1
|
Gavrilov Y, Kümmerer F, Orioli S, Prestel A, Lindorff-Larsen K, Teilum K. Double Mutant of Chymotrypsin Inhibitor 2 Stabilized through Increased Conformational Entropy. Biochemistry 2022; 61:160-170. [PMID: 35019273 DOI: 10.1021/acs.biochem.1c00749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational heterogeneity of a folded protein can affect not only its function but also stability and folding. We recently discovered and characterized a stabilized double mutant (L49I/I57V) of the protein CI2 and showed that state-of-the-art prediction methods could not predict the increased stability relative to the wild-type protein. Here, we have examined whether changed native-state dynamics, and resulting entropy changes, can explain the stability changes in the double mutant protein, as well as the two single mutant forms. We have combined NMR relaxation measurements of the ps-ns dynamics of amide groups in the backbone and the methyl groups in the side chains with molecular dynamics simulations to quantify the native-state dynamics. The NMR experiments reveal that the mutations have different effects on the conformational flexibility of CI2: a reduction in conformational dynamics (and entropy estimated from this) of the native state of the L49I variant correlates with its decreased stability, while increased dynamics of the I57V and L49I/I57V variants correlates with their increased stability. These findings suggest that explicitly accounting for changes in native-state entropy might be needed to improve the predictions of the effect of mutations on protein stability.
Collapse
Affiliation(s)
- Yulian Gavrilov
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Felix Kümmerer
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simone Orioli
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.,Structural Biophysics, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| |
Collapse
|
2
|
Siemons L, Uluca-Yazgi B, Pritchard RB, McCarthy S, Heise H, Hansen DF. Determining isoleucine side-chain rotamer-sampling in proteins from 13C chemical shift. Chem Commun (Camb) 2019; 55:14107-14110. [PMID: 31642826 PMCID: PMC7138115 DOI: 10.1039/c9cc06496f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A framework is presented to derive the conformational sampling of isoleucine side chains from nuclear magnetic resonance 13C chemical shifts.
Chemical shifts are often the only nuclear magnetic resonance parameter that can be obtained for challenging macromolecular systems. Here we present a framework to derive the conformational sampling of isoleucine side chains from 13C chemical shifts and demonstrate that side-chain conformations in a low-populated folding intermediate can be determined.
Collapse
Affiliation(s)
- Lucas Siemons
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UKWC1E 6BT.
| | - Boran Uluca-Yazgi
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany and Institute of Complex Systems, ICS-6: Structural Biochemistry and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ruth B Pritchard
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UKWC1E 6BT.
| | - Stephen McCarthy
- Department of Chemistry, University College London, 20, Gordon Street, London, WC1H 0AJ, UK
| | - Henrike Heise
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany and Institute of Complex Systems, ICS-6: Structural Biochemistry and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UKWC1E 6BT.
| |
Collapse
|
3
|
Modulation of allosteric coupling by mutations: from protein dynamics and packing to altered native ensembles and function. Curr Opin Struct Biol 2018; 54:1-9. [PMID: 30268910 PMCID: PMC6420056 DOI: 10.1016/j.sbi.2018.09.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 01/12/2023]
Abstract
A large body of work has gone into understanding the effect of mutations on protein structure and function. Conventional treatments have involved quantifying the change in stability, activity and relaxation rates of the mutants with respect to the wild-type protein. However, it is now becoming increasingly apparent that mutational perturbations consistently modulate the packing and dynamics of a significant fraction of protein residues, even those that are located >10–15 Å from the mutated site. Such long-range modulation of protein features can distinctly tune protein stability and the native conformational ensemble contributing to allosteric modulation of function. In this review, I summarize a series of experimental and computational observations that highlight the incredibly pliable nature of proteins and their response to mutational perturbations manifested via the intra-protein interaction network. I highlight how an intimate understanding of mutational effects could pave the way for integrating stability, folding, cooperativity and even allostery within a single physical framework.
Collapse
|
4
|
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
|
5
|
Cournia Z, Allen B, Sherman W. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. J Chem Inf Model 2017; 57:2911-2937. [PMID: 29243483 DOI: 10.1021/acs.jcim.7b00564] [Citation(s) in RCA: 401] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects. This advance arises from accumulating developments in the underlying scientific methods (decades of research on force fields and sampling algorithms) coupled with vast increases in computational resources (graphics processing units and cloud infrastructures). Mounting evidence from retrospective validation studies, blind challenge predictions, and prospective applications suggests that RBFE simulations can now predict the affinity differences for congeneric ligands with sufficient accuracy and throughput to deliver considerable value in hit-to-lead and lead optimization efforts. Here, we present an overview of current RBFE implementations, highlighting recent advances and remaining challenges, along with examples that emphasize practical considerations for obtaining reliable RBFE results. We focus specifically on relative binding free energies because the calculations are less computationally intensive than absolute binding free energy (ABFE) calculations and map directly onto the hit-to-lead and lead optimization processes, where the prediction of relative binding energies between a reference molecule and new ideas (virtual molecules) can be used to prioritize molecules for synthesis. We describe the critical aspects of running RBFE calculations, from both theoretical and applied perspectives, using a combination of retrospective literature examples and prospective studies from drug discovery projects. This work is intended to provide a contemporary overview of the scientific, technical, and practical issues associated with running relative binding free energy simulations, with a focus on real-world drug discovery applications. We offer guidelines for improving the accuracy of RBFE simulations, especially for challenging cases, and emphasize unresolved issues that could be improved by further research in the field.
Collapse
Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens , 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Bryce Allen
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
| | - Woody Sherman
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
| |
Collapse
|
6
|
Rajasekaran N, Suresh S, Gopi S, Raman K, Naganathan AN. A General Mechanism for the Propagation of Mutational Effects in Proteins. Biochemistry 2016; 56:294-305. [DOI: 10.1021/acs.biochem.6b00798] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nandakumar Rajasekaran
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Soundhararajan Gopi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| |
Collapse
|
7
|
Perticaroli S, Russo D, Paolantoni M, Gonzalez MA, Sassi P, Nickels JD, Ehlers G, Comez L, Pellegrini E, Fioretto D, Morresi A. Painting biological low-frequency vibrational modes from small peptides to proteins. Phys Chem Chem Phys 2015; 17:11423-31. [DOI: 10.1039/c4cp05388e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We use experiments and simulation to investigate the validity of different model systems used to study the low-frequency vibrations of proteins.
Collapse
Affiliation(s)
- S. Perticaroli
- Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Chemical and Materials Sciences Division
| | - D. Russo
- CNR-IOM
- Italy c/o Institut Laue Langevin
- France
- Institut Lumière Matière
- Université de Lyon 1
| | - M. Paolantoni
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| | | | - P. Sassi
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| | - J. D. Nickels
- Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Department of Chemistry
| | - G. Ehlers
- Quantum Condensed Matter Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - L. Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia
- Università di Perugia
- I-06123 Perugia
- Italy
- Dipartimento di Fisica e Geologia
| | | | - D. Fioretto
- Dipartimento di Fisica e Geologia
- Università di Perugia
- I-06123 Perugia
- Italy
- Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN)
| | - A. Morresi
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| |
Collapse
|
8
|
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
|
9
|
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
|
10
|
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
|
11
|
Verma D, Jacobs DJ, Livesay DR. Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. PLoS Comput Biol 2012; 8:e1002409. [PMID: 22396637 PMCID: PMC3291535 DOI: 10.1371/journal.pcbi.1002409] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 01/11/2012] [Indexed: 11/18/2022] Open
Abstract
We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility index quantify differences within backbone flexibility, whereas changes in the cooperativity correlation quantify differences within pairwise mechanical couplings. Regardless of metric, the same general conclusions are drawn. That is, small structural perturbations introduced by single point mutations have a frequent and pronounced affect on lysozyme flexibility that can extend over long distances. Specifically, an appreciable change occurs in backbone flexibility for 48% of the residues, and a change in cooperativity occurs in 42% of residue pairs. The average distance from mutation to a site with a change in flexibility is 17–20 Å. Interestingly, the frequency and scale of the changes within single point mutant structures are generally larger than those observed in the hen egg white lysozyme (HEWL) ortholog, which shares 61% sequence identity with human lysozyme. For example, point mutations often lead to substantial flexibility increases within the β-subdomain, which is consistent with experimental results indicating that it is the nucleation site for amyloid formation. However, β-subdomain flexibility within the human and HEWL orthologs is more similar despite the lowered sequence identity. These results suggest compensating mutations in HEWL reestablish desired properties. The functional importance of protein dynamics is universally accepted, making the study of dynamical similarities and differences among proteins of the same function an intriguing problem. While some metrics are likely to be conserved across family, differences are also very common. In previous works we have used a Distance Constraint Model to quantify flexibility differences across sets of orthologous proteins, which reproduce this diversity. In the same manner, this work investigates changes occurring upon individual point mutations. Somewhat surprisingly, the small structural perturbations caused by mutation lead to changes throughout the protein. These changes can be quite large, actually surpassing the scale for differences between ortholog pairs. Moreover, changes in flexibility frequently occur at sites far from the mutation site. These results underscore the sensitivity of protein dynamics in connection with allostery, and help explain why differences across protein families are so common.
Collapse
Affiliation(s)
- Deeptak Verma
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Donald J. Jacobs
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail: (DJJ); (DRL)
| | - Dennis R. Livesay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail: (DJJ); (DRL)
| |
Collapse
|
12
|
Shi P, Li D, Chen H, Xiong Y, Wang Y, Tian C. In situ 19F NMR studies of an E. coli membrane protein. Protein Sci 2012; 21:596-600. [PMID: 22362702 DOI: 10.1002/pro.2040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/26/2012] [Accepted: 01/28/2012] [Indexed: 12/16/2022]
Abstract
In this report, (19)F spin incorporation in a specific site of a specific membrane protein in E. coli was accomplished via trifluoromethyl-phenylalanine ((19) F-tfmF). Site-specific (19)F chemical shifts and longitudinal relaxation times of diacylglycerol kinase (DAGK), an E. coli membrane protein, were measured in its native membrane using in situ magic angle spinning (MAS) solid state nuclear magnetic resonance (NMR). Comparing with solution NMR data of the purified DAGK in detergent micelles, the in situ MAS-NMR data illustrated that (19)F chemical shift values of residues at different membrane protein locations were influenced by interactions between membrane proteins and their surrounding lipid or lipid mimic environments, while (19)F side chain longitudinal relaxation values were probably affected by different interactions of DAGK with planar lipid bilayer versus globular detergent micelles.
Collapse
Affiliation(s)
- Pan Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | | | | | | | | | | |
Collapse
|
13
|
Vugmeyster L, Ostrovsky D, Khadjinova A, Ellden J, Hoatson GL, Vold RL. Slow motions in the hydrophobic core of chicken villin headpiece subdomain and their contributions to configurational entropy and heat capacity from solid-state deuteron NMR measurements. Biochemistry 2011; 50:10637-46. [PMID: 22085262 PMCID: PMC3366553 DOI: 10.1021/bi201515b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated microsecond to millisecond time scale dynamics in several key hydrophobic core methyl groups of chicken villin headpiece subdomain protein (HP36) using a combination of single-site labeling, deuteron solid-state NMR line shape analysis, and computational modeling. Deuteron line shapes of hydrated powder samples are dominated by rotameric jumps and show a large variability of rate constants, activation energies, and rotameric populations. Site-specific activation energies vary from 6 to 38 kJ/mol. An additional mode of diffusion on a restricted arc is significant for some sites. In dry samples, the dynamics is quenched. Parameters of the motional models allow for calculations of configurational entropy and heat capacity, which, together with the rate constants, allow for observation of interplay between thermodynamic and kinetic picture of the landscape. Mutations at key phenylalanine residues at both distal (F47L&F51L) and proximal (F58L) locations to a relatively rigid side chain of L69 have a pronounced effect on alleviating the rigidity of this side chain at room temperature and demonstrate the sensitivity of the hydrophobic core environment to such perturbations.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska, Anchorage, Alaska 99508, United States.
| | | | | | | | | | | |
Collapse
|
14
|
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
|
15
|
DuBay KH, Bothma JP, Geissler PL. Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone. PLoS Comput Biol 2011; 7:e1002168. [PMID: 21980271 PMCID: PMC3182858 DOI: 10.1371/journal.pcbi.1002168] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 07/05/2011] [Indexed: 11/30/2022] Open
Abstract
Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate their potential utility using Monte Carlo sampling of side-chain torsional angles on a fixed backbone to quantify correlations amongst side-chain inter-rotameric motions. Results indicate that long-range correlations of side-chain fluctuations can arise independently from several different types of interactions: steric repulsions, implicit solvent interactions, or hydrogen bonding and salt-bridge interactions. These robust correlations persist across the entire protein (up to 60 Å in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations. Allosteric regulation occurs when the function of one part of a protein changes in response to a signal recognized by another part of the protein. Such intra-protein communication is essential for many biochemical processes, allowing the cell to adapt its behavior to a dynamic environment. Most studies of the information conveyance underlying allostery have to date focused on the role of backbone motions in mediating large structural changes. Here we focus instead on more subtle contributions, arising from fluctuations of side-chain torsions. Using a model for side-chain bond rotations in the tightly packed environment imposed by native backbone conformations, we observed significant sensitivity of side-chain organization to small, localized perturbations. This susceptibility arises from correlations among side-chain motions that can propagate information within a protein in complex, heterogeneous ways. Specifically, we found appreciable correlations even between side-chains distant from one another, so that the effect of a minor perturbation at one site on the protein could be observed in the altered fluctuations of side-chains throughout the protein. In conclusion, we have demonstrated that the statistical mechanics of correlated side-chain fluctuations within a model of the folded protein provides the basis for an unconventional but potentially important means of allostery.
Collapse
Affiliation(s)
- Kateri H. DuBay
- Department of Chemistry, University of California at Berkeley, Berkeley, California, United States of America
- Chemical Sciences, Physical Biosciences, and Materials Sciences Divisions, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Jacques P. Bothma
- Biophysical Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Phillip L. Geissler
- Department of Chemistry, University of California at Berkeley, Berkeley, California, United States of America
- Chemical Sciences, Physical Biosciences, and Materials Sciences Divisions, Lawrence Berkeley National Lab, Berkeley, California, United States of America
- Biophysical Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
- * E-mail:
| |
Collapse
|
16
|
Erez Y, Gepshtein R, Presiado I, Trujillo K, Kallio K, Remington SJ, Huppert D. Structure and Excited-State Proton Transfer in the GFP S205A Mutant. J Phys Chem B 2011; 115:11776-85. [DOI: 10.1021/jp2052689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuval Erez
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry Tel Aviv University, Tel Aviv 69978, Israel
| | - Rinat Gepshtein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry Tel Aviv University, Tel Aviv 69978, Israel
| | - Itay Presiado
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry Tel Aviv University, Tel Aviv 69978, Israel
| | - Kristina Trujillo
- Institute of Molecular Biology and Department of Physics, University of Oregon 97403-1229, United States
| | - Karen Kallio
- Institute of Molecular Biology and Department of Physics, University of Oregon 97403-1229, United States
| | - S. James Remington
- Institute of Molecular Biology and Department of Physics, University of Oregon 97403-1229, United States
| | - Dan Huppert
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
17
|
Hansen DF, Kay LE. Determining Valine Side-Chain Rotamer Conformations in Proteins from Methyl 13C Chemical Shifts: Application to the 360 kDa Half-Proteasome. J Am Chem Soc 2011; 133:8272-81. [DOI: 10.1021/ja2014532] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
18
|
Stewart MD, Morgan B, Massi F, Igumenova TI. Probing the determinants of diacylglycerol binding affinity in the C1B domain of protein kinase Cα. J Mol Biol 2011; 408:949-70. [PMID: 21419781 DOI: 10.1016/j.jmb.2011.03.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/09/2011] [Accepted: 03/10/2011] [Indexed: 01/20/2023]
Abstract
C1 domains are independently folded modules that are responsible for targeting their parent proteins to lipid membranes containing diacylglycerol (DAG), a ubiquitous second messenger. The DAG binding affinities of C1 domains determine the threshold concentration of DAG required for the propagation of signaling response and the selectivity of this response among DAG receptors in the cell. The structural information currently available for C1 domains offers little insight into the molecular basis of their differential DAG binding affinities. In this work, we characterized the C1B domain of protein kinase Cα (C1Bα) and its diagnostic mutant, Y123W, using solution NMR methods and molecular dynamics simulations. The mutation did not perturb the C1Bα structure or the sub-nanosecond dynamics of the protein backbone, but resulted in a >100-fold increase in DAG binding affinity and a substantial change in microsecond timescale conformational dynamics, as quantified by NMR rotating-frame relaxation-dispersion methods. The differences in the conformational exchange behavior between wild type and Y123W C1Bα were localized to the hinge regions of ligand-binding loops. Molecular dynamics simulations provided insight into the identity of the exchanging conformers and revealed the significance of a particular residue (Gln128) in modulating the geometry of the ligand-binding site. Taken together with the results of binding studies, our findings suggest that the conformational dynamics and preferential partitioning of the tryptophan side chain into the water-lipid interface are important factors that modulate the DAG binding properties of the C1 domains.
Collapse
Affiliation(s)
- Mikaela D Stewart
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA
| | | | | | | |
Collapse
|
19
|
Multi-Timescale Dynamics Study of FKBP12 Along the Rapamycin–mTOR Binding Coordinate. J Mol Biol 2011; 405:378-94. [DOI: 10.1016/j.jmb.2010.10.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 08/12/2010] [Accepted: 10/20/2010] [Indexed: 01/11/2023]
|
20
|
Sheppard D, Li DW, Godoy-Ruiz R, Brüschweiler R, Tugarinov V. Variation in quadrupole couplings of alpha deuterons in ubiquitin suggests the presence of C(alpha)-H(alpha)...O=C hydrogen bonds. J Am Chem Soc 2010; 132:7709-19. [PMID: 20476744 DOI: 10.1021/ja101691s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear quadrupolar couplings are sensitive probes of hydrogen bonding. Experimental quadrupolar coupling constants of alpha deuterons (D(alpha) QCC) are reported for the residues of human ubiquitin that do not experience large-amplitude internal dynamics on the pico- to nanosecond time scale. Two different methods for D(alpha) QCC estimation are employed: (i) direct estimation of D(alpha) QCC values from R(1) and R(2) (2)H D(alpha) rates using the dynamics parameters (S(C(alpha)-H(alpha))(2)) derived from 1 micros molecular dynamics simulations as well as from (13)C(alpha) relaxation measurements and (ii) indirect measurements via scalar relaxation of the second kind that affects (13)C(alpha) relaxation rates in (13)C(alpha)-D(alpha) spin systems. A relatively large variability of D(alpha) QCC values is produced by both methods. The average value of 170.6 +/- 3 kHz is derived from the combined data set, with D(alpha) QCC values ranging from 159.2 to 177.2 kHz. The set of lowest quadrupolar couplings in all data sets corresponds to the residues that are likely to form weak C(alpha)-H(alpha)...O=C hydrogen bonds as predicted from the analysis of short H(alpha)...O distances in three-dimensional structures of ubiquitin. These D(alpha) nuclei show up to 10 kHz reduction in their QCC values, which is in agreement with earlier solid-state NMR measurements in alpha deuterons of glycine. A statistically significant correlation is observed between the QCC values of alpha-deuterons and the inverse cube of C(alpha)-H(alpha)...O=C distances in ubiquitin.
Collapse
Affiliation(s)
- Devon Sheppard
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | | | | | | | | |
Collapse
|
21
|
Sheppard D, Tugarinov V. Estimating quadrupole couplings of amide deuterons in proteins from direct measurements of 2H spin relaxation rates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 203:316-322. [PMID: 20053572 DOI: 10.1016/j.jmr.2009.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 12/15/2009] [Accepted: 12/19/2009] [Indexed: 05/28/2023]
Abstract
The measurements of longitudinal and transverse 2H spin relaxation rates of backbone amide deuterons (D(N)) in the [U-13C,15N]-labeled protein ubiquitin show that the utility of amide deuterons as probes of backbone order in proteins is compromised by substantial variability of D(N) quadrupolar coupling constants (QCC) from one amide site to another. However, using the dynamics parameters of 15N-2H bond vectors evaluated from 15N relaxation data, site-specific QCC values can be estimated directly from D(N)R1 and R2 rates providing useful information on hydrogen bonding in proteins. In agreement with previous indirect scalar relaxation-based measurements, the D(N) QCC values estimated directly from R1 and R2 2H relaxation rates correlate with the inverse cube of the X-ray structure-derived hydrogen bond distances in ubiquitin: QCC=(232+/-2.3)+(118+/-17) summation operator(i)(cosalpha)r(i)(-3) where r is the inter-nuclear hydrogen bond distance in ångströms, and alpha is the N-D....O(i) angle.
Collapse
Affiliation(s)
- Devon Sheppard
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | | |
Collapse
|
22
|
Tadeo X, López-Méndez B, Castaño D, Trigueros T, Millet O. Protein stabilization and the Hofmeister effect: the role of hydrophobic solvation. Biophys J 2009; 97:2595-603. [PMID: 19883603 PMCID: PMC2770621 DOI: 10.1016/j.bpj.2009.08.029] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 08/18/2009] [Accepted: 08/21/2009] [Indexed: 11/21/2022] Open
Abstract
Using the IGg binding domain of protein L from Streptoccocal magnus (ProtL) as a case study, we investigated how the anions of the Hofmeister series affect protein stability. To that end, a suite of lysine-to-glutamine modifications were obtained and structurally and thermodynamically characterized. The changes in stability introduced with the mutation are related to the solvent-accessible area of the side chain, specifically to the solvation of the nonpolar moiety of the residue. The thermostability for the set of ProtL mutants was determined in the presence of varying concentrations (0-1 M) of six sodium salts from the Hofmeister series: sulfate, phosphate, fluoride, nitrate, perchlorate, and thiocyanate. For kosmotropic anions (sulfate, phosphate, and fluoride), the stability changes induced by the cosolute (encoded in m(3)=deltaDeltaG(0)/deltaC(3)) are proportional to the surface changes introduced with the mutation. In contrast, the m(3) values measured for chaotropic anions are much more independent of such surface modifications. Our results are consistent with a model in which the increase in the solution surface tension induced by the anion stabilizes the folded conformation of the protein. This contribution complements the nonspecific and weak interactions between the ions and the protein backbone that shift the equilibrium toward the unfolded state.
Collapse
Affiliation(s)
| | | | | | | | - Oscar Millet
- Structural Biology Unit, Centro de Investigación Cooperativa bioGUNE, Derio, Spain
| |
Collapse
|
23
|
Sheppard D, Li DW, Brüschweiler R, Tugarinov V. Deuterium spin probes of backbone order in proteins: 2H NMR relaxation study of deuterated carbon alpha sites. J Am Chem Soc 2009; 131:15853-65. [PMID: 19821582 PMCID: PMC2770885 DOI: 10.1021/ja9063958] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(2)H spin relaxation NMR experiments to study the dynamics of deuterated backbone alpha-positions, D(alpha), are developed. To date, solution-state (2)H relaxation measurements in proteins have been confined to side-chain deuterons-primarily (13)CH(2)D or (13)CHD(2) methyl groups. It is shown that quantification of (2)H relaxation rates at D(alpha) backbone positions and the derivation of associated order parameters of C(alpha)-D(alpha) bond vector motions in small [U-(15)N,(13)C,(2)H]-labeled proteins is feasible with reasonable accuracy. The utility of the developed methodology is demonstrated on a pair of proteins-ubiquitin (8.5 kDa) at 10, 27, and 40 degrees C, and a variant of GB1 (6.5 kDa) at 22 degrees C. In both proteins, the D(alpha)-derived parameters of the global rotational diffusion tensor are in good agreement with those obtained from (15)N relaxation rates. Semiquantitative solution-state NMR measurements yield an average value of the quadrupolar coupling constant, QCC, for D(alpha) sites in proteins equal to 174 kHz. Using a uniform value of QCC for all D(alpha) sites, we show that C(alpha)-D(alpha) bond vectors are motionally distinct from the backbone amide N-H bond vectors, with (2)H-derived squared order parameters of C(alpha)-D(alpha) bond vector motions, S(2)(CalphaDalpha), on average slightly higher than their N-H amides counterparts, S(2)(NH). For ubiquitin, the (2)H-derived backbone mobility compares well with that found in a 1-mus molecular dynamics simulation.
Collapse
Affiliation(s)
| | | | | | - Vitali Tugarinov
- Address correspondence to this author: Vitali Tugarinov, Biomolecular Sci. Bldg./CBSO, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742. ; Tel: +1-301-4051504; Fax: +1-301-3140386
| |
Collapse
|
24
|
Mulder FAA. Leucine side-chain conformation and dynamics in proteins from 13C NMR chemical shifts. Chembiochem 2009; 10:1477-9. [PMID: 19466705 DOI: 10.1002/cbic.200900086] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Frans A A Mulder
- Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, NL.
| |
Collapse
|
25
|
Xu J, Xue Y, Skrynnikov NR. Detection of nanosecond time scale side-chain jumps in a protein dissolved in water/glycerol solvent. JOURNAL OF BIOMOLECULAR NMR 2009; 45:57-72. [PMID: 19582374 DOI: 10.1007/s10858-009-9336-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 06/06/2009] [Indexed: 05/28/2023]
Abstract
In solution, the correlation time of the overall protein tumbling, tau(R), plays a role of a natural dynamics cutoff-internal motions with correlation times on the order of tau ( R ) or longer cannot be reliably identified on the basis of spin relaxation data. It has been proposed some time ago that the 'observation window' of solution experiments can be expanded by changing the viscosity of solvent to raise the value of tau(R). To further explore this concept, we prepared a series of samples of alpha-spectrin SH3 domain in solvent with increasing concentration of glycerol. In addition to the conventional (15)N labeling, the protein was labeled in the Val, Leu methyl positions ((13)CHD(2) on a deuterated background). The collected relaxation data were used in asymmetric fashion: backbone (15)N relaxation rates were used to determine tau(R) across the series of samples, while methyl (13)C data were used to probe local dynamics (side-chain motions). In interpreting the results, it has been initially suggested that addition of glycerol leads only to increases in tau(R), whereas local motional parameters remain unchanged. Thus the data from multiple samples can be analyzed jointly, with tau(R) playing the role of experimentally controlled variable. Based on this concept, the extended model-free model was constructed with the intent to capture the effect of ns time-scale rotameric jumps in valine and leucine side chains. Using this model, we made a positive identification of nanosecond dynamics in Val-23 where ns motions were already observed earlier. In several other cases, however, only tentative identification was possible. The lack of definitive results was due to the approximate character of the model-contrary to what has been assumed, addition of glycerol led to a gradual 'stiffening' of the protein. This and other observations also shed light on the interaction of the protein with glycerol, which is one of the naturally occurring osmoprotectants. In particular, it has been found that the overall protein tumbling is controlled by the bulk solvent, and not by a thin solvation layer which contains a higher proportion of water.
Collapse
Affiliation(s)
- Jun Xu
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | | | | |
Collapse
|
26
|
Farès C, Lakomek NA, Walter KFA, Frank BTC, Meiler J, Becker S, Griesinger C. Accessing ns-micros side chain dynamics in ubiquitin with methyl RDCs. JOURNAL OF BIOMOLECULAR NMR 2009; 45:23-44. [PMID: 19652920 PMCID: PMC2728246 DOI: 10.1007/s10858-009-9354-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 06/27/2009] [Indexed: 05/19/2023]
Abstract
This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-tau (c) dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time tau (c). In fact, the average amplitude of motion expressed in terms of order parameters S (2) associated with the supra-tau (c) window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains.
Collapse
Affiliation(s)
- Christophe Farès
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
- University Health Network, Max Bell Research Center, University of Toronto, Toronto, ON Canada
| | - Nils-Alexander Lakomek
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD USA
| | - Korvin F. A. Walter
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Benedikt T. C. Frank
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jens Meiler
- Department of Chemistry, Center of Structural Biology, Vanderbilt University, Nashville, TN USA
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
27
|
Whitley MJ, Lee AL. Frameworks for understanding long-range intra-protein communication. Curr Protein Pept Sci 2009; 10:116-27. [PMID: 19355979 DOI: 10.2174/138920309787847563] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phenomenon of intra-protein communication is fundamental to such processes as allostery and signaling, yet comparatively little is understood about its physical origins despite notable progress in recent years. This review introduces contemporary but distinct frameworks for understanding intra-protein communication by presenting both the ideas behind them and a discussion of their successes and shortcomings. The first framework holds that intra-protein communication is accomplished by the sequential mechanical linkage of residues spanning a gap between distal sites. According to the second framework, proteins are best viewed as ensembles of distinct structural microstates, the dynamical and thermodynamic properties of which contribute to the experimentally observable macroscale properties. Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for studying intra-protein communication, and the insights into both frameworks it provides are presented through a discussion of numerous examples from the literature. Distinct from mechanical and thermodynamic considerations of intra-protein communication are recently applied graph and network theoretic analyses. These computational methods reduce complex three dimensional protein architectures to simple maps comprised of nodes (residues) connected by edges (inter-residue "interactions"). Analysis of these graphs yields a characterization of the protein's topology and network characteristics. These methods have shown proteins to be "small world" networks with moderately high local residue connectivities existing concurrently with a small but significant number of long range connectivities. However, experimental studies of the tantalizing idea that these putative long range interaction pathways facilitate one or several macroscopic protein characteristics are unfortunately lacking at present. This review concludes by comparing and contrasting the presented frameworks and methodologies for studying intra-protein communication and suggests a manner in which they can be brought to bear simultaneously to further enhance our understanding of this important fundamental phenomenon.
Collapse
Affiliation(s)
- Matthew J Whitley
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | | |
Collapse
|
28
|
Agarwal V, Xue Y, Reif B, Skrynnikov NR. Protein Side-Chain Dynamics As Observed by Solution- and Solid-State NMR Spectroscopy: A Similarity Revealed. J Am Chem Soc 2008; 130:16611-21. [PMID: 19049457 DOI: 10.1021/ja804275p] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vipin Agarwal
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Yi Xue
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Bernd Reif
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Nikolai R. Skrynnikov
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| |
Collapse
|
29
|
Rodriguez-Granillo A, Sedlak E, Wittung-Stafshede P. Stability and ATP binding of the nucleotide-binding domain of the Wilson disease protein: effect of the common H1069Q mutation. J Mol Biol 2008; 383:1097-111. [PMID: 18692069 DOI: 10.1016/j.jmb.2008.07.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/18/2008] [Accepted: 07/24/2008] [Indexed: 01/23/2023]
Abstract
Perturbation of the human copper-transporter Wilson disease protein (ATP7B) causes intracellular copper accumulation and severe pathology, known as Wilson disease (WD). Several WD mutations are clustered within the nucleotide-binding subdomain (N-domain), including the most common mutation, H1069Q. To gain insight into the biophysical behavior of the N-domain under normal and disease conditions, we have characterized wild-type and H1069Q recombinant N-domains in vitro and in silico. The mutant has only twofold lower ATP affinity compared to that of the wild-type N-domain. Both proteins unfold in an apparent two-state reaction at 20 degrees C and ATP stabilizes the folded state. The thermal unfolding reactions are irreversible and, for the same scan rate, the wild-type protein is more resistant to perturbation than the mutant. For both proteins, ATP increases the activation barrier towards thermal denaturation. Molecular dynamics simulations identify specific differences in both ATP orientation and protein structure that can explain the absence of catalytic activity for the mutant N-domain. Taken together, our results provide biophysical characteristics that may be general to N-domains in other P(1B)-ATPases as well as identify changes that may be responsible for the H1069Q WD phenotype in vivo.
Collapse
|
30
|
Whitley MJ, Zhang J, Lee AL. Hydrophobic core mutations in CI2 globally perturb fast side-chain dynamics similarly without regard to position. Biochemistry 2008; 47:8566-76. [PMID: 18656953 DOI: 10.1021/bi8007966] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein dynamics is currently an area of intense research because of its importance as complementary information to the huge quantity of available data relating protein structure and function. Because it is usually the influence of dynamics on function that is studied, the physical determinants of the distribution of flexibility in proteins have not been explored as thoroughly. In the present NMR study, an expanded suite of five (2)H relaxation experiments was used to characterize the picosecond-to-nanosecond side-chain dynamics of chymotrypsin inhibitor 2 (CI2) and five hydrophobic core mutants, some of which are members of the folding nucleus. Because CI2 is a homologue of the serine protease inhibitor eglin c, which has already been extensively characterized in terms of its dynamics, it was possible to compare not only side-chain dynamics but also the responses of these dynamics to analogous mutations. Remarkably, each of the five core mutations in CI2 led to similar and reproducible increases in side-chain flexibility throughout the entire structure. Although the expanded suite of (2)H relaxation experiments does not affect model selection for the vast majority of residues, it did enable the detection of increasing levels of nanosecond-scale motions in CI2's reactive site binding loop as the L68 side chain was progressively shortened by mutation. Collectively, we observed that the CI2 mutants are more dynamically similar to each other than to the more rigid wild-type CI2, from which we propose that wild-type CI2 has been optimized to a specific level of rigidity which may aid in its function as a serine protease inhibitor. We also observed that the pattern of side-chain dynamics of CI2 is quantitatively similar to eglin c, but that this similarity is lost upon mutating both proteins at an equivalent position. Finally, (15)N relaxation was used to characterize the backbone dynamics of wild-type and mutant CI2. Interestingly, mutation at folding nucleus positions led to widespread increases in backbone flexibility, whereas non-folding-nucleus positions led to increases in flexibility in the C-terminal half of the protein only.
Collapse
Affiliation(s)
- Matthew J Whitley
- Department of Biochemistry & Biophysics, School of Medicine, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | | | | |
Collapse
|
31
|
Ingratta M, Duhamel J. Effect of Side-chain Length on the Side-chain Dynamics of α-Helical Poly(l-glutamic acid) as Probed by a Fluorescence Blob Model. J Phys Chem B 2008; 112:9209-18. [DOI: 10.1021/jp8021248] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark Ingratta
- Institute for Polymer Research, Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Jean Duhamel
- Institute for Polymer Research, Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| |
Collapse
|
32
|
Hass MAS, Hansen DF, Christensen HEM, Led JJ, Kay LE. Characterization of Conformational Exchange of a Histidine Side Chain: Protonation, Rotamerization, and Tautomerization of His61 in Plastocyanin from Anabaena variabilis. J Am Chem Soc 2008; 130:8460-70. [DOI: 10.1021/ja801330h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mathias A. S. Hass
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - D. Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Hans E. M. Christensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Jens J. Led
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lewis E. Kay
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| |
Collapse
|
33
|
Friedland GD, Linares AJ, Smith CA, Kortemme T. A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol 2008; 380:757-74. [PMID: 18547586 DOI: 10.1016/j.jmb.2008.05.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 04/08/2008] [Accepted: 05/07/2008] [Indexed: 10/22/2022]
Abstract
The considerable flexibility of side-chains in folded proteins is important for protein stability and function, and may have a role in mediating allosteric interactions. While sampling side-chain degrees of freedom has been an integral part of several successful computational protein design methods, the predictions of these approaches have not been directly compared to experimental measurements of side-chain motional amplitudes. In addition, protein design methods frequently keep the backbone fixed, an approximation that may substantially limit the ability to accurately model side-chain flexibility. Here, we describe a Monte Carlo approach to modeling side-chain conformational variability and validate our method against a large dataset of methyl relaxation order parameters derived from nuclear magnetic resonance (NMR) experiments (17 proteins and a total of 530 data points). We also evaluate a model of backbone flexibility based on Backrub motions, a type of conformational change frequently observed in ultra-high-resolution X-ray structures that accounts for correlated side-chain backbone movements. The fixed-backbone model performs reasonably well with an overall rmsd between computed and predicted side-chain order parameters of 0.26. Notably, including backbone flexibility leads to significant improvements in modeling side-chain order parameters for ten of the 17 proteins in the set. Greater accuracy of the flexible backbone model results from both increases and decreases in side-chain flexibility relative to the fixed-backbone model. This simple flexible-backbone model should be useful for a variety of protein design applications, including improved modeling of protein-protein interactions, design of proteins with desired flexibility or rigidity, and prediction of correlated motions within proteins.
Collapse
Affiliation(s)
- Gregory D Friedland
- Graduate Group in Biophysics, University of California at San Francisco, 1700 4th St, UCSF MC 2540, San Francisco, CA 94158-2330, USA
| | | | | | | |
Collapse
|
34
|
Krishnan M, Kurkal-Siebert V, Smith JC. Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin. J Phys Chem B 2008; 112:5522-33. [DOI: 10.1021/jp076641z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Krishnan
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
| | - V. Kurkal-Siebert
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
| | - Jeremy C. Smith
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
| |
Collapse
|
35
|
Zhuravleva A, Orekhov VY. Divided evolution: a scheme for suppression of line broadening induced by conformational exchange. J Am Chem Soc 2008; 130:3260-1. [PMID: 18293983 DOI: 10.1021/ja710056t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anastasia Zhuravleva
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
| | | |
Collapse
|
36
|
LeMaster DM, Anderson JS, Wang L, Guo Y, Li H, Hernández G. NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin. BMC STRUCTURAL BIOLOGY 2007; 7:81. [PMID: 18053245 PMCID: PMC2249605 DOI: 10.1186/1472-6807-7-81] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 12/05/2007] [Indexed: 12/03/2022]
Abstract
Background Chimeric hybrids derived from the rubredoxins of Pyrococcus furiosus (Pf) and Clostridium pasteurianum (Cp) provide a robust system for the characterization of protein conformational stability and dynamics in a differential mode. Interchange of the seven nonconserved residues of the metal binding site between the Pf and Cp rubredoxins yields a complementary pair of hybrids, for which the sum of the thermodynamic stabilities is equal to the sum for the parental proteins. Furthermore, the increase in amide hydrogen exchange rates for the hyperthermophile-derived metal binding site hybrid is faithfully mirrored by a corresponding decrease for the complementary hybrid that is derived from the less thermostable rubredoxin, indicating a degree of additivity in the conformational fluctuations that underlie these exchange reactions. Results Initial NMR studies indicated that the structures of the two complementary hybrids closely resemble "cut-and-paste" models derived from the parental Pf and Cp rubredoxins. This protein system offers a robust opportunity to characterize differences in solution structure, permitting the quantitative NMR chemical shift and NOE peak intensity data to be analyzed without recourse to the conventional conversion of experimental NOE peak intensities into distance restraints. The intensities for 1573 of the 1652 well-resolved NOE crosspeaks from the hybrid rubredoxins were statistically indistinguishable from the intensities of the corresponding parental crosspeaks, to within the baseplane noise level of these high sensitivity data sets. The differences in intensity for the remaining 79 NOE crosspeaks were directly ascribable to localized dynamical processes. Subsequent X-ray analysis of the metal binding site-swapped hybrids, to resolution limits of 0.79 Å and 1.04 Å, demonstrated that the backbone and sidechain heavy atoms in the NMR-derived structures lie within the range of structural variability exhibited among the individual molecules in the crystallographic asymmetric unit (~0.3 Å), indicating consistency with the "cut-and-paste" structuring of the hybrid rubredoxins in both crystal and solution. Conclusion Each of the significant energetic interactions in the metal binding site-swapped hybrids appears to exhibit a 1-to-1 correspondence with the interactions present in the corresponding parental rubredoxin structure, thus providing a structural basis for the observed additivity in conformational stability and dynamics. The congruence of these X-ray and NMR experimental data offers additional support for the interpretation that the conventional treatment of NOE distance restraints contributes substantially to the systematic differences that are commonly reported between NMR- and X-ray-derived protein structures.
Collapse
Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York 12201, USA.
| | | | | | | | | | | |
Collapse
|
37
|
Tadeo X, Castaño D, Millet O. Anion modulation of the 1H/2H exchange rates in backbone amide protons monitored by NMR spectroscopy. Protein Sci 2007; 16:2733-40. [PMID: 17965190 DOI: 10.1110/ps.073027007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The ability of three anionic cosolutes (sulfate, thiocyanate, and chloride) in modulating the (1)H/(2)H exchange rates for backbone amide protons has been investigated using nuclear magnetic resonance (NMR) for two different proteins: the IGg-binding domain of protein L (ProtL) and the glucose-galactose-binding protein (GGBP). Our results show that moderate anion concentrations (0.2 M-1 M) regulate the exchange rate following the Hofmeister series: Addition of thiocyanate increases the exchange rates for both proteins, while sulfate and chloride (to a less extent) slow down the exchange reaction. In the presence of the salt, no alteration of the protein structure and minimal variations in the number of measurable peaks are observed. Experiments with model compounds revealed that the unfolded state is modulated in an equivalent way by these cosolutes. For ProtL, the estimated values for the local free energy change upon salt addition (m (3,DeltaG )) are consistent with the previously reported free energy contribution from the cosolute's preferential interaction/exclusion term indicating that nonspecific weak interactions between the anion and the amide groups constitute the dominant mechanism for the exchange-rate modulation. The same trend is also found for GGBP in the presence of thiocyanate, underlining the generality of the exchange-rate modulation mechanism, complementary to more investigated effects like the electrostatic interactions or specific anion binding to protein sites.
Collapse
Affiliation(s)
- Xavier Tadeo
- Structural Biology Unit, CIC bioGUNE, 48160 Derio, Spain
| | | | | |
Collapse
|
38
|
Houben K, Blanchard L, Blackledge M, Marion D. Intrinsic dynamics of the partly unstructured PX domain from the Sendai virus RNA polymerase cofactor P. Biophys J 2007; 93:2830-44. [PMID: 17586564 PMCID: PMC1989709 DOI: 10.1529/biophysj.107.108829] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite their evident importance for function, dynamics of intrinsically unstructured proteins are poorly understood. Sendai virus phosphoprotein, cofactor of the RNA polymerase, contains a partly unstructured protein domain. The phosphoprotein X domain (PX) is responsible for binding the polymerase to the nucleocapsid assembling the viral RNA. For RNA synthesis, the interplay of the dynamics of the unstructured and structured PX subdomains is thought to drive progression of the RNA polymerase along the nucleocapsid. Here we present a detailed study of the dynamics of PX using hydrogen/deuterium exchange and different NMR relaxation measurements. In the unstructured subdomain, large amplitude fast motions were found to be fine-tuned by the presence of residues with short side chains. In the structured subdomain, where fast motions of both backbone and side chains are fairly restricted, the first helix undergoes slow conformational exchange corresponding to a local unfolding event. The other two helices, which represent the nucleocapsid binding site, were found to be more stable and to reorient with respect to each other, as probed by slow conformational exchange identified for residues on the third helix. The study illustrates the intrinsically differential dynamics of this partly unstructured protein and proposes the relation between these dynamics and its function.
Collapse
Affiliation(s)
- Klaartje Houben
- Institut de Biologie Structurale Jean-Pierre Ebel, CNRS, CEA, UJF, UMR-5075, 38027 Grenoble cedex 1, France
| | | | | | | |
Collapse
|
39
|
Xue Y, Pavlova MS, Ryabov YE, Reif B, Skrynnikov NR. Methyl rotation barriers in proteins from 2H relaxation data. Implications for protein structure. J Am Chem Soc 2007; 129:6827-38. [PMID: 17488010 DOI: 10.1021/ja0702061] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Side-chain 2H and backbone 15N relaxation data have been collected at multiple temperatures in the samples of the SH3 domain from alpha-spectrin. Combined analyses of the data allowed for determination of the temperature-dependent correlation times tauf characterizing fast methyl motion. Molecular dynamics simulations confirmed that tauf are dominated by methyl rotation; the corresponding activation energies approximate methyl rotation barriers. For 33 methyl groups in the alpha-spectrin SH3 domain the average barrier height was thus determined to be 2.8 +/- 0.9 kcal/mol. This value is deemed representative of the "fluid" hydrophobic protein core where some barriers are increased and others are lowered because of the contacts with surrounding atoms, but there is no local order that could produce systematically higher (lower) barriers. For comparison, the MD simulation predicts the average barrier of 3.1 kcal/mol (calculated via the potential of mean force) or 3.4-3.5 kcal/mol (rigid barriers after appropriate averaging over multiple MD snapshots). The latter result prompted us to investigate rigid methyl rotation barriers in a series of NMR structures from the Protein Databank. In most cases the barriers proved to be higher than expected, 4-6 kcal/mol. To a certain degree, this is caused by tight packing of the side chains in the NMR structures and stems from the structure calculation procedure where the coordinates are first annealed toward the temperature of 0 K and then subjected to energy minimization. In several cases the barriers >10 kcal/mol are indicative of van der Waals violations. The notable exceptions are (i) the structures solved using the GROMOS force field where tight methyl packing is avoided (3.0-3.6 kcal/mol) and (ii) the structure solved by means of the dynamic ensemble refinement method (Lindorff-Larsen, K.; Best, R. B.; DePristo, M. A.; Dobson, C. M.; Vendruscolo, M. Nature 2005, 433, 128) (3.5 kcal/mol). These results demonstrate that methyl rotation barriers, derived from the experiments that are traditionally associated with studies of protein dynamics, can be also used in the context of structural work. This is particularly interesting in view of the recent efforts to incorporate dynamics data in the process of protein structure elucidation.
Collapse
Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette Indiana 47907-2084, USA
| | | | | | | | | |
Collapse
|
40
|
Zhuravleva A, Korzhnev DM, Nolde SB, Kay LE, Arseniev AS, Billeter M, Orekhov VY. Propagation of Dynamic Changes in Barnase Upon Binding of Barstar: An NMR and Computational Study. J Mol Biol 2007; 367:1079-92. [PMID: 17306298 DOI: 10.1016/j.jmb.2007.01.051] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 01/09/2007] [Accepted: 01/19/2007] [Indexed: 11/20/2022]
Abstract
NMR spectroscopy and computer simulations were used to examine changes in chemical shifts and in dynamics of the ribonuclease barnase that result upon binding to its natural inhibitor barstar. Although the spatial structures of free and bound barnase are very similar, binding results in changes of the dynamics of both fast side-chains, as revealed by (2)H relaxation measurements, and NMR chemical shifts in an extended beta-sheet that is located far from the binding interface. Both side-chain dynamics and chemical shifts are sensitive to variations in the ensemble populations of the inter-converting molecular states, which can escape direct structural observation. Molecular dynamics simulations of free barnase and barnase in complex with barstar, as well as a normal mode analysis of barnase using a Gaussian network model, reveal relatively rigid domains that are separated by the extended beta-sheet mentioned above. The observed changes in NMR parameters upon ligation can thus be rationalized in terms of changes in inter-domain dynamics and in populations of exchanging states, without measurable structural changes. This provides an alternative model for the propagation of a molecular response to ligand binding across a protein that is based exclusively on changes in dynamics.
Collapse
|
41
|
LeMaster DM, Hernández G. Additivity of Differential Conformational Dynamics in Hyperthermophile/Mesophile Rubredoxin Chimeras as Monitored by Hydrogen Exchange. Chembiochem 2006; 7:1886-9. [PMID: 17068837 DOI: 10.1002/cbic.200600276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health, University at Albany-SUNY, Empire State Plaza, Albany, NY 12201-0509, USA
| | | |
Collapse
|
42
|
Fuentes EJ, Gilmore SA, Mauldin RV, Lee AL. Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. J Mol Biol 2006; 364:337-51. [PMID: 17011581 DOI: 10.1016/j.jmb.2006.08.076] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 08/17/2006] [Accepted: 08/26/2006] [Indexed: 11/21/2022]
Abstract
A number of computational and experimental studies have identified intramolecular communication "pathways" or "networks" important for transmitting allostery. Here, we have used mutagenesis and NMR relaxation methods to investigate the scope and nature of the communication networks found in the second post-synaptic density-95/discs large/zonula occludens-1 (PDZ) domain of the human protein tyrosine phosphatase 1E protein (hPTP1E) (PDZ2). It was found that most mutations do not have a significant energetic contribution to peptide ligand binding. Three mutants that showed significant changes in binding also displayed context-dependent dynamic effects. Both a mutation at a partially exposed site (H71Y) and a buried core position (I35V) had a limited response in side-chain (2)H-based dynamics when compared to wild-type PDZ2. In contrast, a change at a second core position (I20F) that had previously been shown to be part of an energetic and dynamic network, resulted in extensive changes in side-chain dynamics. This response is reminiscent to that seen previously upon peptide ligand binding. These results shed light on the nature of the PDZ2 dynamic network and suggest that position 20 in PDZ2 acts as a "hub" that is energetically and dynamically critical for transmitting changes in dynamics throughout the PDZ domain.
Collapse
Affiliation(s)
- Ernesto J Fuentes
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | |
Collapse
|
43
|
Igumenova TI, Frederick KK, Wand AJ. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 2006; 106:1672-99. [PMID: 16683749 PMCID: PMC2547146 DOI: 10.1021/cr040422h] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tatyana I Igumenova
- Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | |
Collapse
|
44
|
Zhang X, Sui X, Yang D. Probing Methyl Dynamics from 13C Autocorrelated and Cross-Correlated Relaxation. J Am Chem Soc 2006; 128:5073-81. [PMID: 16608341 DOI: 10.1021/ja057579r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An understanding of side-chain motions in protein is of great interest since side chains often play an important role in protein folding and intermolecular interactions. A novel method for measuring dipole-dipole cross-correlated relaxation in methyl groups of uniformly 13C-labeled proteins without deuteration has been developed by our group. The excellent agreement between dynamic parameters of methyl groups in ubiquitin obtained from the cross-correlated relaxation and 13C spin-lattice relaxation and those derived previously from 2H relaxation data demonstrates the reliability of the method. This method was applied to the study of side-chain dynamics of human intestinal fatty acid binding protein (IFABP) with and without its ligand. Binding of oleic acid to the protein results in decreased mobility of most of the methyl groups in the binding region, whereas no significant change in mobility was observed for methyl groups in the nonbinding region.
Collapse
Affiliation(s)
- Xu Zhang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | | | | |
Collapse
|
45
|
Tugarinov V, Kay LE. Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. Chembiochem 2006; 6:1567-77. [PMID: 16075427 DOI: 10.1002/cbic.200500110] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Vitali Tugarinov
- Department of Medical Genetics and Microbiology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | | |
Collapse
|
46
|
Igumenova TI, Lee AL, Wand AJ. Backbone and side chain dynamics of mutant calmodulin-peptide complexes. Biochemistry 2005; 44:12627-39. [PMID: 16171378 PMCID: PMC1343484 DOI: 10.1021/bi050832f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of long-range coupling of allosteric sites in calcium-saturated calmodulin (CaM) has been explored by characterizing structural and dynamics effects of mutants of calmodulin in complex with a peptide corresponding to the smooth muscle myosin light chain kinase calmodulin-binding domain (smMLCKp). Four CaM mutants were examined: D95N and D58N, located in Ca2+-binding loops; and M124L and E84K, located in the target domain-binding site of CaM. Three of these mutants have altered allosteric coupling either between Ca2+-binding sites (D58N and D95N) or between the target- and Ca2+-binding sites (E84K). The structure and dynamics of the mutant calmodulins in complex with smMLCKp were characterized using solution NMR. Analysis of chemical shift perturbations was employed to detect largely structural perturbations. 15N and 2H relaxation was employed to detect perturbations of the dynamics of the backbone and methyl-bearing side chains of calmodulin. The least median squares method was found to be robust in the detection of perturbed sites. The main chain dynamics of calmodulin are found to be largely unresponsive to the mutations. Three mutants show significantly perturbed dynamics of methyl-bearing side chains. Despite the pseudosymmetric location of Ca2+-binding loop mutations D58N and D95N, the dynamic response of CaM is asymmetric, producing long-range perturbation in D58N and almost none in D95N. The mutations located at the target domain-binding site have quite different effects. For M124L, a local perturbation of the methyl dynamics is observed, while the E84K mutation produces a long-range propagation of dynamic perturbations along the target domain-binding site.
Collapse
Affiliation(s)
- Tatyana I Igumenova
- Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | |
Collapse
|
47
|
Diercks T, Orekhov VY. qTROSY--a novel scheme for recovery of the anti-TROSY magnetisation. JOURNAL OF BIOMOLECULAR NMR 2005; 32:113-27. [PMID: 16034663 DOI: 10.1007/s10858-005-5618-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Revised: 03/29/2005] [Accepted: 04/07/2005] [Indexed: 05/03/2023]
Abstract
In TROSY experiments, spin state selection (S3) retains only the single HSQC sub-spectrum with minimal T2 relaxation and maximal resolution, yet at the cost of eliminating half of the available polarisation as undesired anti-TROSY component. We here introduce queued TROSY (qTROSY) as a novel scheme to partially recover and exploit this anti-TROSY polarisation in two concatenated scans. After initial orthogonal spin state separation (oS3), anti-TROSY polarisation is explicitly stored while its TROSY counterpart follows the desired coherence pathway recorded in a first scan A. The immediately appended scan B then quantitatively converts the recovered anti-TROSY polarisation into a second TROSY spectrum, skipping the time-limiting long reequilibration delay. Both concatenated qTROSY scans thus ideally exploit the full initial polarisation within almost the same measurement time. In practice, T2 relaxation losses accruing during the coupling evolution delays reduced anti-TROSY polarisation recovery below 40%, obviating sensitivity enhancement through addition of both qTROSY scans; yet, scan B retained a complete scan A spectrum with up to 75% intensity. We therefore propose to employ qTROSY asymmetrically, compacting two separate conventional into one queued TROSY-type experiment with significantly reduced measurement time, implying primarily the concatenation of different three- or higher-dimensional experiments. Both anti-TROSY polarisation recoveries and possible time savings are largest for deuterated and smaller non-deuterated proteins, extending the rentability limit of the TROSY principle towards smaller molecular weights.
Collapse
Affiliation(s)
- Tammo Diercks
- Swedish NMR Centre at Göteborg University, P.O.Box 465, Göteborg, SE, 40530, Sweden
| | | |
Collapse
|
48
|
Clarkson MW, Lee AL. Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c. Biochemistry 2004; 43:12448-58. [PMID: 15449934 DOI: 10.1021/bi0494424] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Long-range interactions are fundamental to protein behaviors such as cooperativity and allostery. In an attempt to understand the role protein flexibility plays in such interactions, the distribution of local fluctuations in a globular protein was monitored in response to localized, nonelectrostatic perturbations. Two valine-to-alanine mutations were introduced into the small serine protease inhibitor eglin c, and the (15)N and (2)H NMR spin relaxation properties of these variants were analyzed in terms of the Lipari-Szabo dynamics formalism and compared to those of the wild type. Significant changes in picosecond to nanosecond dynamics were observed in side chains located as much as 13 A from the point of mutation. Additionally, those residues experiencing altered dynamics appear to form contiguous surfaces within the protein. In the case of V54A, the large-to-small mutation results in a rigidification of connected residues, even though this mutation decreases the global stability. These findings suggest that dynamic perturbations arising from single mutations may propagate away from the perturbed site through networks of interacting side chains. That this is observed in eglin c, a classically nonallosteric protein, suggests that such behavior will be observed in many, if not all, globular proteins. Differences in behavior between the two mutants suggest that dynamic responses will be context-dependent.
Collapse
Affiliation(s)
- Michael W Clarkson
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7360, USA
| | | |
Collapse
|
49
|
Mittermaier A, Kay LE. The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase. Protein Sci 2004; 13:1088-99. [PMID: 15044737 PMCID: PMC2280047 DOI: 10.1110/ps.03502504] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have used (15)N- and (2)H-NMR spin relaxation experiments to study the response of backbone and side-chain dynamics when a leucine or valine is substituted for a completely buried phenylalanine residue in the SH3 domain from the Fyn tyrosine kinase. Several residues show differences in the time scales and temperature dependences of internal motions when data for the three proteins are compared. Changes were also observed in the magnitude of dynamics, with the valine, and to a lesser extent leucine mutant, showing enhanced flexibility compared to the wild-type (WT) protein. The motions of many of the same amide and methyl groups are affected by both mutations, identifying a set of loci where dynamics are sensitive to interactions involving the targeted side chain. These results show that contacts within the hydrophobic core affect many aspects of internal mobility throughout the Fyn SH3 domain.
Collapse
Affiliation(s)
- Anthony Mittermaier
- Departments of Biochemistry, Chemistry and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
| | | |
Collapse
|
50
|
Tugarinov V, Kay LE. Stereospecific NMR Assignments of Prochiral Methyls, Rotameric States and Dynamics of Valine Residues in Malate Synthase G. J Am Chem Soc 2004; 126:9827-36. [PMID: 15291587 DOI: 10.1021/ja048738u] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Near complete stereospecific assignments of the prochiral methyl carbons of Leu and Val residues in malate synthase G, a 723 residue enzyme, are reported. Assignments were obtained on the basis of a 10% fractional (13)C-labeling strategy developed by Wüthrich and co-workers [Neri, D; Szyperski, T; Otting, G; Senn, H; Wüthrich, K. Biochemistry 1989, 28, 7510-7516] and, in the case of Val residues, supplemented with results from a series of new methyl-TROSY quantitative J experiments for measuring (3)J(C)(gamma)(N) and (3)J(C)(gamma)(C)' couplings. The measured (3)J couplings were also used to probe Val side chain dynamics. A strong correlation is observed between rotamer averaging established on the basis of the couplings and side chain millisecond time scale dynamics measured using methyl-TROSY based (1)H-(13)C multiple quantum relaxation dispersion experiments.
Collapse
Affiliation(s)
- Vitali Tugarinov
- Protein Engineering Network Centres of Excellence and the Department of Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | | |
Collapse
|