51
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Combining NMR and molecular dynamics studies for insights into the allostery of small GTPase-protein interactions. Methods Mol Biol 2012; 796:235-59. [PMID: 22052494 DOI: 10.1007/978-1-61779-334-9_13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Combinations of experimentally derived data from nuclear magnetic resonance spectroscopy and analyses of molecular dynamics trajectories increasingly allow us to obtain a detailed description of the molecular mechanisms by which proteins function in signal transduction. This chapter provides an introduction into these two methodologies, illustrated by example of a small GTPase-effector interaction. It is increasingly becoming clear that new insights are provided by the combination of experimental and computational methods. Understanding the structural and protein dynamical contributions to allostery will be useful for the engineering of new binding interfaces and protein functions, as well as for the design/in silico screening of chemical agents that can manipulate the function of small GTPase-protein interactions in diseases such as cancer.
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52
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Landström J, Bergström M, Hamark C, Ohlson S, Widmalm G. Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate–lysozyme interaction studies. Org Biomol Chem 2012; 10:3019-32. [DOI: 10.1039/c2ob07066a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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53
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Eichenberger AP, Smith LJ, van Gunsteren WF. Ester-linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation - possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold. FEBS J 2011; 279:299-315. [DOI: 10.1111/j.1742-4658.2011.08424.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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54
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Vostrikov VV, Gu H, Ingólfsson HI, Hinton JF, Andersen OS, Roux B, Koeppe RE. Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments. J Phys Chem B 2011; 115:7427-32. [PMID: 21574558 PMCID: PMC3114435 DOI: 10.1021/jp200906y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motional properties are important for understanding protein function and are accessible to NMR relaxation measurements. The goal of this study is to investigate the internal dynamics occurring in gramicidin A (gA) channels in order to provide benchmark experimental data for comparison with the results of molecular dynamics simulations. We therefore synthesized several (15)N isotope-enriched gA samples, covering all backbone residues as well as the Trp indole side chains for NMR relaxation experiments. On the basis of the (15)N NMR spectra for labeled gA samples incorporated in sodium dodecylsulfate (SDS) micelles, we determined T(1), T(2), and heteronuclear NOE values for backbone and indole (15)NH groups. The results indicate that the SDS-incorporated gA channel is a constrained structure without an especially "floppy" region. The NMR observables, particularly those for backbone groups, are predicted well by the molecular dynamics simulations in the accompanying article (DOI 10.1021/jp200904d ).
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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55
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Cavity hydration as a gateway to unfolding: An NMR study of hen lysozyme at high pressure and low temperature. Biophys Chem 2011; 156:24-30. [DOI: 10.1016/j.bpc.2011.01.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 01/25/2011] [Indexed: 11/18/2022]
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56
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Sziegat F, Wirmer-Bartoschek J, Schwalbe H. Characteristics of Human Lysozyme and Its Disease-Related Mutants in their Unfolded States. Angew Chem Int Ed Engl 2011; 50:5514-8. [DOI: 10.1002/anie.201008040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 04/06/2011] [Indexed: 11/10/2022]
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57
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Sziegat F, Wirmer-Bartoschek J, Schwalbe H. Characteristics of Human Lysozyme and Its Disease-Related Mutants in their Unfolded States. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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58
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Li DW, Brüschweiler R. Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins. J Chem Theory Comput 2011; 7:1773-82. [PMID: 26596440 DOI: 10.1021/ct200094b] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
High quality molecular mechanics force fields of proteins are key for the quantitative interpretation of experimental data and the predictive understanding of protein function based on computer simulations. A strategy is presented for the optimization of protein force fields based on full-length proteins in their native environment that is guided by experimental NMR chemical shifts and residual dipolar couplings (RDCs). An energy-based reweighting approach is applied to a long molecular dynamics trajectory, performed with a parent force field, to efficiently screen a large number of trial force fields. The force field that yields the best agreement with the experimental data is then used as the new parent force field, and the procedure is repeated until no further improvement is obtained. This method is demonstrated for the optimization of the backbone φ,ψ dihedral angle potential of the Amber ff99SB force field using six trial proteins and another 17 proteins for cross-validation using (13)C chemical shifts with and without backbone RDCs. The φ,ψ dihedral angle potential is systematically improved by the inclusion of correlation effects through the addition of up to 24 bivariate Gaussian functions of variable height, width, and tilt angle. The resulting force fields, termed ff99SB_φψ(g24;CS) and ff99SB_φψ(g8;CS,RDC), perform significantly better than their parent force field in terms of both NMR data reproduction and Cartesian coordinate root-mean-square deviations between the MD trajectories and the X-ray crystal structures. The strategy introduced here represents a powerful addition to force field optimization approaches by overcoming shortcomings of methods that are solely based on quantum-chemical calculations of small molecules and protein fragments in the gas phase.
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Affiliation(s)
- Da-Wei Li
- Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32306, United States
| | - Rafael Brüschweiler
- Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32306, United States
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59
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Khodadadi S, Curtis JE, Sokolov AP. Nanosecond Relaxation Dynamics of Hydrated Proteins: Water versus Protein Contributions. J Phys Chem B 2011; 115:6222-6. [DOI: 10.1021/jp1122213] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. Khodadadi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - J. E. Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - A. P. Sokolov
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States, and Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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60
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Sinha SK, Bandyopadhyay S. Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules. J Chem Phys 2011; 134:115101. [DOI: 10.1063/1.3560442] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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61
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Calandrini V, Abergel D, Kneller GR. Fractional protein dynamics seen by nuclear magnetic resonance spectroscopy: Relating molecular dynamics simulation and experiment. J Chem Phys 2011; 133:145101. [PMID: 20950048 DOI: 10.1063/1.3486195] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We propose a fractional Brownian dynamics model for time correlation functions characterizing the internal dynamics of proteins probed by NMR relaxation spectroscopy. The time correlation functions are represented by a broad distribution of exponential functions which are characterized by two parameters. We show that the model describes well the restricted rotational motion of N-H vectors in the amide groups of lysozyme obtained from molecular dynamics simulation and that reliable predictions of experimental relaxation rates can be obtained on that basis.
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Affiliation(s)
- Vania Calandrini
- Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans, France.
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62
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Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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63
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Yamane T, Okamura H, Nishimura Y, Kidera A, Ikeguchi M. Side-chain conformational changes of transcription factor PhoB upon DNA binding: a population-shift mechanism. J Am Chem Soc 2011; 132:12653-9. [PMID: 20722414 DOI: 10.1021/ja103218x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using molecular dynamics (MD) simulations and analyses of NMR relaxation order parameters, we investigated conformational changes of side chains in hydrophobic cores upon DNA binding for the DNA binding/transactivation domain of the transcription factor PhoB, in which backbone conformational changes upon DNA binding are small. The simulation results correlated well with experimental order parameters for the backbone and side-chain methyl groups, showing that the order parameters generally represent positional fluctuations of the backbone and side-chain methyl groups. However, topological effects of the side chains on the order parameters were also found and could be eliminated using normalized order parameters for each amino acid type. Consistent with the NMR experiments, the normalized order parameters from the MD simulations showed that the side chains in one of the two hydrophobic cores (the soft core) were highly flexible in comparison with those in the other hydrophobic core (the hard core) before DNA binding and that the flexibility of the hydrophobic cores, particularly of the soft core, was reduced upon DNA binding. Principal component analysis of methyl group configurations revealed strikingly different side-chain dynamics for the soft and hard cores. In the hard core, side-chain configurations were simply distributed around one or two average configurations. In contrast, the side chains in the soft core dynamically varied their configurations in an equilibrium ensemble that included binding configurations as minor components before DNA binding. DNA binding led to a restriction of the side-chain dynamics and a shift in the equilibrium toward binding configurations, in clear correspondence with a population-shift model.
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Affiliation(s)
- Tsutomu Yamane
- Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan
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64
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Higman VA, Boyd J, Smith LJ, Redfield C. Residual dipolar couplings: are multiple independent alignments always possible? JOURNAL OF BIOMOLECULAR NMR 2011; 49:53-60. [PMID: 21184138 PMCID: PMC3020303 DOI: 10.1007/s10858-010-9457-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/19/2010] [Indexed: 05/30/2023]
Abstract
RDCs for the 14 kDa protein hen egg-white lysozyme (HEWL) have been measured in eight different alignment media. The elongated shape and strongly positively charged surface of HEWL appear to limit the protein to four main alignment orientations. Furthermore, low levels of alignment and the protein's interaction with some alignment media increases the experimental error. Together with heterogeneity across the alignment media arising from constraints on temperature, pH and ionic strength for some alignment media, these data are suitable for structure refinement, but not the extraction of dynamic parameters. For an analysis of protein dynamics the data must be obtained with very low errors in at least three or five independent alignment media (depending on the method used) and so far, such data have only been reported for three small 6-8 kDa proteins with identical folds: ubiquitin, GB1 and GB3. Our results suggest that HEWL is likely to be representative of many other medium to large sized proteins commonly studied by solution NMR. Comparisons with over 60 high-resolution crystal structures of HEWL reveal that the highest resolution structures are not necessarily always the best models for the protein structure in solution.
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Affiliation(s)
- Victoria A. Higman
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Jonathan Boyd
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Lorna J. Smith
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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65
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Jaremko Ł, Jaremko M, Elfaki I, Mueller JW, Ejchart A, Bayer P, Zhukov I. Structure and dynamics of the first archaeal parvulin reveal a new functionally important loop in parvulin-type prolyl isomerases. J Biol Chem 2010; 286:6554-65. [PMID: 21138844 PMCID: PMC3057832 DOI: 10.1074/jbc.m110.160713] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Parvulins are a group of peptidyl-prolyl isomerases (PPIases) responsible for important biological processes in all kingdoms of life. The PinA protein from the psychrophilic archaeon Cenarchaeum symbiosum is a parvulin-like PPIase. Due to its striking similarity to the human parvulins Pin1 and Par14, PinA constitutes an interesting subject for structural and functional studies. Here, we present the first high resolution NMR structure of an archaeal parvulin, PinA, based on 1798 conformational restraints. Structure calculation yields an ensemble of 20 convergent low energy structures with a backbone r.m.s.d. value of 0.6 Å within the secondary structure elements. The overall fold of PinA comprises the β-α(3)-β-α-β(2) fold typical for all parvulin structures known so far, but with helix III being a short 3(10)-helix. A detailed comparison of this high resolution structure of the first archaeal PinA protein with bacterial and eukaryotic parvulin PPIase structures reveals an atypically large catalytic binding site. This feature provides an explanation for cold-adapted protein function. Moreover, the residues in and around 3(10)-helix III exhibit strong intramolecular dynamics on a microsecond to millisecond timescale and display structural heterogeneity within the NMR ensemble. A putative peptide ligand was found for PinA by phage display and was used for (1)H-(15)N-HSQC titrations. Again, the flexible region around 3(10)-helix III as well as residues of the peptide binding pocket showed the strongest chemical shift perturbations upon peptide binding. The local flexibility of this region also was modulated by ligand binding. A glycine and two positively charged residues are conserved in most parvulin proteins in this flexible loop region, which may be of general functional importance for parvulin-type PPIases.
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Affiliation(s)
- Łukasz Jaremko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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66
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Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol 2010; 6. [PMID: 20865158 PMCID: PMC2928775 DOI: 10.1371/journal.pcbi.1000911] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Accepted: 07/28/2010] [Indexed: 11/21/2022] Open
Abstract
It is widely recognized that representing a protein as a single static conformation is inadequate to describe the dynamics essential to the performance of its biological function. We contrast the amino acid displacements below and above the protein dynamical transition temperature, TD∼215K, of hen egg white lysozyme using X-ray crystallography ensembles that are analyzed by molecular dynamics simulations as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above TD, and they remain virtually identical to structural motions measured at 300K. Our results highlight the ability to observe functional structural variations across an ensemble of X-ray crystallographic data, and that residue fluctuations measured in MD simulations at room temperature are in quantitative agreement with the experimental observable. There is a well-recognized gap between the dynamical motions of proteins required to execute function and the experimental techniques capable of capturing that motion at the atomic level. We show that much experimental detail of dynamical motion is already present in X-ray crystallographic data, which arises from being solved by different research groups using different methodologies under different crystallization conditions, which then capture an ensemble of structures whose variations can be quantified on a residue-by-residue level using local density correlations. We contrast the amino acid displacements below and above the protein dynamical transition temperature, TD∼215K, of hen egg white lysozyme by comparing the X-ray ensemble to MD ensembles as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above TD and they remain virtually identical to structural motions measured at 300K. It provides a novel analysis of large X-ray ensemble data that is useful for the broader structural biology community.
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Affiliation(s)
- Jonathan E. Kohn
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jory Z. Ruscio
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Paul D. Adams
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Teresa Head-Gordon
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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67
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Olson AL, Cai S, Herdendorf TJ, Miziorko HM, Sem DS. NMR dynamics investigation of ligand-induced changes of main and side-chain arginine N-H's in human phosphomevalonate kinase. J Am Chem Soc 2010; 132:2102-3. [PMID: 20112895 DOI: 10.1021/ja906244j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphomevalonate kinase (PMK) catalyzes phosphoryl transfer from adenosine triphosphate (ATP) to mevalonate 5-phosphate (M5P) on the pathway for synthesizing cholesterol and other isoprenoids. To permit this reaction, its substrates must be brought proximal, which would result in a significant and repulsive buildup of negative charge. To facilitate this difficult task, PMK contains 17 arginines and eight lysines. However, the way in which this charge neutralization and binding is achieved, from a structural and dynamics perspective, is not known. More broadly, the role of arginine side-chain dynamics in binding of charged substrates has not been experimentally defined for any protein to date. Herein we report a characterization of changes to the dynamical state of the arginine side chains in PMK due to binding of its highly charged substrates, ATP and M5P. These studies were facilitated by the use of arginine-selective labeling to eliminate spectral overlap. Model-free analysis indicated that while substrate binding has little effect on the arginine backbone dynamics, binding of either substrate leads to significant rigidification of the arginine side chains throughout the protein, even those that are >8 A from the binding site. Such a global rigidification of arginine side chains is unprecedented and suggests that there are long-range electrostatic interactions of sufficient strength to restrict the motion of arginine side chains on the picosecond-to-nanosecond time scale. It will be interesting to see whether such effects are general for arginine residues in proteins that bind highly charged substrates, once additional studies of arginine side-chain dynamics are reported.
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Affiliation(s)
- Andrew L Olson
- Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201, USA
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68
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Bruylants G, Redfield C. (15)N NMR relaxation data reveal significant chemical exchange broadening in the alpha-domain of human alpha-lactalbumin. Biochemistry 2009; 48:4031-9. [PMID: 19309110 DOI: 10.1021/bi900023m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human alpha-lactalbumin (alpha-LA), a 123-residue calcium-binding protein, has been studied using (15)N NMR relaxation methods in order to characterize backbone dynamics of the native state at the level of individual residues. Relaxation data were collected at three magnetic field strengths and analyzed using the model-free formalism of Lipari and Szabo. The order parameters derived from this analysis are generally high, indicating a rigid backbone. A total of 46 residues required an exchange contribution to T(2); 43 of these residues are located in the alpha-domain of the protein. The largest exchange contributions are observed in the A-, B-, D-, and C-terminal 3(10)-helices of the alpha-domain; these residues have been shown previously to form a highly stable core in the alpha-LA molten globule. The observed exchange broadening, along with previous hydrogen/deuterium amide exchange data, suggests that this part of the alpha-domain may undergo a local structural transition between the well-ordered native structure and a less-ordered molten-globule-like structure.
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Affiliation(s)
- Gilles Bruylants
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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69
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Trbovic N, Cho JH, Abel R, Friesner RA, Rance M, Palmer AG. Protein side-chain dynamics and residual conformational entropy. J Am Chem Soc 2009; 131:615-22. [PMID: 19105660 DOI: 10.1021/ja806475k] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Changes in residual conformational entropy of proteins can be significant components of the thermodynamics of folding and binding. Nuclear magnetic resonance (NMR) spin relaxation is the only experimental technique capable of probing local protein entropy, by inference from local internal conformational dynamics. To assess the validity of this approach, the picosecond-to-nanosecond dynamics of the arginine side-chain N(epsilon)-H(epsilon) bond vectors of Escherichia coli ribonuclease H (RNase H) were determined by NMR spin relaxation and compared to the mechanistic detail provided by molecular dynamics (MD) simulations. The results indicate that arginine N(epsilon) spin relaxation primarily reflects persistence of guanidinium salt bridges and correlates well with simulated side-chain conformational entropy. In particular cases, the simulations show that the aliphatic part of the arginine side chain can retain substantial disorder while the guanidinium group maintains its salt bridges; thus, the N(epsilon)-H(epsilon) bond-vector orientation is conserved and side-chain flexibility is concealed from N(epsilon) spin relaxation. The MD simulations and an analysis of a rotamer library suggest that dynamic decoupling of the terminal moiety from the remainder of the side chain occurs for all five amino acids with more than two side-chain dihedral angles (R, K, E, Q, and M). Dynamic decoupling thus may represent a general biophysical strategy for minimizing the entropic penalties of folding and binding.
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Affiliation(s)
- Nikola Trbovic
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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70
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Giri K, Maynard EL. Conformational analysis of a peptide approximating the HCCH motif in HIV-1 Vif. Biopolymers 2009; 92:417-25. [DOI: 10.1002/bip.21209] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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71
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Paquin R, Ferrage F, Mulder FAA, Akke M, Bodenhausen G. Multiple-Timescale Dynamics of Side-Chain Carboxyl and Carbonyl Groups in Proteins by 13C Nuclear Spin Relaxation. J Am Chem Soc 2008; 130:15805-7. [PMID: 18975903 DOI: 10.1021/ja803794g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raphaël Paquin
- Département de Chimie, associé au CNRS, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris Cedex 05, France, Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Center for Molecular Protein Science, Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, BCH, CH-1015 Lausanne, Switzerland
| | - Fabien Ferrage
- Département de Chimie, associé au CNRS, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris Cedex 05, France, Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Center for Molecular Protein Science, Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, BCH, CH-1015 Lausanne, Switzerland
| | - Frans A. A. Mulder
- Département de Chimie, associé au CNRS, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris Cedex 05, France, Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Center for Molecular Protein Science, Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, BCH, CH-1015 Lausanne, Switzerland
| | - Mikael Akke
- Département de Chimie, associé au CNRS, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris Cedex 05, France, Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Center for Molecular Protein Science, Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, BCH, CH-1015 Lausanne, Switzerland
| | - Geoffrey Bodenhausen
- Département de Chimie, associé au CNRS, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris Cedex 05, France, Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Center for Molecular Protein Science, Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, BCH, CH-1015 Lausanne, Switzerland
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72
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Khodadadi S, Pawlus S, Sokolov AP. Influence of Hydration on Protein Dynamics: Combining Dielectric and Neutron Scattering Spectroscopy Data. J Phys Chem B 2008; 112:14273-80. [PMID: 18942780 DOI: 10.1021/jp8059807] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Khodadadi
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, and Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - S. Pawlus
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, and Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - A. P. Sokolov
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, and Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
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73
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Huang SW, Shih CH, Lin CP, Hwang JK. Prediction of NMR order parameters in proteins using weighted protein contact-number model. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0465-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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74
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Nodet G, Abergel D, Bodenhausen G. Predicting NMR relaxation rates in anisotropically tumbling proteins through networks of coupled rotators. Chemphyschem 2008; 9:625-33. [PMID: 18324719 DOI: 10.1002/cphc.200700732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We show that the prediction of (15)N relaxation rates in proteins can be extended to systems with anisotropic global rotational diffusion by using a network of coupled rotators (NCR), starting from a three-dimensional structure. The relaxation rates predicted by this method are confronted in several examples with experiments performed by other groups. The NCR spectral density functions are compared with the results obtained from reduced spectral density mapping. The consequence of the timescales of internal motions on the predicted relaxation rates and the effects of the predicted local anisotropy-present only in the case of anisotropic overall tumbling-on dynamic parameters, are discussed.
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Affiliation(s)
- Gabrielle Nodet
- Institut de Biologie Structurale Jean-Pierre Ebel (CNRS/CEA/UJF), 41, rue Jules Horowitz, 38027, Grenoble, France
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75
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Go A, Kim S, Baum J, Hecht MH. Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles. Protein Sci 2008; 17:821-32. [PMID: 18436954 DOI: 10.1110/ps.073377908] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4-helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S-836. Protein S-836 proved to be a 4-helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4-helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well-packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue-by-residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core.
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Affiliation(s)
- Abigail Go
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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76
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Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality. Biophys J 2008; 95:L04-6. [PMID: 18441027 DOI: 10.1529/biophysj.108.132811] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparing experimental generalized N-H S(2) order parameters to those calculated from molecular dynamics trajectories is increasingly used to judge force-field quality and completeness of sampling. Herein we demonstrate for the well-investigated system hen egg white lysozyme that different experimental starting structures can lead to significant differences in molecular-dynamics-derived S(2) parameters that can be even larger than S(2) parameter deviations due to different force fields. Caution should thus be taken in general when simulated S(2) parameters are compared to experimental data with the aim of judging force-field quality. We show that adequately sampling flexible regions ( approximately 100 ns) and only calculating S(2) parameters averaged over short time windows proved necessary to obtain consistent results irrespective of the starting structure.
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77
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Miller BT, Zheng W, Venable RM, Pastor RW, Brooks BR. Langevin network model of myosin. J Phys Chem B 2008; 112:6274-81. [PMID: 18311963 DOI: 10.1021/jp077042v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Langevin mode theory and the coarse-grained elastic network model (ENM) for proteins are combined to yield the Langevin network model (LNM). Hydrodynamic radii of 6 A were assigned to each alpha-carbon on the basis of matching experimental translational and rotational diffusion constants of lysozyme, myoglobin, and hemoglobin with those calculated using a rigid body bead model with hydrodynamic interactions described by the Rotne-Prager tensor. LNM analysis of myosin II indicates that all ENM-like modes are overdamped at water viscosities. The low-frequency LNM modes in the pre-power stroke structure (PDB code: 1VOM) are substantially less mixed than the corresponding modes of the post-power stroke structure (1Q5G). Results from a four-bead model of the myosin "lever arm" indicate that coupling between modes increases as the array departs from linearity and are consistent with the results for 1VOM and 1Q5G. The decay times for all overdamped Langevin modes are shorter than the calculated rotational tumbling times found for lysozyme and myosin.
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Affiliation(s)
- Benjamin T Miller
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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78
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Bouguet-Bonnet S, Buck M. Compensatory and long-range changes in picosecond-nanosecond main-chain dynamics upon complex formation: 15N relaxation analysis of the free and bound states of the ubiquitin-like domain of human plexin-B1 and the small GTPase Rac1. J Mol Biol 2008; 377:1474-87. [PMID: 18321527 DOI: 10.1016/j.jmb.2008.01.081] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 01/21/2008] [Accepted: 01/25/2008] [Indexed: 11/28/2022]
Abstract
The formation of a complex between Rac1 and the cytoplasmic domain of plexin-B1 is one of the first documented cases of a direct interaction between a small guanosine 5'-triphosphatase (GTPase) and a transmembrane receptor. Structural studies have begun to elucidate the role of this interaction for the signal transduction mechanism of plexins. Mapping of the Rac1 GTPase surface that contacts the Rho GTPase binding domain of plexin-B1 by solution NMR spectroscopy confirms the plexin domain as a GTPase effector protein. Regions neighboring the GTPase switch I and II regions are also involved in the interaction and there is considerable interest to examine the changes in protein dynamics that take place upon complex formation. Here we present main-chain nitrogen-15 relaxation measurements for the unbound proteins as well as for the Rho GTPase binding domain and Rac1 proteins in their complexed state. Derived order parameters, S2, show that considerable motions are maintained in the bound state of plexin. In fact, some of the changes in S2 on binding appear compensatory, exhibiting decreased as well as increased dynamics. Fluctuations in Rac1, already a largely rigid protein on the picosecond-nanosecond timescale, are overall diminished, but isomerization dynamics in the switch I and II regions of the GTPase are retained in the complex and appear to be propagated to the bound plexin domain. Remarkably, fluctuations in the GTPase are attenuated at sites, including helices alpha6 (the Rho-specific insert helix), alpha7 and alpha8, that are spatially distant from the interaction region with plexin. This effect of binding on long-range dynamics appears to be communicated by hinge sites and by subtle conformational changes in the protein. Similar to recent studies on other systems, we suggest that dynamical protein features are affected by allosteric mechanisms. Altered protein fluctuations are likely to prime the Rho GTPase-plexin complex for interactions with additional binding partners.
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Affiliation(s)
- S Bouguet-Bonnet
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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79
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Nodet G, Abergel D. An overview of recent developments in the interpretation and prediction of fast internal protein dynamics. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:985-93. [PMID: 17562038 DOI: 10.1007/s00249-007-0167-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 04/05/2007] [Accepted: 04/17/2007] [Indexed: 10/23/2022]
Abstract
During the past decades, NMR spectroscopy has emerged as a unique tool for the study of protein dynamics. Indeed, relaxation studies on isotopically labeled proteins can provide information on the overall motions as well as the internal fast, sub-nanosecond, dynamics. Therefore, the interpretation and the prediction of spin relaxation rates in proteins are important issues that have motivated numerous theoretical and methodological developments, including the description of overall dynamics and its possible coupling to internal mobility, the introduction of models of internal dynamics, the determination of correlation functions from experimental data, and the relationship between relaxation and thermodynamical quantities. A brief account of recent developments that have proven useful in this domain are presented.
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Affiliation(s)
- Gabrielle Nodet
- Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231, Paris Cedex 05, France
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80
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Chen Y, Campbell SL, Dokholyan NV. Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophys J 2007; 93:2300-6. [PMID: 17557784 PMCID: PMC1965439 DOI: 10.1529/biophysj.107.104174] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Perhaps one of the most prominent realizations of recent years is the critical role that protein dynamics plays in many facets of cellular function. While characterization of protein dynamics is fundamental to our understanding of protein function, the ability to explicitly detect an ensemble of protein conformations from dynamics data is a paramount challenge in structural biology. Here, we report a new computational method, Sample and Select, for determining the ensemble of protein conformations consistent with NMR dynamics data. This method can be generalized and extended to different sources of dynamics data, enabling broad applicability in deciphering protein dynamics at different timescales. The structural ensemble derived from Sample and Select will provide structural and dynamic information that should aid us in understanding and manipulating protein function.
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Affiliation(s)
- Yiwen Chen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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81
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Hamaneh MB, Buck M. Acceptable protein and solvent behavior in primary hydration shell simulations of hen lysozyme. Biophys J 2007; 92:L49-51. [PMID: 17259273 PMCID: PMC1864839 DOI: 10.1529/biophysj.106.103010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The "primary hydration shell" method in molecular dynamics simulations uses a two- to three-layer thick shell of explicitly represented water molecules as the solvent around the protein of interest. We show that despite its simplicity, this computationally cheap model is capable of predicting acceptable water and protein behavior using the CHARMM22/CMAP potential function. For protein dynamics, comparisons are made with Lipari-Szabo order parameters. These have been derived from NMR relaxation parameters for pico-nano second motions of the NH groups in the main-chain and NH(2) groups in Asn/Gln side chains in hen lysozyme. It is also shown that an even simpler, and therefore faster, water-shell model leads to results in similarly good agreement with experiments, and also compared with simulations using a full box of water with periodic boundary conditions or with an implicit solvation model. Thus, the primary hydration shell method should be useful in making larger systems accessible to extensive simulations.
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82
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Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2007; 65:712-25. [PMID: 16981200 PMCID: PMC4805110 DOI: 10.1002/prot.21123] [Citation(s) in RCA: 5440] [Impact Index Per Article: 320.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over-stabilization of alpha-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "Amber" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in Amber of two sets of backbone phi/psi dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the phi/psi dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems.
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Affiliation(s)
- Viktor Hornak
- Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794
| | - Robert Abel
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL 32611
| | - Asim Okur
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794
| | - Bentley Strockbine
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794
| | - Adrian Roitberg
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL 32611
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794
- Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794
- Computational Science Center, Brookhaven National Laboratory, Upton NY11973
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83
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Povey JF, Smales CM, Hassard SJ, Howard MJ. Comparison of the effects of 2,2,2-trifluoroethanol on peptide and protein structure and function. J Struct Biol 2006; 157:329-38. [PMID: 16979904 DOI: 10.1016/j.jsb.2006.07.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 07/20/2006] [Accepted: 07/22/2006] [Indexed: 10/24/2022]
Abstract
The co-solvent 2,2,2-trifluoroethanol (TFE) has been often used to aid formation of secondary structure in solution peptides or alternately as a denaturant within protein folding studies. Hen egg white lysozyme (HEWL) and a synthetic model peptide defining HEWL helix-4 were used as comparative model systems to systematically investigate the effect of increasing TFE concentrations on the structure of proteins and peptides. HEWL was analyzed using NMR, far-UV CD and fluorescence spectroscopy; with correlation of these results towards changes in enzymatic activity and the helix-4 peptide was analysed using NMR. Data illustrates two conflicting modes of interaction: Low TFE concentrations stabilize tertiary structure, observed from an increase in the number of NMR NOE contacts. Higher TFE concentrations denatured HEWL with the loss of lysozyme tertiary structure. The effects of TFE upon secondary structural elements within HEWL are distinct from those observed for the helix-4 peptide. This illustrates a dissimilar interaction of TFE towards both protein and peptide at equivalent TFE concentrations. The concentration that TFE promotes stabilization over denaturation is likely to be protein dependent although the structural action can be extrapolated to other protein systems with implications for the use of TFE in structural stability studies.
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Affiliation(s)
- Jane F Povey
- Protein Science Group, Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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84
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Dubyna VM, Kovalskyy DB, Ivanova OS, Kornelyuk AI. The improvement of the algorithm for order parameter calculation (S2) from molecular dynamics simulation using the correlation motion function. Biophys Chem 2006; 123:25-8. [PMID: 16698173 DOI: 10.1016/j.bpc.2006.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 03/03/2006] [Accepted: 03/06/2006] [Indexed: 11/18/2022]
Abstract
The generalized order parameter, S2, calculated from MD simulation trajectory using time-dependent internal Correlation Motion Function (CMF) agrees well with NMR derived S2 processed with the extended model-free analysis approach. However, the former lies considerably lower comparing to simple model-free derived data from NMR experiments. In the present study we analyze possible reasons of such disagreement. In the general case we propose to use preexponential factors from expression for internal CMF rather than ordinary S2 values. Particularly, in case of the simple model-free S(2) experimental values we suggest comparing them with S2(eff)=1+S2-Sf2 computed from MD simulation data. We show that the S2(eff) values are in a good agreement with NMR derived S2 values obtained using the simple model-free analysis.
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Affiliation(s)
- V M Dubyna
- Institute of Molecular Biology and Genetics, 150 Akad. Zabolotny Str, Kyiv-143, 03143, Ukraine.
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85
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Kim H, Jeong K, Cho KW, Paik SR, Jung S. Molecular dynamics simulations of a cyclic-β-(1→2) glucan containing an α-(1→6) linkage as a ‘molecular alleviator’ for the macrocyclic conformational strain. Carbohydr Res 2006; 341:1011-9. [PMID: 16546149 DOI: 10.1016/j.carres.2006.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2005] [Revised: 02/18/2006] [Accepted: 02/22/2006] [Indexed: 11/24/2022]
Abstract
The conformational preferences of a cyclic osmoregulated periplasmic glucan of Ralstonia solanacearum (OPGR), which is composed of 13 glucose units and linked entirely via beta-(1-->2) linkages excluding one alpha-(1-->6) linkage, were characterized by molecular dynamics simulations. Of the three force fields modified for carbohydrates that were applied to select a suitable one for the cyclic glucan, the carbohydrate solution force field (CSFF) was found to most accurately simulate the cyclic molecule. To determine the conformational characteristics of OPGR, we investigated the glycosidic dihedral angle distribution, fluctuation, and the potential energy of the glucan and constructed hypothetical cyclic (CYS13) and linear (LINEAR) glucans. All beta-(1-->2)-glycosidic linkages of OPGR adopted stable conformations, and the dihedral angles fluctuated in this energy region with some flexibility. However, despite the inherent flexibility of the alpha-(1-->6) linkage, the dihedral angles have no transition and are more rigid than that in a linear glucan. CYS13, which consists of only beta-(1-->2) linkages, is somewhat less flexible than other glycans, and one of its linkages adopts a higher energy conformation. In addition, the root-mean-square fluctuation of this linkage is lower than that of other linkages. Furthermore, the potential energy of glucans increases in the order of LINEAR, OPGR, and CYS13. These results provide evidence of the existence of conformational constraints in the cyclic glucan. The alpha-(1-->6)-glycosidic linkage can relieve this constraint more efficiently than the beta-(1-->2) linkage. The conformation of OPGR can reconcile the tendency for individual glycosidic bonds to adopt energetically favorable conformations with the requirement for closure of the macrocyclic ring by losing the inherent flexibility of the alpha-(1-->6)-glycosidic linkage.
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Affiliation(s)
- Hyunmyung Kim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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86
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Ivanov KL, Yurkovskaya AV, Hore PJ, Lukzen NN. Theoretical study of the CIDNP kinetics of the reaction of a photo-excited dye with a reactive spot on the surface of a sphere: application to CIDNP of proteins. Mol Phys 2006. [DOI: 10.1080/00268970600618442] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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87
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Ming D, Brüschweiler R. Reorientational contact-weighted elastic network model for the prediction of protein dynamics: comparison with NMR relaxation. Biophys J 2006; 90:3382-8. [PMID: 16500967 PMCID: PMC1440724 DOI: 10.1529/biophysj.105.071902] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new model for the prediction of protein backbone motions is presented. The model, termed reorientational contact-weighted elastic network model, is based on a multidimensional reorientational harmonic potential of the backbone amide bond vector orientations and it is applied to the interpretation of dynamics parameters obtained from NMR relaxation data. The individual energy terms are weighted as a function of the intervector distances and by the contact strengths of each bond vector with respect to its local environment. Correlated reorientational motional properties of the bond vectors are obtained by means of normal mode analysis. Application to a set of proteins with known three-dimensional structures yields good to excellent agreement between predicted and experimental NMR order parameters presenting an improvement over the local contact model. The reorientational eigenmodes of the reorientational contact-weighted elastic network model method provide direct information on the collective nature of protein backbone motions. The dominant eigenmodes have a notably low collectivity, which is consistent with the behavior found for reorientational eigenmodes from molecular dynamics simulations.
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Affiliation(s)
- Dengming Ming
- Computer and Computational Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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88
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Collins ES, Wirmer J, Hirai K, Tachibana H, Segawa SI, Dobson CM, Schwalbe H. Characterisation of disulfide-bond dynamics in non-native states of lysozyme and its disulfide deletion mutants by NMR. Chembiochem 2006; 6:1619-27. [PMID: 16138305 DOI: 10.1002/cbic.200500196] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This report describes NMR-spectroscopic investigations of the conformational dynamics of disulfide bonds in hen-egg-white lysozyme substitution mutants. The following four systems have been investigated: 2SS(alpha), a lysozyme variant that contains C64A, C76A, C80A and C94A substitutions, was studied in water at pH 2 and 3.8 and in urea (8 M, pH 2); 2SS(beta) lysozyme, which has C6S, C30A, C115A and C127A substitutions, was studied in water (pH 2) and urea (8 M, pH 2). The NMR analysis of heteronuclear 15N-relaxation rates shows that the barrier to disulfide-bond isomerisation can vary substantially in different lysozyme mutants and depends on the residual structure present in these states. The investigations reveal cooperativity in the modulation of micro- to millisecond dynamics that is due to the presence of multiple disulfide bridges in lysozyme. Mutation of cysteines in one of the two structural domains substantially diminishes the barrier to rotational isomerisation in the other domain. However, the interactions between hydrophobic clusters within and across the domains remains intact.
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Affiliation(s)
- Emily S Collins
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
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89
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Buck M, Bouguet-Bonnet S, Pastor RW, MacKerell AD. Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J 2005; 90:L36-8. [PMID: 16361340 PMCID: PMC1367299 DOI: 10.1529/biophysj.105.078154] [Citation(s) in RCA: 279] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.
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90
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Schlörb C, Ackermann K, Richter C, Wirmer J, Schwalbe H. Heterologous expression of hen egg white lysozyme and resonance assignment of tryptophan side chains in its non-native states. JOURNAL OF BIOMOLECULAR NMR 2005; 33:95-104. [PMID: 16258828 DOI: 10.1007/s10858-005-2063-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Accepted: 08/05/2005] [Indexed: 05/05/2023]
Abstract
A new protocol is described for the isotope (15N and 13C,15N) enrichment of hen egg white lysozyme. Hen egg white lysozyme and an all-Ala-mutant of this protein have been expressed in E. coli. They formed inclusion bodies from which mg quantities of the proteins were purified and prepared for NMR spectroscopic investigations. 1H,13C and 15N main chain resonances of disulfide reduced and S-methylated lysozyme were assigned and its residual structure in water pH 2 was characterized by chemical shift perturbation analysis. A new NMR experiment has been developed to assign tryptophan side chain indole resonances by correlation of side chain and backbone NH resonances with the Cgamma resonances of these residues. Assignment of tryptophan side chains enables further residue specific investigations on structural and dynamical properties, which are of significant interest for the understanding of non-natives states of lysozyme stabilized by hydrophobic interactions between clusters of tryptophan residues.
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Affiliation(s)
- Christian Schlörb
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Marie-Curie-Strasse 11, D-60439, Frankfurt, Germany
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91
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Rai N, Nöllmann M, Spotorno B, Tassara G, Byron O, Rocco M. SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics. Structure 2005; 13:723-34. [PMID: 15893663 DOI: 10.1016/j.str.2005.02.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 02/02/2005] [Accepted: 02/03/2005] [Indexed: 11/27/2022]
Abstract
Reduced numbers of frictional/scattering centers are essential for tractable hydrodynamic and small-angle scattering data modeling. We present a method for generating medium-resolution models from the atomic coordinates of proteins, basically by using two nonoverlapping spheres of differing radii per residue. The computed rigid-body hydrodynamic parameters of BPTI, RNase A, and lysozyme models were compared with a large database of critically assessed experimental values. Overall, very good results were obtained, but significant discrepancies between X-ray- and NMR-derived models were found. Interestingly, they could be accounted for by properly considering the extent to which highly mobile surface side chains differently affect translational/rotational properties. Models of larger structures, such as fibrinogen fragment D and citrate synthase, also produced consistent results. Foremost among this method's potential applications is the overall conformation and dynamics of modular/multidomain proteins and of supramolecular complexes. The possibility of merging data from high- and low-resolution structures greatly expands its scope.
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Affiliation(s)
- Nithin Rai
- Division of Infection & Immunity, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
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92
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Oostenbrink C, Soares TA, van der Vegt NFA, van Gunsteren WF. Validation of the 53A6 GROMOS force field. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 34:273-84. [PMID: 15803330 DOI: 10.1007/s00249-004-0448-6] [Citation(s) in RCA: 385] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Revised: 11/03/2004] [Accepted: 11/03/2004] [Indexed: 10/25/2022]
Abstract
The quality of biomolecular dynamics simulations relies critically on the force field that is used to describe the interactions between particles in the system. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. Simulations of the well-studied 129 residue protein hen egg-white lysozyme, of the DNA dodecamer d(CGCGAATTCGCG)(2), and a proteinogenic beta(3)-dodecapeptide were performed and analysed. It was found that the new parameter set performs as well as the previous parameter sets in terms of protein (45A3) and DNA (45A4) stability and that it is better at describing the folding-unfolding balance of the peptide. The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized.
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Affiliation(s)
- Chris Oostenbrink
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland.
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93
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Bertini I, Gupta YK, Luchinat C, Parigi G, Schlörb C, Schwalbe H. NMR Spectroscopic Detection of Protein Protons and Longitudinal Relaxation Rates between 0.01 and 50 MHz. Angew Chem Int Ed Engl 2005; 44:2223-5. [PMID: 15751103 DOI: 10.1002/anie.200462344] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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94
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Bertini I, Gupta YK, Luchinat C, Parigi G, Schlörb C, Schwalbe H. NMR Spectroscopic Detection of Protein Protons and Longitudinal Relaxation Rates between 0.01 and 50 MHz. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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95
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Abstract
Infrared spectra of a film of lysozyme 3 mum thick, immersed in an atmosphere displaying a relative humidity, or hygrometry, which spans the whole range from 0 to 1 at room temperature, are recorded. The evolution of the spectra with this relative humidity is quantitatively analyzed on the basis of a newly proposed method. It allows the precise measurement of the quantity of water that remains embedded inside the dried sample at each stage of hydration, and the definition, in terms of chemical reactions of the three hydration mechanisms that correspond to the three hydration spectra on which all experimental spectra can be decomposed. With respect to preceding similar studies, some refinements are introduced that allow improvement of the interpretation, but that also raise some new questions, which mainly concern the structure of the hydrogen-bond network around the carbonyl peptide groups.
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Affiliation(s)
- K Liltorp
- Department of Life Sciences and Chemistry, P. O. Box 260, DK-4000 Roskilde, Denmark
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96
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Soares TA, Daura X, Oostenbrink C, Smith LJ, van Gunsteren WF. Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme. JOURNAL OF BIOMOLECULAR NMR 2004; 30:407-422. [PMID: 15630561 DOI: 10.1007/s10858-004-5430-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Accepted: 10/21/2004] [Indexed: 05/24/2023]
Abstract
The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43Alpha1 and a new set 45Alpha3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, (3)J(NHalpha) and (3)J(alphabeta) coupling constants, and (15)N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45Alpha3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43Alpha1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone (3)J(HNalpha)-coupling constants and (1)H-(15)N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain (3)J(alphabeta)-coupling constants and (1)H-(15)N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result.
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Affiliation(s)
- T A Soares
- Laboratory of Physical Chemistry, ETH Hönggerberg Zürich, 8093 Zürich, Switzerland
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97
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Higman VA, Boyd J, Smith LJ, Redfield C. Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2004; 30:327-346. [PMID: 15754058 DOI: 10.1007/s10858-004-3218-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Accepted: 08/11/2004] [Indexed: 05/24/2023]
Abstract
Experimental (15)N-(1)H and (1)H-(1)H residual dipolar couplings (RDCs) for the asparagine (Asn) and glutamine (Gln) side chains of hen egg-white lysozyme are measured and analysed in conjunction with (1)N relaxation data, information about chi(1) torsion angles in solution and molecular dynamics simulations. The RDCs are compared to values predicted from 16 high-resolution crystal structures. Two distinct groups of Asn and Gln side chains are identified. The first contains residues whose side chains show a fixed, relatively rigid, conformation in solution. For these residues there is good agreement between the experimental and predicted RDCs. This agreement improves when the experimental order parameter, S, is included in the calculation of the RDCs from the crystal structures. The comparison of the experimental RDCs with values calculated from the X-ray structures shows that the similarity between the oxygen and nitrogen electron densities is a limitation to the correct assignment of the Asn and Gln side-chain orientation in X-ray structures. In the majority of X-ray structures a 180 degrees rotation about chi(2) or chi(3), leading to the swapping of N(delta/epsilon 2) and O(delta/epsilon 1), is necessary for at least one Asn or Gln residue in order to achieve good agreement between experimental and predicted RDCs. The second group contains residues whose side chains do not adopt a single, well-defined, conformation in solution. These residues do not show a correlation between the experimental and predicted RDCs. In many cases the family of crystal structures shows a range of orientations for these side chains, but in others the crystal structures show a well-defined side-chain position. In the latter case, this is found to arise from crystallographic contacts and does not represent the behaviour of the side chain in solution.
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98
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Halle B. Protein hydration dynamics in solution: a critical survey. Philos Trans R Soc Lond B Biol Sci 2004; 359:1207-23; discussion 1223-4, 1323-8. [PMID: 15306377 PMCID: PMC1693401 DOI: 10.1098/rstb.2004.1499] [Citation(s) in RCA: 387] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The properties of water in biological systems have been studied for well over a century by a wide range of physical techniques, but progress has been slow and erratic. Protein hydration--the perturbation of water structure and dynamics by the protein surface--has been a particularly rich source of controversy and confusion. Our aim here is to critically examine central concepts in the description of protein hydration, and to assess the experimental basis for the current view of protein hydration, with the focus on dynamic aspects. Recent oxygen-17 magnetic relaxation dispersion (MRD) experiments have shown that the vast majority of water molecules in the protein hydration layer suffer a mere twofold dynamic retardation compared with bulk water. The high mobility of hydration water ensures that all thermally activated processes at the protein-water interface, such as binding, recognition and catalysis, can proceed at high rates. The MRD-derived picture of a highly mobile hydration layer is consistent with recent molecular dynamics simulations, but is incompatible with results deduced from intermolecular nuclear Overhauser effect spectroscopy, dielectric relaxation and fluorescence spectroscopy. It is also inconsistent with the common view of hydration effects on protein hydrodynamics. Here, we show how these discrepancies can be resolved.
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Affiliation(s)
- Bertil Halle
- Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden.
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99
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Sethuraman A, Vedantham G, Imoto T, Przybycien T, Belfort G. Protein unfolding at interfaces: Slow dynamics of α-helix to β-sheet transition. Proteins 2004; 56:669-78. [PMID: 15281120 DOI: 10.1002/prot.20183] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A two-phase sequential dynamic change in the secondary structure of hen egg lysozyme (Lys) adsorbed on solid substrates was observed. The first phase involved fast conversion of alpha-helix to random/turns (within the first minute or at very low coverage or high substrate wettability) with no perceptible change in beta-sheet content. The second phase (1-1200 min), however, involved a relatively slow conversion from alpha-helix to beta-sheet without a noticeable change in random/turns. An important finding of this work is that the concentration of lysozyme in the adsorbed state has a substantial effect on the fractional content of secondary structures. Attenuated total reflection Fourier transform infrared (ATR/FTIR) spectroscopy, along with a newly-developed optimization algorithm for predicting the content of secondary structure motifs, was used to correlate the secondary structure and the amount of adsorbed lysozyme with the surface wettability of six different flat nanoporous substrates. Although three independent variables, surface wettability, solution concentration and time for adsorption, were used to follow the fractional structural changes of lysozyme, the results were all normalized onto a single plot with the amount adsorbed as the universal independent variable. Consequently, lateral interactions among proteins likely drive the transition process. Direct intermolecular force adhesion measurements between lysozyme and different functionalized self-assembled alkanethiol monolayers confirm that hydrophobic surfaces interact strongly with proteins. The lysozyme-unfolding pathway during early adsorption appears to be similar to that predicted by published molecular modeling results.
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Affiliation(s)
- Ananthakrishnan Sethuraman
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
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100
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Kamatari YO, Yamada H, Akasaka K, Jones JA, Dobson CM, Smith LJ. Response of native and denatured hen lysozyme to high pressure studied by 15
N/1
H NMR spectroscopy. ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1432-1327.2001.02050.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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