel F. Cousin
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Pavel Kadeřávek
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Nicolas Bolik-Coulon
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Yina Gu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Cyril Charlier
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Ludovic Carlier
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Jean-Max Tyburn
- Bruker BioSpin, 34 rue de l’Industrie BP 10002, 67166 Wissembourg Cedex, France
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| |
Collapse
|
16
|
Baird-Titus JM, Thapa M, Doerdelmann T, Combs KA, Rance M. Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations. Biochemistry 2018; 57:2796-2813. [PMID: 29664630 DOI: 10.1021/acs.biochem.8b00195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in many cases to the other factors that determine the binding thermodynamics and may, therefore, play a key role in dictating the binding affinity and/or specificity. Because the entropic contributions, including the presence and influence of side-chain dynamics, are especially difficult to estimate based on structural information, it is important to pursue experimental and theoretical studies that can provide direct information regarding these issues. We report on studies of a model system, the homeodomain/DNA complex, focusing on the Lys50 class of homeodomains where a key lysine residue in position 50 was shown previously to be critical for binding site specificity. NMR methodology was employed for determining the dynamics of lysine side-chain amino groups via 15N relaxation measurements in the Lys50-class homeodomains from the Drosophila protein Bicoid and the human protein Pitx2. In the case of Pitx2, complexes with both a consensus and a nonconsensus DNA binding site were examined. NMR-derived order parameters indicated moderate to substantial conformational freedom for the lysine NH3+ group in the complexes studied. To complement the experimental NMR measurements, molecular dynamics simulations were performed for the consensus complexes to gain further, detailed insights regarding the dynamics of the Lys50 side chain and other important residues in the protein-DNA interface.
Collapse
Affiliation(s)
- Jamie M Baird-Titus
- Department of Chemistry and Physical Sciences , Mount St. Joseph University , Cincinnati , Ohio 45233 , United States
| | - Mahendra Thapa
- Department of Physics , University of Cincinnati , Cincinnati , Ohio 45220 , United States
| | - Thomas Doerdelmann
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
| | - Kelly A Combs
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
| | - Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
| |
Collapse
|
17
|
Hoffmann F, Mulder FAA, Schäfer LV. Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. J Phys Chem B 2018; 122:5038-5048. [DOI: 10.1021/acs.jpcb.8b02769] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Falk Hoffmann
- Theoretical Chemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| |
Collapse
|
18
|
Tavagnacco L, Zaccarelli E, Chiessi E. On the molecular origin of the cooperative coil-to-globule transition of poly(N-isopropylacrylamide) in water. Phys Chem Chem Phys 2018; 20:9997-10010. [PMID: 29619464 PMCID: PMC5932979 DOI: 10.1039/c8cp00537k] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cooperativity of PNIPAM coil-to-globule transition in water arises from the structuring of solvent in proximity to hydrophobic groups.
By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer–water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain.
Collapse
Affiliation(s)
- L Tavagnacco
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | | | | |
Collapse
|
19
|
Hoffmann F, Xue M, Schäfer LV, Mulder FAA. Narrowing the gap between experimental and computational determination of methyl group dynamics in proteins. Phys Chem Chem Phys 2018; 20:24577-24590. [DOI: 10.1039/c8cp03915a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A synergistic analysis of methyl NMR relaxation data and MD simulations identifies ways to improve studies of protein dynamics.
Collapse
Affiliation(s)
- Falk Hoffmann
- Theoretical Chemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Mengjun Xue
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry
- University of Aarhus
- DK-8000 Aarhus
- Denmark
| | - Lars V. Schäfer
- Theoretical Chemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry
- University of Aarhus
- DK-8000 Aarhus
- Denmark
| |
Collapse
|
20
|
Lesovoy DM, Mineev KS, Bragin PE, Bocharova OV, Bocharov EV, Arseniev AS. NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 69:165-179. [PMID: 29063258 DOI: 10.1007/s10858-017-0146-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the membrane protein interface mapping based on chemical shifts or other relevant parameters was never assessed. In the present work, we investigate the predictive power of various NMR parameters that can be used for mapping of helix-helix interfaces in dimeric TM domains. These parameters are studied on a dataset containing three structures of helical dimers obtained for two different proteins in various membrane mimetics. We conclude that the amide chemical shifts have very little predictive value, while the methyl chemical shifts could be used to predict interfaces, though with great care. We suggest an approach based on conversion of the carbon NMR relaxation parameters of methyl groups into parameters of motion, and one of such values, the characteristic time of methyl rotation, appears to be a reliable sensor of interhelix contacts in transmembrane domains. The carbon NMR relaxation parameters of methyl groups can be measured accurately and with high sensitivity and resolution, making the proposed parameter a useful tool for investigation of protein-protein interfaces even in large membrane proteins. An approach to build the models of transmembrane dimers based on perturbations of methyl parameters and TMDOCK software is suggested.
Collapse
Affiliation(s)
- D M Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
| | - K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| | - P E Bragin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow, Russian Federation, 119991
| | - O V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| | - E V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997.
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700.
- National Research Centre "Kurchatov Institute", Kurchatov Complex of NBICS-technologies, Akad. Kurchatova Sqr., 1, Moscow, Russian Federation, 123182.
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| |
Collapse
|
21
|
Vugmeyster L, Ostrovsky D. Comparative Dynamics of Methionine Side-Chain in FMOC-Methionine and in Amyloid Fibrils. Chem Phys Lett 2017; 673:108-112. [PMID: 28959059 DOI: 10.1016/j.cplett.2017.02.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We compared the dynamics of key methionine methyl groups in the water-accessible hydrophobic cavity of amyloid fibrils and Fluorenylmethyloxycarbonyl-Methionine (FMOC-Met), which renders general hydrophobicity to the environment without the complexity of the protein. Met35 in the hydrated cavity was recently found to undergo a dynamical cross-over from the dominance of methyl rotations at low temperatures to the dominance of diffusive motion of methyl axis at high temperatures. Current results indicate that in FMOC-Met this cross-over is suppressed, similar to what was observed for the dry fibrils, indicating that hydration of the cavity is driving the onset of the dynamical transition.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, 1201 Larimer Street, University of Colorado at Denver, Denver, CO 80204, USA
| | - Dmitry Ostrovsky
- Department of Mathematics, 1201 Larimer Street, University of Colorado at Denver, Denver, CO 80204, USA
| |
Collapse
|
22
|
Wong YTA, Landmann J, Finze M, Bryce DL. Dynamic Disorder and Electronic Structures of Electron-Precise Dianionic Diboranes: Insights from Solid-State Multinuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2017; 139:8200-8211. [PMID: 28548827 DOI: 10.1021/jacs.7b01783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The J(11B,11B) coupling constants of various salts of the electron-precise hexacyanodiborane(6) dianion, [B2(CN)6]2-, were obtained using 11B double-quantum-filtered (DQF) J-resolved solid-state nuclear magnetic resonance (SSNMR) spectroscopy. Our results show that the magnitude of the DQF J splitting is influenced by both the crystallographic symmetry of the system and the presence of dynamics. The splittings are amplified by a factor of 3 as compared to the corresponding theoretical J coupling constants for cases where (1) there is an absence of dynamics but the boron pairs are crystallographically equivalent or (2) the boron pairs are crystallographically inequivalent but are rendered magnetically equivalent on the time scale of the experiment due to dynamic disorder, which was identified by 11B and 13C SSNMR experiments. Consequently, molecular motions need to be taken into consideration when interpreting the results of DQF J-resolved experiments, and conversely, these experiments may be used to identify dynamic disorder. Variable-temperature NMR data support the notion of three different motional processes with correlation times ranging from 102 to 106 s-1 over the temperature range of 248-306 K. When molecular motion and crystallographic symmetry are both accounted for, the J(11B,11B) coupling constants for various [B2(CN)6]2- salts were measured to range from 29.4 to 35.8 Hz, and their electronic origins were determined using natural localized molecular orbital and natural bond orbital analyses. The coupling constants were found to strongly correlate to the hybridization states of the boron orbitals that form the B-B bonds and to the strength of the B-B bonds. This study provides a novel tool to study dynamics in ordered and disordered solids and provides new perspectives on electron-precise dianionic diboranes featuring two-center-two-electron bonds in the context of related compounds featuring multiply and singly bonded boron spin pairs.
Collapse
Affiliation(s)
- Y T Angel Wong
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa , Ottawa, Ontario, Canada K1N6N5
| | - Johannes Landmann
- Institut für Anorganische Chemie, Institut für nachhaltige Chemie & Katalyse mit Bor (ICB), Julius-Maximilians-Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Maik Finze
- Institut für Anorganische Chemie, Institut für nachhaltige Chemie & Katalyse mit Bor (ICB), Julius-Maximilians-Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa , Ottawa, Ontario, Canada K1N6N5
| |
Collapse
|
23
|
Abstract
Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein-ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or "entropy meter" also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water-protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins.
Collapse
|
24
|
Hansen DF. Measurement of 15N longitudinal relaxation rates in 15NH 4+ spin systems to characterise rotational correlation times and chemical exchange. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 279:91-98. [PMID: 28511856 PMCID: PMC5441844 DOI: 10.1016/j.jmr.2017.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/16/2017] [Accepted: 01/20/2017] [Indexed: 06/07/2023]
Abstract
Many chemical and biological processes rely on the movement of monovalent cations and an understanding of such processes can therefore only be achieved by characterising the dynamics of the involved ions. It has recently been shown that 15N-ammonium can be used as a proxy for potassium to probe potassium binding in bio-molecules such as DNA quadruplexes and enzymes. Moreover, equations have been derived to describe the time-evolution of 15N-based spin density operator elements of 15NH4+ spin systems. Herein NMR pulse sequences are derived to select specific spin density matrix elements of the 15NH4+ spin system and to measure their longitudinal relaxation in order to characterise the rotational correlation time of the 15NH4+ ion as well as report on chemical exchange events of the 15NH4+ ion. Applications to 15NH4+ in acidic aqueous solutions are used to cross-validate the developed pulse sequence while measurements of spin-relaxation rates of 15NH4+ bound to a 41kDa domain of the bacterial Hsp70 homologue DnaK are presented to show the general applicability of the derived pulse sequence. The rotational correlation time obtained for 15N-ammonium bound to DnaK is similar to the correlation time that describes the rotation about the threefold axis of a methyl group. The methodology presented here provides, together with the previous theoretical framework, an important step towards characterising the motional properties of cations in macromolecular systems.
Collapse
Affiliation(s)
- D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
| |
Collapse
|
25
|
Rajeshwar T R, Krishnan M. Direct Determination of Site-Specific Noncovalent Interaction Strengths of Proteins from NMR-Derived Fast Side Chain Motional Parameters. J Phys Chem B 2017; 121:5174-5186. [PMID: 28452484 DOI: 10.1021/acs.jpcb.7b01402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel approach to accurately determine residue-specific noncovalent interaction strengths (ξ) of proteins from NMR-measured fast side chain motional parameters (Oaxis2) is presented. By probing the environmental sensitivity of side chain conformational energy surfaces of individual residues of a diverse set of proteins, the microscopic connections between ξ, Oaxis2, conformational entropy (Sconf), conformational barriers, and rotamer stabilities established here are found to be universal among proteins. The results reveal that side chain flexibility and conformational entropy of each residue decrease with increasing ξ and that for each residue type there exists a critical range of ξ, determined primarily by the mean side chain conformational barriers, within which flexibility of any residue can be reversibly tuned from highly flexible (with Oaxis2 ∼ 0) to highly restricted (with Oaxis2 ∼ 1) by increasing ξ by ∼3 kcal/mol. Beyond this critical range of ξ, both side chain flexibility and conformational entropy are insensitive to ξ. The interrelationships between conformational dynamics, conformational entropy, and noncovalent interactions of protein side chains established here open up new avenues to probe perturbation-induced (for example, ligand-binding, temperature, pressure) changes in fast side chain dynamics and thermodynamics of proteins by comparing their conformational energy surfaces in the native and perturbed states.
Collapse
Affiliation(s)
- Rajitha Rajeshwar T
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Gachibowli, Hyderabad 500 032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Gachibowli, Hyderabad 500 032, India
| |
Collapse
|
26
|
Ni QZ, Markhasin E, Can TV, Corzilius B, Tan KO, Barnes AB, Daviso E, Su Y, Herzfeld J, Griffin RG. Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR. J Phys Chem B 2017; 121:4997-5006. [PMID: 28437077 DOI: 10.1021/acs.jpcb.7b02066] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In DNP MAS NMR experiments at ∼80-110 K, the structurally important -13CH3 and -15NH3+ signals in MAS spectra of biological samples disappear due to the interference of the molecular motions with the 1H decoupling. Here we investigate the effect of these dynamic processes on the NMR line shapes and signal intensities in several typical systems: (1) microcrystalline APG, (2) membrane protein bR, (3) amyloid fibrils PI3-SH3, (4) monomeric alanine-CD3, and (5) the protonated and deuterated dipeptide N-Ac-VL over 78-300 K. In APG, the three-site hopping of the Ala-Cβ peak disappears completely at 112 K, concomitant with the attenuation of CP signals from other 13C's and 15N's. Similarly, the 15N signal from Ala-NH3+ disappears at ∼173 K, concurrent with the attenuation in CP experiments of other 15N's as well as 13C's. In bR and PI3-SH3, the methyl groups are attenuated at ∼95 K, while all other 13C's remain unaffected. However, both systems exhibit substantial losses of intensity at ∼243 K. Finally, with spectra of Ala and N-Ac-VL, we show that it is possible to extract site specific dynamic data from the temperature dependence of the intensity losses. Furthermore, 2H labeling can assist with recovering the spectral intensity. Thus, our study provides insight into the dynamic behavior of biological systems over a wide range of temperatures, and serves as a guide to optimizing the sensitivity and resolution of structural data in low temperature DNP MAS NMR spectra.
Collapse
Affiliation(s)
- Qing Zhe Ni
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Evgeny Markhasin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Thach V Can
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Björn Corzilius
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kong Ooi Tan
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander B Barnes
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eugenio Daviso
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Yongchao Su
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Judith Herzfeld
- Department of Chemistry, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
27
|
Vugmeyster L, Ostrovsky D, Clark MA, Falconer IB, Hoatson GL, Qiang W. Fast Motions of Key Methyl Groups in Amyloid-β Fibrils. Biophys J 2016; 111:2135-2148. [PMID: 27851938 PMCID: PMC5113154 DOI: 10.1016/j.bpj.2016.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/18/2016] [Accepted: 10/05/2016] [Indexed: 11/28/2022] Open
Abstract
Amyloid-β (Aβ) peptide is the major component of plaques found in Alzheimer's disease patients. Using solid-state 2H NMR relaxation performed on selectively deuterated methyl groups, we probed the dynamics in the threefold symmetric and twofold symmetric polymorphs of native Aβ as well as the protofibrils of the D23N mutant. Specifically, we investigated the methyl groups of two leucine residues that belong to the hydrophobic core (L17 and L34) as well as M35 residues belonging to the hydrophobic interface between the cross-β subunits, which has been previously found to be water-accessible. Relaxation measurements performed over 310-140 K and two magnetic field strengths provide insights into conformational variability within and between polymorphs. Core packing variations within a single polymorph are similar to what is observed for globular proteins for the core residues, whereas M35 exhibits a larger degree of variability. M35 site is also shown to undergo a solvent-dependent dynamical transition in which slower amplitude motions of methyl axes are activated at high temperature. The motions, modeled as a diffusion of methyl axis, have activation energy by a factor of 2.7 larger in the twofold compared with the threefold polymorph, whereas D23N protofibrils display a value similar to the threefold polymorph. This suggests enhanced flexibility of the hydrophobic interface in the threefold polymorph. This difference is only observed in the hydrated state and is absent in the dry fibrils, highlighting the role of solvent at the cavity. In contrast, the dynamic behavior of the core is hydration-independent.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado at Denver, Denver, Colorado
| | - Matthew A Clark
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska
| | - Isaac B Falconer
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado
| | - Gina L Hoatson
- Department of Physics, College of William and Mary, Williamsburg, Virginia
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York
| |
Collapse
|
28
|
Tchaicheeyan O, Meirovitch E. An SRLS Study of 2H Methyl-Moiety Relaxation and Related Conformational Entropy in Free and Peptide-Bound PLCγ1C SH2. J Phys Chem B 2016; 120:10695-10705. [DOI: 10.1021/acs.jpcb.6b08264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oren Tchaicheeyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
29
|
Beckmann PA, Rheingold AL. 1H and 19F spin-lattice relaxation and CH3 or CF3 reorientation in molecular solids containing both H and F atoms. J Chem Phys 2016; 144:154308. [DOI: 10.1063/1.4944981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
Vugmeyster L, Ostrovsky D, Villafranca T, Sharp J, Xu W, Lipton AS, Hoatson GL, Vold RL. Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR. J Phys Chem B 2015; 119:14892-904. [PMID: 26529128 PMCID: PMC4970646 DOI: 10.1021/acs.jpcb.5b09299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298-80 K temperature range. Our main tools were static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is nonexponential at all temperatures with the extent of nonexponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al. J. Phys. Chem. B 2013, 117, 6129-6137), suggests that the hydrophobic core undergoes slow concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The crossover temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in softening the core and highlights aromatic residues as markers of the protein dynamical transitions.
Collapse
Affiliation(s)
| | | | | | - Janelle Sharp
- University of Alaska Anchorage, Anchorage, Alaska, 99508
| | - Wei Xu
- College of William and Mary, Williamsburg, Virginia, 23187
| | - Andrew S. Lipton
- Pacific Northwest National Laboratory, Richland, Washington, 99354
| | | | - Robert L. Vold
- College of William and Mary, Williamsburg, Virginia, 23187
| |
Collapse
|
31
|
Observing the overall rocking motion of a protein in a crystal. Nat Commun 2015; 6:8361. [PMID: 26436197 PMCID: PMC4600728 DOI: 10.1038/ncomms9361] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/13/2015] [Indexed: 12/25/2022] Open
Abstract
The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments. Small-amplitude overall motion of molecules in crystals limits the achievable resolution in X-ray diffraction, yet little is known about its exact nature. Here, the authors obtain NMR, XRD and MD data from three different crystal forms of a protein (ubiquitin) to gain insight into amplitude and timescale of such motions.
Collapse
|
32
|
Zandarashvili L, Iwahara J. Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds. Biochemistry 2014; 54:538-45. [PMID: 25489884 DOI: 10.1021/bi5012749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although charged side chains play important roles in protein function, their dynamic properties are not well understood. Nuclear magnetic resonance methods for investigating the dynamics of lysine side-chain NH3(+) groups were established recently. Using this methodology, we have studied the temperature dependence of the internal motions of the lysine side-chain NH3(+) groups that form ion pairs with DNA phosphate groups in the HoxD9 homeodomain-DNA complex. For these NH3(+) groups, we determined order parameters and correlation times for bond rotations and reorientations at 15, 22, 28, and 35 °C. The order parameters were found to be virtually constant in this temperature range. In contrast, the bond-rotation correlation times of the NH3(+) groups were found to depend strongly on temperature. On the basis of transition state theory, the energy barriers for NH3(+) rotations were analyzed and compared to those for CH3 rotations. Enthalpies of activation for NH3(+) rotations were found to be significantly higher than those for CH3 rotations, which can be attributed to the requirement of hydrogen bond breakage. However, entropies of activation substantially reduce the overall free energies of activation for NH3(+) rotations to a level comparable to those for CH3 rotations. This entropic reduction in energy barriers may accelerate molecular processes requiring hydrogen bond breakage and play a kinetically important role in protein function.
Collapse
Affiliation(s)
- Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555-1068, United States
| | | |
Collapse
|
33
|
Xue Y, Yuwen T, Zhu F, Skrynnikov NR. Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos. Biochemistry 2014; 53:6473-95. [PMID: 25207671 DOI: 10.1021/bi500904f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intrinsically disordered proteins (IDPs) often rely on electrostatic interactions to bind their structured targets. To obtain insight into the mechanism of formation of the electrostatic encounter complex, we investigated the binding of the peptide Sos (PPPVPPRRRR), which serves as a minimal model for an IDP, to the c-Crk N-terminal SH3 domain. Initially, we measured ¹⁵N relaxation rates at two magnetic field strengths and determined the binding shifts for the complex of Sos with wild-type SH3. We have also recorded a 3 μs molecular dynamics (MD) trajectory of this complex using the Amber ff99SB*-ILDN force field. The comparison of the experimental and simulated data shows that MD simulation consistently overestimates the strength of salt bridge interactions at the binding interface. The series of simulations using other advanced force fields also failed to produce any satisfactory results. To address this issue, we have devised an empirical correction to the Amber ff99SB*-ILDN force field whereby the Lennard-Jones equilibrium distance for the nitrogen-oxygen pair across the Arg-to-Asp and Arg-to-Glu salt bridges has been increased by 3%. Implementing this correction resulted in a good agreement between the simulations and the experiment. Adjusting the strength of salt bridge interactions removed a certain amount of strain contained in the original MD model, thus improving the binding of the hydrophobic N-terminal portion of the peptide. The arginine-rich C-terminal portion of the peptide, freed from the effect of the overstabilized salt bridges, was found to interconvert more rapidly between its multiple conformational states. The modified MD protocol has also been successfully used to simulate the entire binding process. In doing so, the peptide was initially placed high above the protein surface. It then arrived at the correct bound pose within ∼2 Å of the crystallographic coordinates. This simulation allowed us to analyze the details of the dynamic binding intermediate, i.e., the electrostatic encounter complex. However, an experimental characterization of this transient, weakly populated state remains out of reach. To overcome this problem, we designed the double mutant of c-Crk N-SH3 in which mutations Y186L and W169F abrogate tight Sos binding and shift the equilibrium toward the intermediate state resembling the electrostatic encounter complex. The results of the combined NMR and MD study of this engineered system will be reported in the next part of this paper.
Collapse
Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | | | | | | |
Collapse
|
34
|
del Amo JML, Agarwal V, Sarkar R, Porter J, Asami S, Rübbelke M, Fink U, Xue Y, Lange OF, Reif B. Site-specific analysis of heteronuclear Overhauser effects in microcrystalline proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 59:241-9. [PMID: 24989039 DOI: 10.1007/s10858-014-9843-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/20/2014] [Indexed: 05/14/2023]
Abstract
Relaxation parameters such as longitudinal relaxation are susceptible to artifacts such as spin diffusion, and can be affected by paramagnetic impurities as e.g. oxygen, which make a quantitative interpretation difficult. We present here the site-specific measurement of [(1)H](13)C and [(1)H](15)N heteronuclear rates in an immobilized protein. For methyls, a strong effect is expected due to the three-fold rotation of the methyl group. Quantification of the [(1)H](13)C heteronuclear NOE in combination with (13)C-R 1 can yield a more accurate analysis of side chain motional parameters. The observation of significant [(1)H](15)N heteronuclear NOEs for certain backbone amides, as well as for specific asparagine/glutamine sidechain amides is consistent with MD simulations. The measurement of site-specific heteronuclear NOEs is enabled by the use of highly deuterated microcrystalline protein samples in which spin diffusion is reduced in comparison to protonated samples.
Collapse
Affiliation(s)
- Juan Miguel Lopez del Amo
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
T. RR, Smith JC, Krishnan M. Hidden Regularity and Universal Classification of Fast Side Chain Motions in Proteins. J Am Chem Soc 2014; 136:8590-605. [DOI: 10.1021/ja5024783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Rajitha Rajeshwar T.
- Center
for Computational Natural Sciences and Bioinformatics, International
Institute of Information Technology, Gachibowli, Hyderabad 500 032, India
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Molecular and Cellular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Marimuthu Krishnan
- Center
for Computational Natural Sciences and Bioinformatics, International
Institute of Information Technology, Gachibowli, Hyderabad 500 032, India
| |
Collapse
|
36
|
Vugmeyster L, Ostrovsky D. Restricted diffusion of methyl groups in proteins revealed by deuteron NMR: manifestation of intra-well dynamics. J Chem Phys 2014; 140:075101. [PMID: 24559369 DOI: 10.1063/1.4865412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The three-site hops of methyl groups are usually used as an approximation of the mechanistic description of motions responsible for the longitudinal NMR relaxation. Distinguishing between three-site hops and a more realistic mechanism of diffusion in a potential requires extended experimental and computational analysis. In order to achieve this goal, in this work the restricted diffusion is decomposed into two independent modes, namely, the jumps between potential wells and intra-well fluctuations, assuming time scale separation between these modes. This approach allows us to explain the rise in the theoretical value of T1 minimum for the restricted diffusion mechanism compared with the three-site hops mechanism via rescaling the three-site hops correlation function by the order parameter of intra-well motions. The main result of the paper is that, in general, intra-well dynamics can be visible in NMR even in the limit of large barrier heights in contrast to the common view that this limit converges to the three-site hops mechanism. Based on a previously collected detailed set of deuteron NMR relaxation and spectral data in the villin headpiece subdomain protein over a wide temperature range of 300-31 K, we are then able to conclude that the mechanism of diffusion in the threefold potential is likely to be the main source of the dynamics in this system.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska 99508, USA
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Alaska Anchorage, Anchorage, Alaska 99508, USA
| |
Collapse
|
37
|
Meirovitch E. The Slowly Relaxing Local Structure Perspective of Protein Dynamics by NMR Relaxation. Isr J Chem 2014. [DOI: 10.1002/ijch.201300090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
38
|
Tugarinov V. Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 77:49-68. [PMID: 24411830 DOI: 10.1016/j.pnmrs.2013.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/15/2013] [Indexed: 06/03/2023]
Abstract
A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R1 and R2 rates) of nuclei directly attached to one or more deuterons as well as protons of methyl groups in a highly deuterated environment, (4) scalar relaxation of 15N and 13C nuclei in 15N-D and 13C-D spin systems as a measure of hydrogen bonding strength, and (5) NOE-based applications of deuteration in NMR studies of protein structure. The discussion is restricted to the 'indirect' use of deuterium in the sense that the description of NMR parameters and properties of the nuclei affected by nearby deuterons (15N, 13C, 1H) is provided rather than those of deuterium itself.
Collapse
Affiliation(s)
- Vitali Tugarinov
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States.
| |
Collapse
|
39
|
Martínez JI, Alonso PJ, García-Rubio I, Medina M. Methyl rotors in flavoproteins. Phys Chem Chem Phys 2014; 16:26203-12. [DOI: 10.1039/c4cp03115f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ENDOR evidence shows that methyl groups in flavin behave as quantum locked rotors.
Collapse
Affiliation(s)
- Jesús I. Martínez
- Instituto de Ciencia de Materiales de Aragón
- Universidad de Zaragoza-Consejo Superior de Investigaciones Científicas
- Facultad de Ciencias
- 50009 Zaragoza, Spain
| | - Pablo J. Alonso
- Instituto de Ciencia de Materiales de Aragón
- Universidad de Zaragoza-Consejo Superior de Investigaciones Científicas
- Facultad de Ciencias
- 50009 Zaragoza, Spain
| | - Inés García-Rubio
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zürich, Switzerland
- Centro Universitario de la Defensa
- 50090 Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)
- Universidad de Zaragoza
- 50009 Zaragoza, Spain
| |
Collapse
|
40
|
Beckmann PA, Conn KG, Mallory CW, Mallory FB, Rheingold AL, Rotkina L, Wang X. Distributions of methyl group rotational barriers in polycrystalline organic solids. J Chem Phys 2013; 139:204501. [DOI: 10.1063/1.4830411] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
41
|
Vugmeyster L, Do T, Ostrovsky D, Fu R. Effect of subdomain interactions on methyl group dynamics in the hydrophobic core of villin headpiece protein. Protein Sci 2013; 23:145-56. [PMID: 24243806 DOI: 10.1002/pro.2398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/16/2013] [Accepted: 11/06/2013] [Indexed: 11/06/2022]
Abstract
Thermostable villin headpiece protein (HP67) consists of the N-terminal subdomain (residues 10-41) and the autonomously folding C-terminal subdomain (residues 42-76) which pack against each other to form a structure with a unified hydrophobic core. The X-ray structures of the isolated C-terminal subdomain (HP36) and its counterpart in HP67 are very similar for the hydrophobic core residues. However, fine rearrangements of the free energy landscape are expected to occur because of the interactions between the two subdomains. We detect and characterize these changes by comparing the µs-ms time scale dynamics of the methyl-bearing side chains in isolated HP36 and in HP67. Specifically, we probe three hydrophobic side chains at the interface of the two subdomains (L42, V50, and L75) as well as at two residues far from the interface (L61 and L69). Solid-state deuteron NMR techniques are combined with computational modeling for the detailed characterization of motional modes in terms of their kinetic and thermodynamic parameters. The effect of interdomain interactions on side chain dynamics is seen for all residues but L75. Thus, changes in dynamics because of subdomain interactions are not confined to the site of perturbation. One of the main results is a two- to threefold increase in the value of the activation energies for the rotameric mode of motions in HP67 compared with HP36. Detailed analysis of configurational entropies and heat capacities complement the kinetic view of the degree of the disorder in the folded state.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska
| | | | | | | |
Collapse
|
42
|
Vugmeyster L, Ostrovsky D, Lipton AS. Origin of abrupt rise in deuteron NMR longitudinal relaxation times of protein methyl groups below 90 K. J Phys Chem B 2013; 117:6129-37. [PMID: 23627365 DOI: 10.1021/jp4021596] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In order to examine the origin of the abrupt change in the temperature dependence of (2)H NMR longitudinal relaxation times observed previously for methyl groups of L69 in the hydrophobic core of villin headpiece protein at around 90 K (Vugmeyster et al. J. Am. Chem. Soc. 2010, 132, 4038-4039), we extended the measurements to several other methyl groups in the hydrophobic core. We show that, for all methyl groups, relaxation times experience a dramatic jump several orders of magnitude around this temperature. Theoretical modeling supports the conclusion that the origin of the apparent transition in the relaxation times is due to the existence of the distribution of conformers distinguished by their activation energy for methyl three-site hops. It is also crucial to take into account the differential contribution of individual conformers into overall signal intensity. When a particular conformer approaches the regime at which its three-site hop rate constant is on the order of the quadrupolar coupling interaction constant, the intensity of the signal due to this conformer experiences a sharp drop, thus changing the balance of the contributions of different conformers into the overall signal. As a result, the observed apparent transition in the relaxation rates can be explained without the assumption of an underlying transition in the rate constants. This work in combination with earlier results also shows that the model based on the distribution of conformers explains the relaxation behavior in the entire temperature range between 300 and 70 K.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, Alaska 99508, United States.
| | | | | |
Collapse
|
43
|
Gascooke JR, Lawrance WD. The toluene-Ar complex: S0 and S1 van der Waals modes, changes to methyl rotation, and torsion-van der Waals vibration coupling. J Chem Phys 2013; 138:084304. [DOI: 10.1063/1.4792642] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jason R Gascooke
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | | |
Collapse
|
44
|
Vugmeyster L, Ostrovsky D, Penland K, Hoatson GL, Vold RL. Glassy dynamics of protein methyl groups revealed by deuteron NMR. J Phys Chem B 2013; 117:1051-61. [PMID: 23301823 DOI: 10.1021/jp311112j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated site-specific dynamics of key methyl groups in the hydrophobic core of chicken villin headpiece subdomain (HP36) over the temperature range between 298 and 140 K using deuteron solid-state NMR longitudinal relaxation measurements. The relaxation of the longitudinal magnetization is weakly nonexponential (glassy) at high temperatures and exhibits a stronger degree of nonexponentiality below about 175 K. In addition, the characteristic relaxation times deviate from the simple Arrhenius law. We interpret this behavior via the existence of distribution of activation energy barriers for the three-site methyl jumps, which originates from somewhat different methyl environments within the local energy landscape. The width of the distribution of the activation barriers for methyl jumps is rather significant, about 1.4 kJ/mol. Our experimental results and modeling allow for the description of the apparent change at about 175 K without invoking a specific transition temperature. For most residues in the core, the relaxation behavior at high temperatures points to the existence of conformational exchange between the substates of the landscape, and our model takes into account the kinetics of this process. The observed dynamics are the same for dry and hydrated protein. We also looked at the effect of F58L mutation inside the hydrophobic core on the dynamics of one of the residues and observed a significant increase in its conformational exchange rate constant at high temperatures.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska 99508, USA.
| | | | | | | | | |
Collapse
|
45
|
Miao Y, Yi Z, Glass DC, Hong L, Tyagi M, Baudry J, Jain N, Smith JC. Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein. J Am Chem Soc 2012; 134:19576-9. [DOI: 10.1021/ja3097898] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yinglong Miao
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Zheng Yi
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dennis C. Glass
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Graduate School of Genome Science
and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Liang Hong
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899, United States
- Department of Materials Science, University of Maryland, College Park, Maryland 20742,
United States
| | - Jerome Baudry
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Nitin Jain
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
46
|
Miao Y, Yi Z, Cantrell C, Glass DC, Baudry J, Jain N, Smith JC. Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation. Biophys J 2012. [PMID: 23200050 DOI: 10.1016/j.bpj.2012.10.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Neutron scattering and nuclear magnetic resonance relaxation experiments are combined with molecular dynamics (MD) simulations in a novel, to our knowledge, approach to investigate the change in internal dynamics on substrate (camphor) binding to a protein (cytochrome P450cam). The MD simulations agree well with both the neutron scattering, which furnishes information on global flexibility, and the nuclear magnetic resonance data, which provides residue-specific order parameters. Decreased fluctuations are seen in the camphor-bound form using all three techniques, dominated by changes in specific regions of the protein. The combined experimental and simulation results permit a detailed description of the dynamical change, which involves modifications in the coupling between the dominant regions and concomitant substrate access channel closing, via specific salt-bridge, hydrogen-bonding, and hydrophobic interactions. The work demonstrates how the combination of complementary experimental spectroscopies with MD simulation can provide an in-depth description of functional dynamical protein changes.
Collapse
Affiliation(s)
- Yinglong Miao
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Liao X, Long D, Li DW, Brüschweiler R, Tugarinov V. Probing side-chain dynamics in proteins by the measurement of nine deuterium relaxation rates per methyl group. J Phys Chem B 2011; 116:606-20. [PMID: 22098066 DOI: 10.1021/jp209304c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We demonstrate the feasibility of the measurement of up to nine deuterium spin relaxation rates in 13CHD2 and 13CH2D methyl isotopomers of small proteins. In addition to five measurable 2H relaxation rates in a 13CH2D methyl group (Millet, O.; Muhandiram, D. R.; Skrynnikov, N. R.; Kay, L. E. J. Am. Chem. Soc. 2002, 124, 6439-48), the measurement of additional four rates of (nearly) single-exponentially decaying magnetization terms in methyl groups of the 13CHD2 variety is reported. Consistency relationships between 2H spin relaxation rates measured in the two different types of methyl groups are derived and verified experimentally for a subset of methyl-containing side chains in the protein ubiquitin. A detailed comparison of methyl-bearing side-chain dynamics parameters obtained from relaxation measurements in 13CH2D and 13CHD2 methyls of ubiquitin at 10, 27, and 40 °C reveals that transverse 2H relaxation rates in 13CHD2 groups are reliable and accurate reporters of the amplitudes of methyl 3-fold axis motions (S(axis)2) for protein molecules with global molecular tumbling times τ(C) >~9 ns. For smaller molecules, simple correction of transverse 2H relaxation rates in 13CHD2 groups is sufficient for the derivation of robust measures of order. Residue-specific distributions of S(axis)2 are consistent with atomic-detail molecular dynamics (MD) results. Both 13CHD2- and 13CH2D-derived S(axis)2 values are in good overall agreement with those obtained from 1 μs MD simulations at all the three temperatures, although some differences in the site-specific temperature dependence between MD- and 2H-relaxation-derived S(axis)2 values are observed.
Collapse
Affiliation(s)
- Xinli Liao
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | | | | | | | | |
Collapse
|
48
|
Hong L, Smolin N, Lindner B, Sokolov AP, Smith JC. Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. PHYSICAL REVIEW LETTERS 2011; 107:148102. [PMID: 22107237 DOI: 10.1103/physrevlett.107.148102] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Indexed: 05/31/2023]
Abstract
A simplified description of the 295 K dynamics of a globular protein over a wide frequency range (1-1000 GHz) is obtained by combining neutron scattering of lysozyme with molecular dynamics simulation. The molecular dynamics simulation agrees quantitatively with experiment for both the protein and the hydration water and shows that, whereas the hydration water molecules subdiffuse, the protein atoms undergo confined motion decomposable into three distinct classes: localized diffusion, methyl group rotations, and jumps. Each of the three classes gives rise to a characteristic neutron susceptibility signal.
Collapse
Affiliation(s)
- Liang Hong
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, P.O.Box 2008, Oak Ridge Tennessee 37831-6164, USA
| | | | | | | | | |
Collapse
|
49
|
Xue Y, Skrynnikov NR. Motion of a disordered polypeptide chain as studied by paramagnetic relaxation enhancements, 15N relaxation, and molecular dynamics simulations: how fast is segmental diffusion in denatured ubiquitin? J Am Chem Soc 2011; 133:14614-28. [PMID: 21819149 DOI: 10.1021/ja201605c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics (MD) simulations have been widely used to analyze dynamic conformational equilibria of folded proteins, especially in relation to NMR observables. However, this approach found little use in the studies of disordered proteins, where the sampling of vast conformational space presents a serious problem. In this paper, we demonstrate that the latest advances in computation technology make it possible to overcome this limitation. The experimentally validated (calibrated) MD models allow for new insights into structure/dynamics of disordered proteins. As a test system, we have chosen denatured ubiquitin in solution with 8 M urea at pH 2. High-temperature MD simulations in implicit solvent have been carried out for the wild-type ubiquitin as well as MTSL-tagged Q2C, D32C, and R74C mutants. To recalibrate the MD data (500 K) in relation to the experimental conditions (278 K, 8 M urea), the time axes of the MD trajectories were rescaled. The scaling factor was adjusted such as to maximize the agreement between the simulated and experimental (15)N relaxation rates. The resulting effective length of the trajectories, 311 μs, ensures good convergence properties of the MD model. The constructed MD model was validated against the array of experimental data, including additional (15)N relaxation parameters, multiple sets of paramagnetic relaxation enhancements (PREs), and the radius of gyration. In each case, a near-quantitative agreement has been obtained, suggesting that the model is successful. Of note, the MD-based approach rigorously predicts the quantities that are inherently dynamic, i.e., dependent on the motional correlation times. This cannot be accomplished, other than in empirical fashion, on the basis of static structural models (conformational ensembles). The MD model was further used to investigate the relative translational motion of the MTSL label and the individual H(N) atoms. The derived segmental diffusion coefficients proved to be nearly uniform along the peptide chain, averaging to D = 0.49-0.55 × 10(-6) cm(2)/s. This result was verified by direct analysis of the experimental PRE data using the recently proposed Ullman-Podkorytov model. In this model, MTSL and H(N) moieties are treated as two tethered spheres undergoing mutual diffusion in a harmonic potential. The fitting of the experimental data involving D as a single adjustable parameter leads to D = 0.45 × 10(-6) cm(2)/s, in good agreement with the MD-based analyses. This result can be compared with the range of estimates obtained from the resonance energy transfer experiments, D = 0.2-6.0 × 10(-6) cm(2)/s.
Collapse
Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
| | | |
Collapse
|
50
|
Esadze A, Li DW, Wang T, Brüschweiler R, Iwahara J. Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H−15N NMR spectroscopy. J Am Chem Soc 2011; 133:909-19. [PMID: 21186799 DOI: 10.1021/ja107847d] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics of lysine NH3(+) groups by NMR spectroscopy and computation. By using 1H−15N heteronuclear correlation experiments optimized for 15NH3(+) moieties, we have analyzed the dynamic behavior of individual lysine NH3(+) groups in human ubiquitin at 2 °C and pH 5. We modified the theoretical framework developed previously for CH3 groups and used it to analyze 15N relaxation data for the NH3(+) groups. For six lysine NH3(+) groups out of seven in ubiquitin, we have determined model-free order parameters, correlation times for bond rotation, and reorientation of the symmetry axis occurring on a pico- to nanosecond time scale. From CPMG relaxation dispersion experiment for lysine NH3(+) groups, slower dynamics occurring on a millisecond time scale have also been detected for Lys27. The NH3(+) groups of Lys48, which plays a key role as the linkage site in ubiquitination for proteasomal degradation, was found to be highly mobile with the lowest order parameter among the six NH3(+) groups analyzed by NMR. We compared the experimental order parameters for the lysine NH3(+) groups with those from a 1 μs molecular dynamics simulation in explicit solvent and found good agreement between the two. Furthermore, both the computer simulation and the experimental correlation times for the bond rotations of NH3(+) groups suggest that their hydrogen bonding is highly dynamic with a subnanosecond lifetime. This study demonstrates the utility of combining NMR experiment and simulation for an in-depth characterization of the dynamics of these functionally most important side-chains of ubiquitin.
Collapse
Affiliation(s)
- Alexandre Esadze
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | | | | | | | | |
Collapse
|