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Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. J Am Chem Soc 2023; 145:22964-22978. [PMID: 37831584 DOI: 10.1021/jacs.3c04614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Knowing the 3D structures formed by the various conformations populating the RNA free-energy landscape, their relative abundance, and kinetic interconversion rates is required to obtain a quantitative and predictive understanding of how RNAs fold and function at the atomic level. While methods integrating ensemble-averaged experimental data with computational modeling are helping define the most abundant conformations in RNA ensembles, elucidating their kinetic rates of interconversion and determining the 3D structures of sparsely populated short-lived RNA excited conformational states (ESs) remains challenging. Here, we developed an approach integrating Rosetta-FARFAR RNA structure prediction with NMR residual dipolar couplings and relaxation dispersion that simultaneously determines the 3D structures formed by the ground-state (GS) and ES subensembles, their relative abundance, and kinetic rates of interconversion. The approach is demonstrated on HIV-1 TAR, whose six-nucleotide apical loop was previously shown to form a sparsely populated (∼13%) short-lived (lifetime ∼ 45 μs) ES. In the GS, the apical loop forms a broad distribution of open conformations interconverting on the pico-to-nanosecond time scale. Most residues are unpaired and preorganized to bind the Tat-superelongation protein complex. The apical loop zips up in the ES, forming a narrow distribution of closed conformations, which sequester critical residues required for protein recognition. Our work introduces an approach for determining the 3D ensemble models formed by sparsely populated RNA conformational states, provides a rare atomic view of an RNA ES, and kinetically resolves the atomic 3D structures of RNA conformational substates, interchanging on time scales spanning 6 orders of magnitude, from picoseconds to microseconds.
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Affiliation(s)
- Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Elizabeth A Dethoff
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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2
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Almeida FCL, Sanches K, Caruso IP, Melo FA. NMR Relaxation Dispersion Experiments to Study Phosphopeptide Recognition by SH2 Domains: The Grb2-SH2-Phosphopeptide Encounter Complex. Methods Mol Biol 2023; 2705:135-151. [PMID: 37668973 DOI: 10.1007/978-1-0716-3393-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Protein interactions are at the essence of life. Proteins evolved not to have stable structures, but rather to be specialized in participating in a network of interactions. Every interaction involving proteins comprises the formation of an encounter complex, which may have two outcomes: (i) the dissociation or (ii) the formation of the final specific complex. Here, we present a methodology to characterize the encounter complex of the Grb2-SH2 domain with a phosphopeptide. This method can be generalized to other protein partners. It consists of the measurement of 15N CPMG relaxation dispersion (RD) profiles of the protein in the free state, which describes the residues that are in conformational exchange. We then acquire the dispersion profiles of the protein at a semisaturated concentration of the ligand. At this condition, the chemical exchange between the free and bound state leads to the observation of dispersion profiles in residues that are not in conformational exchange in the free state. This is due to fuzzy interactions that are typical of the encounter complexes. The transient "touching" of the ligand in the protein partner generates these new relaxation dispersion profiles. For the Grb2-SH2 domain, we observed a wider surface at SH2 for the encounter complex than the phosphopeptide (pY) binding site, which might explain the molecular recognition of remote phosphotyrosine. The Grb2-SH2-pY encounter complex is dominated by electrostatic interactions, which contribute to the fuzziness of the complex, but also have contribution of hydrophobic interactions.
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Affiliation(s)
- Fabio C L Almeida
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Institute of Medical Biochemistry - IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Karoline Sanches
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC, Australia
| | - Icaro P Caruso
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), Sao Jose do Rio Preto, Sao Paulo, Brazil
| | - Fernando A Melo
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), Sao Jose do Rio Preto, Sao Paulo, Brazil
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3
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Russo L, Salzano G, Corvino A, Bistaffa E, Moda F, Celauro L, D'Abrosca G, Isernia C, Milardi D, Giachin G, Malgieri G, Legname G, Fattorusso R. Structural and dynamical determinants of a β-sheet-enriched intermediate involved in amyloid fibrillar assembly of human prion protein. Chem Sci 2022; 13:10406-10427. [PMID: 36277622 PMCID: PMC9473526 DOI: 10.1039/d2sc00345g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/04/2022] [Indexed: 12/02/2022] Open
Abstract
The conformational conversion of the cellular prion protein (PrPC) into a misfolded, aggregated and infectious scrapie isoform is associated with prion disease pathology and neurodegeneration. Despite the significant number of experimental and theoretical studies the molecular mechanism regulating this structural transition is still poorly understood. Here, via Nuclear Magnetic Resonance (NMR) methodologies we investigate at the atomic level the mechanism of the human HuPrP(90–231) thermal unfolding and characterize the conformational equilibrium between its native structure and a β-enriched intermediate state, named β-PrPI. By comparing the folding mechanisms of metal-free and Cu2+-bound HuPrP(23–231) and HuPrP(90–231) we show that the coupling between the N- and C-terminal domains, through transient electrostatic interactions, is the key molecular process in tuning long-range correlated μs–ms dynamics that in turn modulate the folding process. Moreover, via thioflavin T (ThT)-fluorescence fibrillization assays we show that β-PrPI is involved in the initial stages of PrP fibrillation, overall providing a clear molecular description of the initial phases of prion misfolding. Finally, we show by using Real-Time Quaking-Induced Conversion (RT-QuIC) that the β-PrPI acts as a seed for the formation of amyloid aggregates with a seeding activity comparable to that of human infectious prions. The N-ter domain in HuPrP regulates the folding mechanism by tuning the long-range μs–ms dynamics. Removal of the N-ter domain triggers the formation of a stable β-enriched intermediate state inducing amyloid aggregates with HuPrPSc seeding activity.![]()
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Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Giulia Salzano
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Andrea Corvino
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Edoardo Bistaffa
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Division of Neurology 5 and Neuropathology, Milano, Italy
| | - Fabio Moda
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Division of Neurology 5 and Neuropathology, Milano, Italy
| | - Luigi Celauro
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Danilo Milardi
- Institute of Crystallography, National Research Council, Catania, Italy
| | - Gabriele Giachin
- Department of Chemical Sciences (DiSC), University of Padua, Padova, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- ELETTRA Laboratory, Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
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4
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Ban D, Rice CT, McCoy MA. Quantification of natural abundance NMR data differentiates the solution behavior of monoclonal antibodies and their fragments. MAbs 2021; 13:1978132. [PMID: 34612804 PMCID: PMC8496538 DOI: 10.1080/19420862.2021.1978132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Biotherapeutics are an important class of molecules for the treatment of a wide range of diseases. They include low molecular weight peptides, highly engineered protein scaffolds and monoclonal antibodies. During their discovery and development, assessments of the biophysical attributes is critical to understanding the solution behavior of therapeutic proteins and for de-risking liabilities. Thus, methods that can quantify, characterize, and provide a basis to inform risks and drive the selection of more optimal antibody and alternative scaffolds are needed. Nuclear Magnetic Resonance (NMR) spectroscopy is a technique that provides a means to probe antibody and antibody-like molecules in solution, at atomic resolution, under any formulated conditions. Here, all samples were profiled at natural abundance requiring no isotope enrichment. We present a numerical approach that quantitates two-dimensional methyl spectra. The approach was tested with a reference dataset that contained different types of antibody and antibody-like molecules. This dataset was processed through a procedure we call a Random Sampling of NMR Peaks for Covariance Analysis. This analysis revealed that the first two components were well correlated with the hydrodynamic radius of the molecules included in the reference set. Higher-order principal components were also linked to dynamic features between different tethered antibody-like molecules and contributed to decisions around candidate selection. The reference set provides a basis to characterize molecules with unknown solution behavior and is sensitive to the behavior of a molecule formulated under different conditions. The approach is independent of protein design, scaffold, formulation and provides a facile method to quantify solution behavior.
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Affiliation(s)
- David Ban
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Cory T Rice
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Mark A McCoy
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
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5
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Kinetic Constraints in the Specific Interaction between Phosphorylated Ubiquitin and Proteasomal Shuttle Factors. Biomolecules 2021; 11:biom11071008. [PMID: 34356632 PMCID: PMC8301994 DOI: 10.3390/biom11071008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Ubiquitin (Ub) specifically interacts with the Ub-associating domain (UBA) in a proteasomal shuttle factor, while the latter is involved in either proteasomal targeting or self-assembly coacervation. PINK1 phosphorylates Ub at S65 and makes Ub alternate between C-terminally relaxed (pUbRL) and retracted conformations (pUbRT). Using NMR spectroscopy, we show that pUbRL but not pUbRT preferentially interacts with the UBA from two proteasomal shuttle factors Ubqln2 and Rad23A. Yet discriminatorily, Ubqln2-UBA binds to pUb more tightly than Rad23A does and selectively enriches pUbRL upon complex formation. Further, we determine the solution structure of the complex between Ubqln2-UBA and pUbRL and uncover the thermodynamic basis for the stronger interaction. NMR kinetics analysis at different timescales further suggests an indued-fit binding mechanism for pUb-UBA interaction. Notably, at a relatively low saturation level, the dissociation rate of the UBA-pUbRL complex is comparable with the exchange rate between pUbRL and pUbRT. Thus, a kinetic constraint would dictate the interaction between Ub and UBA, thus fine-tuning the functional state of the proteasomal shuttle factors.
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6
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Sanches K, Caruso IP, Almeida FCL, Melo FA. The dynamics of free and phosphopeptide-bound Grb2-SH2 reveals two dynamically independent subdomains and an encounter complex with fuzzy interactions. Sci Rep 2020; 10:13040. [PMID: 32747626 PMCID: PMC7398917 DOI: 10.1038/s41598-020-70034-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/20/2020] [Indexed: 01/18/2023] Open
Abstract
The growth factor receptor-bound protein 2 (Grb2) is a key factor in the regulation of cell survival, proliferation, differentiation, and metabolism. In its structure, the central Src homology 2 (SH2) domain is flanked by two Src homology 3 (SH3). SH2 is the most important domain in the recognition of phosphotyrosines. Here, we present the first dynamical characterization of Grb2-SH2 domain in the free state and in the presence of phosphopeptide EpYINSQV at multiple timescales, which revealed valuable information to the understanding of phophotyrosine sensing mechanism. Grb2-SH2 presented two dynamically independent subdomains, subdomain I involved in pY recognition and subdomain II is the pY + 2 specificity pocket. Under semi-saturated concentrations of pY-pep we observed fuzzy interactions, which led to chemical exchange observed by NMR. This information was used to describe the encounter complex. The association with pY-pep is dynamic, involving fuzzy interactions and multiple conformations of pY-pep with negative and hydrophobic residues, creating an electrostatic-potential that drives the binding of pY-pep. The recognition face is wider than the binding site, with many residues beyond the central SH2 binding site participating in the association complex, which contribute to explain previously reported capability of Grb2 to recognize remote pY.
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Affiliation(s)
- Karoline Sanches
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto, São Paulo, Brazil
| | - Icaro P Caruso
- Institute of Medical Biochemistry - IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto, São Paulo, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry - IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil. .,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fernando A Melo
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto, São Paulo, Brazil.
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7
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Petrović D, Wang X, Strodel B. How accurately do force fields represent protein side chain ensembles? Proteins 2018; 86:935-944. [DOI: 10.1002/prot.25525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/02/2018] [Accepted: 05/14/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Dušan Petrović
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Department of Cell and Molecular Biology; Uppsala University, BMC Box 596; Uppsala, 751 24 Sweden
| | - Xue Wang
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf, Universitätsstraße 1; Düsseldorf, 40225 Germany
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf, Universitätsstraße 1; Düsseldorf, 40225 Germany
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8
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Erman B. A computational model for controlling conformational cooperativity and function in proteins. Proteins 2018; 86:1001-1009. [PMID: 30051502 DOI: 10.1002/prot.25535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/08/2018] [Accepted: 06/02/2018] [Indexed: 01/02/2023]
Abstract
We present a computational model that allows for rapid prediction of correlations among a set of residue pairs when the fluctuations of another set of residues are perturbed. The simple theory presented here is based on the knowledge of the fluctuation covariance matrix only. In this sense, the theory is model independent and therefore universal. Perturbation of any set of fluctuations and the resulting response of the remaining set are calculated using conditional probabilities of a multivariate normal distribution. The model is expected to rapidly and accurately map the consequences of mutations in proteins, as well as allosteric activity and ligand binding. Knowledge of triple correlations of fluctuations of residues i, j, and k, 〈 Δ R i Δ R j Δ R k 〉 emerges as the necessary source of information for controlling residue pairs by perturbing a distant residue. Triple correlations have not received wide attention in literature. Perturbation-response-function relations for ubiquitin (UBQ) are discussed as an example. Covariance matrix for UBQ obtained from the Gaussian Network Model combined with the present computational algorithm is able to reflect the millisecond molecular dynamics correlations and observed NMR results. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Burak Erman
- Department of Chemical and Biological Engineering; Koc University; Sariyer Istanbul Turkey
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9
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Reddy JG, Pratihar S, Ban D, Frischkorn S, Becker S, Griesinger C, Lee D. Simultaneous determination of fast and slow dynamics in molecules using extreme CPMG relaxation dispersion experiments. JOURNAL OF BIOMOLECULAR NMR 2018; 70:1-9. [PMID: 29188417 DOI: 10.1007/s10858-017-0155-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/20/2017] [Indexed: 06/07/2023]
Abstract
Molecular dynamics play a significant role in how molecules perform their function. A critical method that provides information on dynamics, at the atomic level, is NMR-based relaxation dispersion (RD) experiments. RD experiments have been utilized for understanding multiple biological processes occurring at micro-to-millisecond time, such as enzyme catalysis, molecular recognition, ligand binding and protein folding. Here, we applied the recently developed high-power RD concept to the Carr-Purcell-Meiboom-Gill sequence (extreme CPMG; E-CPMG) for the simultaneous detection of fast and slow dynamics. Using a fast folding protein, gpW, we have shown that previously inaccessible kinetics can be accessed with the improved precision and efficiency of the measurement by using this experiment.
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Affiliation(s)
- Jithender G Reddy
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- NMR & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
| | - Supriya Pratihar
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
| | - Sebastian Frischkorn
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA.
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10
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Ban D, Iconaru LI, Ramanathan A, Zuo J, Kriwacki RW. A Small Molecule Causes a Population Shift in the Conformational Landscape of an Intrinsically Disordered Protein. J Am Chem Soc 2017; 139:13692-13700. [PMID: 28885015 PMCID: PMC5962290 DOI: 10.1021/jacs.7b01380] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Intrinsically disordered proteins (IDPs) have roles in myriad biological processes and numerous human diseases. However, kinetic and amplitude information regarding their ground-state conformational fluctuations has remained elusive. We demonstrate using nuclear magnetic resonance (NMR)-based relaxation dispersion that the D2 domain of p27Kip1, a prototypical IDP, samples multiple discrete, rapidly exchanging conformational states. By combining NMR with mutagenesis and small-angle X-ray scattering (SAXS), we show that these states involve aromatic residue clustering through long-range hydrophobic interactions. Theoretical studies have proposed that small molecules bind promiscuously to IDPs, causing expansion of their conformational landscapes. However, on the basis of previous NMR-based screening results, we show here that compound binding only shifts the populations of states that existed within the ground state of apo p27-D2 without changing the barriers between states. Our results provide atomic resolution insight into how a small molecule binds an IDP and emphasize the need to examine motions on the low microsecond time scale when probing these types of interactions.
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Affiliation(s)
- David Ban
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Luigi I. Iconaru
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Arvind Ramanathan
- Computational Science and Engineering Division, Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Jian Zuo
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, Tennessee 38105, USA
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11
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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12
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Combining experimental and simulation data of molecular processes via augmented Markov models. Proc Natl Acad Sci U S A 2017; 114:8265-8270. [PMID: 28716931 DOI: 10.1073/pnas.1704803114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.
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13
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Lakomek NA, Penzel S, Lends A, Cadalbert R, Ernst M, Meier BH. Microsecond Dynamics in Ubiquitin Probed by Solid-State 15
N NMR Spectroscopy R
1ρ
Relaxation Experiments under Fast MAS (60-110 kHz). Chemistry 2017; 23:9425-9433. [DOI: 10.1002/chem.201701738] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Nils-Alexander Lakomek
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Susanne Penzel
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Alons Lends
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Matthias Ernst
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Beat H. Meier
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
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14
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Ban D, Smith CA, de Groot BL, Griesinger C, Lee D. Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy. Arch Biochem Biophys 2017; 628:81-91. [PMID: 28576576 DOI: 10.1016/j.abb.2017.05.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 12/25/2022]
Abstract
Protein function can be modulated or dictated by the amplitude and timescale of biomolecular motion, therefore it is imperative to study protein dynamics. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique capable of studying timescales of motion that range from those faster than molecular reorientation on the picosecond timescale to those that occur in real-time. Across this entire regime, NMR observables can report on the amplitude of atomic motion, and the kinetics of atomic motion can be ascertained with a wide variety of experimental techniques from real-time to milliseconds and several nanoseconds to picoseconds. Still a four orders of magnitude window between several nanoseconds and tens of microseconds has remained elusive. Here, we highlight new relaxation dispersion NMR techniques that serve to cover this "hidden-time" window up to hundreds of nanoseconds that achieve atomic resolution while studying the molecule under physiological conditions.
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Affiliation(s)
- David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Colin A Smith
- Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077 Germany; Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077 Germany
| | - Bert L de Groot
- Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077 Germany
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077 Germany
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
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15
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Hacisuleyman A, Erman B. Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions. Proteins 2017; 85:1056-1064. [PMID: 28241380 DOI: 10.1002/prot.25272] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/19/2017] [Accepted: 02/12/2017] [Indexed: 11/06/2022]
Abstract
A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence. Proteins 2017; 85:1056-1064. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Aysima Hacisuleyman
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
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16
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Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin. PLoS Comput Biol 2017; 13:e1005319. [PMID: 28095404 PMCID: PMC5283753 DOI: 10.1371/journal.pcbi.1005319] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/31/2017] [Accepted: 12/20/2016] [Indexed: 02/07/2023] Open
Abstract
It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.
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17
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Braun D, Schmollngruber M, Steinhauser O. Towards a complete characterization of the δ-dispersion in dielectric spectroscopy of protein–water systems. Phys Chem Chem Phys 2017; 19:26980-26985. [DOI: 10.1039/c7cp05216b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The δ-process in dielectric spectroscopy of protein–water systems is computationally analyzed in great detail, in relation to other experiments.
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Affiliation(s)
- Daniel Braun
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- 1090 Vienna
- Austria
| | - Michael Schmollngruber
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- 1090 Vienna
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- 1090 Vienna
- Austria
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18
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Olsson S, Noé F. Mechanistic Models of Chemical Exchange Induced Relaxation in Protein NMR. J Am Chem Soc 2016; 139:200-210. [DOI: 10.1021/jacs.6b09460] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Simon Olsson
- Computational Molecular
Biology,
FB Mathematik und Informatik, Freie Universität Berlin, Berlin 14195, Germany
| | - Frank Noé
- Computational Molecular
Biology,
FB Mathematik und Informatik, Freie Universität Berlin, Berlin 14195, Germany
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19
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The Dynamic Basis for Signal Propagation in Human Pin1-WW. Structure 2016; 24:1464-75. [PMID: 27499442 DOI: 10.1016/j.str.2016.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/11/2016] [Accepted: 06/14/2016] [Indexed: 12/23/2022]
Abstract
Allostery is the structural manifestation of information transduction in biomolecules. Its hallmark is conformational change induced by perturbations at a distal site. An increasing body of evidence demonstrates the presence of allostery in very flexible and even disordered proteins, encouraging a thermodynamic description of this phenomenon. Still, resolving such processes at atomic resolution is difficult. Here we establish a protocol to determine atomistic thermodynamic models of such systems using high-resolution solution state nuclear magnetic resonance data and extensive molecular simulations. Using this methodology, we study information transduction in the WW domain of a key cell-cycle regulator Pin1. Pin1 binds promiscuously to phospho-Ser/Thr-Pro motifs, however, disparate structural and dynamic responses have been reported upon binding different ligands. Our model consists of two topologically distinct states whose relative population may be specifically skewed by an incoming ligand. This model provides a canonical basis for the understanding of multi-functionality in Pin1.
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20
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Chakrabarti KS, Ban D, Pratihar S, Reddy JG, Becker S, Griesinger C, Lee D. High-power (1)H composite pulse decoupling provides artifact free exchange-mediated saturation transfer (EST) experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 269:65-69. [PMID: 27240144 DOI: 10.1016/j.jmr.2016.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/16/2016] [Accepted: 05/20/2016] [Indexed: 05/25/2023]
Abstract
Exchange-mediated saturation transfer (EST) provides critical information regarding dynamics of molecules. In typical applications EST is studied by either scanning a wide range of (15)N chemical shift offsets where the applied (15)N irradiation field strength is on the order of hundreds of Hertz or, scanning a narrow range of (15)N chemical shift offsets where the applied (15)N irradiation field-strength is on the order of tens of Hertz during the EST period. The (1)H decoupling during the EST delay is critical as incomplete decoupling causes broadening of the EST profile, which could possibly result in inaccuracies of the extracted kinetic parameters and transverse relaxation rates. Currently two different (1)H decoupling schemes have been employed, intermittently applied 180° pulses and composite-pulse-decoupling (CPD), for situations where a wide range, or narrow range of (15)N chemical shift offsets are scanned, respectively. We show that high-power CPD provides artifact free EST experiments, which can be universally implemented regardless of the offset range or irradiation field-strengths.
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Affiliation(s)
- Kalyan S Chakrabarti
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - David Ban
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Supriya Pratihar
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jithender G Reddy
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Donghan Lee
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
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21
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Pratihar S, Sabo TM, Ban D, Fenwick RB, Becker S, Salvatella X, Griesinger C, Lee D. Kinetics of the Antibody Recognition Site in the Third IgG-Binding Domain of Protein G. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Supriya Pratihar
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - T. Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
| | - R. Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Department of Integrative Structural and Computational Biology; Skaggs Institute for Chemical Biology, The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
| | - Stefan Becker
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Barcelona Spain
| | - Christian Griesinger
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - Donghan Lee
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
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22
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Pratihar S, Sabo TM, Ban D, Fenwick RB, Becker S, Salvatella X, Griesinger C, Lee D. Kinetics of the Antibody Recognition Site in the Third IgG-Binding Domain of Protein G. Angew Chem Int Ed Engl 2016; 55:9567-70. [PMID: 27345359 DOI: 10.1002/anie.201603501] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 05/20/2016] [Indexed: 12/31/2022]
Abstract
Protein dynamics occurring on a wide range of timescales play a crucial role in governing protein function. Particularly, motions between the globular rotational correlation time (τc ) and 40 μs (supra-τc window), strongly influence molecular recognition. This supra-τc window was previously hidden, owing to a lack of experimental methods. Recently, we have developed a high-power relaxation dispersion (RD) experiment for measuring kinetics as fast as 4 μs. For the first time, this method, performed under super-cooled conditions, enabled us to detect a global motion in the first β-turn of the third IgG-binding domain of protein G (GB3), which was extrapolated to 371±115 ns at 310 K. Furthermore, the same residues show the plasticity in the model-free residual dipolar coupling (RDC) order parameters and in an ensemble encoding the supra-τc dynamics. This β-turn is involved in antibody binding, exhibiting the potential link of the observed supra-τc motion with molecular recognition.
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Affiliation(s)
- Supriya Pratihar
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
| | - R Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.,Department of Integrative Structural and Computational Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Donghan Lee
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany. .,Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA.
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23
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Lindorff-Larsen K, Maragakis P, Piana S, Shaw DE. Picosecond to Millisecond Structural Dynamics in Human Ubiquitin. J Phys Chem B 2016; 120:8313-20. [DOI: 10.1021/acs.jpcb.6b02024] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Paul Maragakis
- D. E. Shaw Research, New York, New York 10036, United States
| | - Stefano Piana
- D. E. Shaw Research, New York, New York 10036, United States
| | - David E. Shaw
- D. E. Shaw Research, New York, New York 10036, United States
- Department
of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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24
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Allosteric switch regulates protein-protein binding through collective motion. Proc Natl Acad Sci U S A 2016; 113:3269-74. [PMID: 26961002 DOI: 10.1073/pnas.1519609113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Many biological processes depend on allosteric communication between different parts of a protein, but the role of internal protein motion in propagating signals through the structure remains largely unknown. Through an experimental and computational analysis of the ground state dynamics in ubiquitin, we identify a collective global motion that is specifically linked to a conformational switch distant from the binding interface. This allosteric coupling is also present in crystal structures and is found to facilitate multispecificity, particularly binding to the ubiquitin-specific protease (USP) family of deubiquitinases. The collective motion that enables this allosteric communication does not affect binding through localized changes but, instead, depends on expansion and contraction of the entire protein domain. The characterization of these collective motions represents a promising avenue for finding and manipulating allosteric networks.
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25
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Wang H, Hosoda K, Ishii T, Arai R, Kohno T, Terawaki SI, Wakamatsu K. Protein stabilizer, NDSB-195, enhances the dynamics of the β4 -α2 loop of ubiquitin. J Pept Sci 2016; 22:174-80. [PMID: 26856691 DOI: 10.1002/psc.2855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 12/21/2022]
Abstract
Non-detergent sulfobetaines (NDSBs) are a new group of small, synthetic protein stabilizers, which have advantages over classical compatible osmolytes, such as polyol, amines, and amino acids: they do not increase solution viscosity, unlike polyols, and they are zwitterionic at all pH ranges, unlike amines and amino acids. NDSBs also facilitate the crystallization and refolding of proteins. The mechanism whereby NDSBs exhibit such activities, however, remains elusive. To gain insight into this mechanism, we studied, using nuclear magnetic resonance (NMR), the effects of dimethylethylammonium propane sulfonate (NDSB-195) on the dynamics of ubiquitin, on which a wealth of information has been accumulated. By analyzing the line width of amide proton resonances and the transverse relaxation rates of nitrogen atoms, we found that NDSB-195 enhances the microsecond-millisecond dynamics of a β4 -α2 loop of ubiquitin. Although those compounds that enhance protein dynamics are generally considered to destabilize protein molecules, NDSB-195 enhanced the stability of ubiquitin against guanidium chloride denaturation. Thus, the simultaneous enhancement of stability and flexibility by a single compound can be attained.
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Affiliation(s)
- Haimei Wang
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Kazuo Hosoda
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Takeshi Ishii
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Ryo Arai
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Toshiyuki Kohno
- Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Shin-Ichi Terawaki
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Kaori Wakamatsu
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
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26
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Carneiro MG, Reddy JG, Griesinger C, Lee D. Speeding-up exchange-mediated saturation transfer experiments by Fourier transform. JOURNAL OF BIOMOLECULAR NMR 2015; 63:237-244. [PMID: 26350257 DOI: 10.1007/s10858-015-9985-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/02/2015] [Indexed: 06/05/2023]
Abstract
Protein motions over various time scales are crucial for protein function. NMR relaxation dispersion experiments play a key role in explaining these motions. However, the study of slow conformational changes with lowly populated states remained elusive. The recently developed exchange-mediated saturation transfer experiments allow the detection and characterization of such motions, but require extensive measurement time. Here we show that, by making use of Fourier transform, the total acquisition time required to measure an exchange-mediated saturation transfer profile can be reduced by twofold in case that one applies linear prediction. In addition, we demonstrate that the analytical solution for R1ρ experiments can be used for fitting the exchange-mediated saturation transfer profile. Furthermore, we show that simultaneous analysis of exchange-mediated saturation transfer profiles with two different radio-frequency field strengths is required for accurate and precise characterization of the exchange process and the exchanging states.
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Affiliation(s)
- Marta G Carneiro
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical chemistry, Am Fassberg 11, 37077, Goettingen, Germany
| | - Jithender G Reddy
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical chemistry, Am Fassberg 11, 37077, Goettingen, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical chemistry, Am Fassberg 11, 37077, Goettingen, Germany
| | - Donghan Lee
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical chemistry, Am Fassberg 11, 37077, Goettingen, Germany.
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 529 South Jackson Street, Louisville, KY, 40202, USA.
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27
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Sabo TM, Trent JO, Lee D. Population shuffling between ground and high energy excited states. Protein Sci 2015; 24:1714-9. [PMID: 26316263 DOI: 10.1002/pro.2797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/26/2015] [Indexed: 12/14/2022]
Abstract
Stochastic processes powered by thermal energy lead to protein motions traversing time-scales from picoseconds to seconds. Fundamental to protein functionality is the utilization of these dynamics for tasks such as catalysis, folding, and allostery. A hierarchy of motion is hypothesized to connect and synergize fast and slow dynamics toward performing these essential activities. Population shuffling predicts a "top-down" temporal hierarchy, where slow time-scale conformational interconversion leads to a shuffling of the free energy landscape for fast time-scale events. Until now, population shuffling was only applied to interconverting ground states. Here, we extend the framework of population shuffling to be applicable for a system interconverting between low energy ground and high energy excited states, such as the SH3 domain mutants G48M and A39V/N53P/V55L from the Fyn tyrosine kinase, providing another tool for accessing the structural dynamics of high energy excited states. Our results indicate that the higher energy gauche - rotameric state for the leucine χ2 dihedral angle contributes significantly to the distribution of rotameric states in both the major and minor forms of the SH3 domain. These findings are corroborated with unrestrained molecular dynamics (MD) simulations on both the major and minor states of the SH3 domain demonstrating high correlations between experimental and back-calculated leucine χ2 rotameric populations. Taken together, we demonstrate how fast time-scale rotameric side-chain population distributions can be extracted from slow time-scale conformational exchange data further extending the scope and the applicability of the population shuffling model.
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Affiliation(s)
- T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202
| | - John O Trent
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202.,Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany
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28
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Phillips AH, Corn JE. Using protein motion to read, write, and erase ubiquitin signals. J Biol Chem 2015; 290:26437-44. [PMID: 26354440 DOI: 10.1074/jbc.r115.653675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotes use a tiny protein called ubiquitin to send a variety of signals, most often by post-translationally attaching ubiquitins to substrate proteins and to each other, thereby forming polyubiquitin chains. A combination of biophysical, biochemical, and biological studies has shown that complex macromolecular dynamics are central to many aspects of ubiquitin signaling. This review focuses on how equilibrium fluctuations and coordinated motions of ubiquitin itself, the ubiquitin conjugation machinery, and deubiquitinating enzymes enable activity and regulation on many levels, with implications for how such a tiny protein can send so many signals.
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Affiliation(s)
- Aaron H Phillips
- From the Innovative Genomics Initiative, University of California, Berkeley, California 94702
| | - Jacob E Corn
- From the Innovative Genomics Initiative, University of California, Berkeley, California 94702
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29
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Wolf M, Emmert S, Gulich R, Lunkenheimer P, Loidl A. Dynamics of protein hydration water. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:032727. [PMID: 26465518 DOI: 10.1103/physreve.92.032727] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Indexed: 06/05/2023]
Abstract
We present the frequency- and temperature-dependent dielectric properties of lysozyme solutions in a broad concentration regime, measured at subzero temperatures, and compare the results with measurements above the freezing point of water and on hydrated lysozyme powder. Our experiments allow examining the dynamics of unfreezable hydration water in a broad temperature range. The obtained results prove the bimodality of the hydration shell dynamics. In addition, we find indications of a fragile-to-strong transition of hydration water.
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Affiliation(s)
- M Wolf
- Experimental Physics V, Center for Electronic Correlations and Magnetism, University of Augsburg, Universitätsstr. 2, 86135 Augsburg, Germany
| | - S Emmert
- Experimental Physics V, Center for Electronic Correlations and Magnetism, University of Augsburg, Universitätsstr. 2, 86135 Augsburg, Germany
| | - R Gulich
- Experimental Physics V, Center for Electronic Correlations and Magnetism, University of Augsburg, Universitätsstr. 2, 86135 Augsburg, Germany
| | - P Lunkenheimer
- Experimental Physics V, Center for Electronic Correlations and Magnetism, University of Augsburg, Universitätsstr. 2, 86135 Augsburg, Germany
| | - A Loidl
- Experimental Physics V, Center for Electronic Correlations and Magnetism, University of Augsburg, Universitätsstr. 2, 86135 Augsburg, Germany
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30
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Fasshuber HK, Lakomek NA, Habenstein B, Loquet A, Shi C, Giller K, Wolff S, Becker S, Lange A. Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR. Protein Sci 2015; 24:592-8. [PMID: 25644665 DOI: 10.1002/pro.2654] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 01/07/2023]
Abstract
By applying [1-(13) C]- and [2-(13) C]-glucose labeling schemes to the folded globular protein ubiquitin, a strong reduction of spectral crowding and increase in resolution in solid-state NMR (ssNMR) spectra could be achieved. This allowed spectral resonance assignment in a straightforward manner and the collection of a wealth of long-range distance information. A high precision solid-state NMR structure of microcrystalline ubiquitin was calculated with a backbone rmsd of 1.57 to the X-ray structure and 1.32 Å to the solution NMR structure. Interestingly, we can resolve structural heterogeneity as the presence of three slightly different conformations. Structural heterogeneity is most significant for the loop region β1-β2 but also for β-strands β1, β2, β3, and β5 as well as for the loop connecting α1 and β3. This structural polymorphism observed in the solid-state NMR spectra coincides with regions that showed dynamics in solution NMR experiments on different timescales.
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Affiliation(s)
- Hannes Klaus Fasshuber
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany; Institut für Biologie, Humboldt-Universität, zu Berlin, Berlin, Germany
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31
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Jha RK, Strauss CEM. 3D structure analysis of PAKs: A clue to the rational design for affinity reagents and blockers. CELLULAR LOGISTICS 2014; 2:69-77. [PMID: 23162739 PMCID: PMC3490965 DOI: 10.4161/cl.21883] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The p21-activated kinase (PAK) family plays a versatile role in cell signaling by forming a hub of interactions. PAKs bind the GTPases like RAC and CDC42. Their proline-rich motifs bind SH3 adaptor proteins such as PIX and NCK. PAKs display nuclear localization signal sites and a potential Integrin binding site. No fully complete structure of the PAKs has been published; partial 3D structures of the PAK family kinases include portions of the auto-inhibited PAK1, GTPase bound to small peptides from PAKs, and the kinase domains from PAK1 and PAK4–6 (with small ligands in a few cases). This review focuses on exploring the intermolecular interaction regions in these 3D structures and we offer insights on the missing regions in crystal structure of the auto-inhibited PAK1. Understanding and modulation of PAK intermolecular interactions can pave the way for PAK blockers and biosensors.
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Affiliation(s)
- Ramesh K Jha
- Bioscience Division; Los Alamos National Laboratory; Los Alamos, NM USA
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32
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D'Abramo M, Besker N, Chillemi G, Grottesi A. Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges. Front Genet 2014; 5:128. [PMID: 24860596 PMCID: PMC4026744 DOI: 10.3389/fgene.2014.00128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 04/22/2014] [Indexed: 12/26/2022] Open
Abstract
Protein kinases work because their flexibility allows to continuously switch from inactive to active form. Despite the large number of structures experimentally determined in such states, the mechanism of their conformational transitions as well as the transition pathways are not easily to capture. In this regard, computational methods can help to shed light on such an issue. However, due to the intrinsic sampling limitations, much efforts have been done to model in a realistic way the conformational changes occurring in protein kinases. In this review we will address the principal biological achievements and structural aspects in studying kinases conformational transitions and will focus on the main challenges related to computational approaches such as molecular modeling and MD simulations.
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Affiliation(s)
- Marco D'Abramo
- CINECA Rome, Italy ; Dipartimento di Chimica, Sapienza University of Rome Rome, Italy
| | - Neva Besker
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata," Rome, Italy
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33
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Sabo TM, Smith CA, Ban D, Mazur A, Lee D, Griesinger C. ORIUM: optimized RDC-based Iterative and Unified Model-free analysis. JOURNAL OF BIOMOLECULAR NMR 2014; 58:287-301. [PMID: 24013952 PMCID: PMC3982212 DOI: 10.1007/s10858-013-9775-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/23/2013] [Indexed: 05/31/2023]
Abstract
Residual dipolar couplings (RDCs) are NMR parameters that provide both structural and dynamic information concerning inter-nuclear vectors, such as N-H(N) and Cα-Hα bonds within the protein backbone. Two approaches for extracting this information from RDCs are the model free analysis (MFA) (Meiler et al. in J Am Chem Soc 123:6098-6107, 2001; Peti et al. in J Am Chem Soc 124:5822-5833, 2002) and the direct interpretation of dipolar couplings (DIDCs) (Tolman in J Am Chem Soc 124:12020-12030, 2002). Both methods have been incorporated into iterative schemes, namely the self-consistent RDC based MFA (SCRM) (Lakomek et al. in J Biomol NMR 41:139-155, 2008) and iterative DIDC (Yao et al. in J Phys Chem B 112:6045-6056, 2008), with the goal of removing the influence of structural noise in the MFA and DIDC formulations. Here, we report a new iterative procedure entitled Optimized RDC-based Iterative and Unified Model-free analysis (ORIUM). ORIUM unifies theoretical concepts developed in the MFA, SCRM, and DIDC methods to construct a computationally less demanding approach to determine these structural and dynamic parameters. In all schemes, dynamic averaging reduces the actual magnitude of the alignment tensors complicating the determination of the absolute values for the generalized order parameters. To readdress this scaling issue that has been previously investigated (Lakomek et al. in J Biomol NMR 41:139-155, 2008; Salmon et al. in Angew Chem Int Edit 48:4154-4157, 2009), a new method is presented using only RDC data to establish a lower bound on protein motion, bypassing the requirement of Lipari-Szabo order parameters. ORIUM and the new scaling procedure are applied to the proteins ubiquitin and the third immunoglobulin domain of protein G (GB3). Our results indicate good agreement with the SCRM and iterative DIDC approaches and signify the general applicability of ORIUM and the proposed scaling for the extraction of inter-nuclear vector structural and dynamic content.
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Affiliation(s)
- T. Michael Sabo
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Colin A. Smith
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - David Ban
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Adam Mazur
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Donghan Lee
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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34
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Palmer AG. Chemical exchange in biomacromolecules: past, present, and future. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:3-17. [PMID: 24656076 PMCID: PMC4049312 DOI: 10.1016/j.jmr.2014.01.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 05/08/2023]
Abstract
The perspective reviews quantitative investigations of chemical exchange phenomena in proteins and other biological macromolecules using NMR spectroscopy, particularly relaxation dispersion methods. The emphasis is on techniques and applications that quantify the populations, interconversion kinetics, and structural features of sparsely populated conformational states in equilibrium with a highly populated ground state. Applications to folding, molecular recognition, catalysis, and allostery by proteins and nucleic acids are highlighted.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States.
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35
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Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK. Protein conformational populations and functionally relevant substates. Acc Chem Res 2014; 47:149-56. [PMID: 23988159 DOI: 10.1021/ar400084s] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.
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Affiliation(s)
- Arvind Ramanathan
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Andrej Savol
- Joint Carnegie Mellon University−University of Pittsburgh Ph.D Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Virginia Burger
- Joint Carnegie Mellon University−University of Pittsburgh Ph.D Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chakra S. Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pratul K. Agarwal
- Annavitas Biosciences, 2519 Caspian Drive, Knoxville, Tennessee 37932, United States
- Computational Biology Institute, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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36
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Al-Hashimi HM. NMR studies of nucleic acid dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 237:191-204. [PMID: 24149218 PMCID: PMC3984477 DOI: 10.1016/j.jmr.2013.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 08/23/2013] [Indexed: 05/12/2023]
Abstract
Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.
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Affiliation(s)
- Hashim M Al-Hashimi
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.
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37
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Charlier C, Khan SN, Marquardsen T, Pelupessy P, Reiss V, Sakellariou D, Bodenhausen G, Engelke F, Ferrage F. Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry. J Am Chem Soc 2013; 135:18665-72. [PMID: 24228712 PMCID: PMC3865798 DOI: 10.1021/ja409820g] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Understanding
the molecular determinants underlying protein function
requires the characterization of both structure and dynamics at atomic
resolution. Nuclear relaxation rates allow a precise characterization
of protein dynamics at the Larmor frequencies of spins. This usually
limits the sampling of motions to a narrow range of frequencies corresponding
to high magnetic fields. At lower fields one cannot achieve sufficient
sensitivity and resolution in NMR. Here, we use a fast shuttle device
where the polarization builds up and the signals are detected at high
field, while longitudinal relaxation takes place at low fields 0.5
< B0 < 14.1 T. The sample is propelled
over a distance up to 50 cm by a blowgun-like system in about 50 ms.
The analysis of nitrogen-15 relaxation in the protein ubiquitin over
such a wide range of magnetic fields offers unprecedented insights
into molecular dynamics. Some key regions of the protein feature structural
fluctuations on nanosecond time scales, which have so far been overlooked
in high-field relaxation studies. Nanosecond motions in proteins may
have been underestimated by traditional high-field approaches, and
slower supra-τc motions that have no effect on relaxation
may have been overestimated. High-resolution relaxometry thus opens
the way to a quantitative characterization of nanosecond motions in
proteins.
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Affiliation(s)
- Cyril Charlier
- Laboratoire des Biomolécules, Département de Chimie, UMR 7203 CNRS-UPMC-ENS, Ecole Normale Supérieure , 24 Rue Lhomond, 75231 Paris Cedex 05, France
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38
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Ganoth A, Tsfadia Y, Wiener R. Ubiquitin: Molecular modeling and simulations. J Mol Graph Model 2013; 46:29-40. [DOI: 10.1016/j.jmgm.2013.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/18/2023]
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39
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Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. JOURNAL OF BIOMOLECULAR NMR 2013; 57:263-80. [PMID: 24105432 PMCID: PMC3840295 DOI: 10.1007/s10858-013-9787-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/23/2013] [Indexed: 05/21/2023]
Abstract
Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps-μs motions in proteins by solid-state NMR.
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Affiliation(s)
- Jens D. Haller
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), 38027 Grenoble, France
- CEA, DSV, IBS, 38027 Grenoble, France
- CNRS, IBS, 38027 Grenoble, France
| | - Paul Schanda
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), 38027 Grenoble, France
- CEA, DSV, IBS, 38027 Grenoble, France
- CNRS, IBS, 38027 Grenoble, France
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40
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Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy. Molecules 2013; 18:11904-37. [PMID: 24077173 PMCID: PMC6270068 DOI: 10.3390/molecules181011904] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/28/2013] [Accepted: 09/17/2013] [Indexed: 11/16/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-tc window (defined as τ(c) < supra-τ(c) < 40 μs; in which tc is the overall tumbling time of a molecule) from the perspective of local inter-nuclear vector dynamics extracted from residual dipolar couplings (RDCs) and from the perspective of conformational exchange captured by relaxation dispersion measurements (RD). The goal of the first section is to present a detailed analysis of how to extract protein dynamics encoded in RDCs and how to relate this information to protein functionality within the previously inaccessible supra-τ(c) window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τ(c) scale by up to a factor of two (motion up to 25 μs). From the data obtained with these techniques and methodology, the importance of the supra-τ(c) scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τ(c) scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.
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41
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Ban D, Mazur A, Carneiro MG, Sabo TM, Giller K, Koharudin LMI, Becker S, Gronenborn AM, Griesinger C, Lee D. Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2013; 57:73-82. [PMID: 23949308 DOI: 10.1007/s10858-013-9769-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/05/2013] [Indexed: 06/02/2023]
Abstract
Micro-to-millisecond motions of proteins transmit pivotal signals for protein function. A powerful technique for the measurement of these motions is nuclear magnetic resonance spectroscopy. One of the most widely used methodologies for this purpose is the constant-time Carr-Purcell-Meiboom-Gill (CT-CPMG) relaxation dispersion experiment where kinetic and structural information can be obtained at atomic resolution. Extraction of accurate kinetics determined from CT-CPMG data requires refocusing frequencies that are much larger than the nuclei's exchange rate between states. We investigated the effect when fast processes are probed by CT-CPMG experiments via simulation and show that if the intrinsic relaxation rate (R(CT-CPMG)(2,0)) is not known a priori the extraction of accurate kinetics is hindered. Errors on the order of 50 % in the exchange rate are attained when processes become fast, but are minimized to 5 % with a priori (CT-CPMG)(2,0)) information. To alleviate this shortcoming, we developed an experimental scheme probing (CT-CPMG)(2,0)) with large amplitude spin-lock fields, which specifically contains the intrinsic proton longitudinal Eigenrelaxation rate. Our approach was validated with ubiquitin and the Oscillatoria agardhii agglutinin (OAA). For OAA, an underestimation of 66 % in the kinetic rates was observed if (CT-CPMG)(2,0)) is not included during the analysis of CT-CPMG data and result in incorrect kinetics and imprecise amplitude information. This was overcome by combining CT-CPMG with (CT-CPMG)(2,0)) measured with a high power R1ρ experiment. In addition, the measurement of (CT-CPMG)(2,0)) removes the ambiguities in choosing between different models that describe CT-CPMG data.
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Affiliation(s)
- David Ban
- Department for NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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42
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Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling. Proc Natl Acad Sci U S A 2013; 110:11379-84. [PMID: 23801757 DOI: 10.1073/pnas.1302407110] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Ubiquitin is a highly conserved eukaryotic protein that interacts with a diverse set of partners to act as a cellular signaling hub. Ubiquitin's conformational flexibility has been postulated to underlie its multifaceted recognition. Here we use computational and library-based means to interrogate core mutations that modulate the conformational dynamics of human ubiquitin. These ubiquitin variants exhibit increased affinity for the USP14 deubiquitinase, with concomitantly reduced affinity for other deubiquitinases. Strikingly, the kinetics of conformational motion are dramatically slowed in these variants without a detectable change in either the ground state fold or excited state population. These variants can be ligated into substrate-linked chains in vitro and in vivo but cannot solely support growth in eukaryotic cells. Proteomic analyses reveal nearly identical interaction profiles between WT ubiquitin and the variants but identify a small subset of altered interactions. Taken together, these results show that conformational dynamics are critical for ubiquitin-deubiquitinase interactions and imply that the fine tuning of motion has played a key role in the evolution of ubiquitin as a signaling hub.
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43
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Sfriso P, Hospital A, Emperador A, Orozco M. Exploration of conformational transition pathways from coarse-grained simulations. ACTA ACUST UNITED AC 2013; 29:1980-6. [PMID: 23740746 DOI: 10.1093/bioinformatics/btt324] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MOTIVATION A new algorithm to trace conformational transitions in proteins is presented. The method uses discrete molecular dynamics as engine to sample protein conformational space. A multiple minima Go-like potential energy function is used in combination with several enhancing sampling strategies, such as metadynamics, Maxwell Demon molecular dynamics and essential dynamics. The method, which shows an unprecedented computational efficiency, is able to trace a wide range of known experimental transitions. Contrary to simpler methods our strategy does not introduce distortions in the chemical structure of the protein and is able to reproduce well complex non-linear conformational transitions. The method, called GOdMD, can easily introduce additional restraints to the transition (presence of ligand, known intermediate, known maintained contacts, …) and is freely distributed to the community through the Spanish National Bioinformatics Institute (http://mmb.irbbarcelona.org/GOdMD). AVAILABILITY Freely available on the web at http://mmb.irbbarcelona.org/GOdMD.
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Affiliation(s)
- Pedro Sfriso
- Institute for Research in Biomedicine (IRB Barcelona), Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10, Barcelona, Spain
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44
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45
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46
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Pons C, Fenwick RB, Esteban-Martín S, Salvatella X, Fernandez-Recio J. Validated Conformational Ensembles Are Key for the Successful Prediction of Protein Complexes. J Chem Theory Comput 2013; 9:1830-7. [DOI: 10.1021/ct300990h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carles Pons
- Joint BSC-IRB research programme
in Computational Biology, Barcelona Supercomputing Center (BSC), Jordi Girona 29, Barcelona 08034, Spain
- Computational Bioinformatics, National Institute of Bioinformatics (INB), Jordi Girona
29, Barcelona 08034, Spain
| | - R. Bryn Fenwick
- Joint BSC-IRB Research Programme
in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona,
Spain
| | - Santiago Esteban-Martín
- Joint BSC-IRB research programme
in Computational Biology, Barcelona Supercomputing Center (BSC), Jordi Girona 29, Barcelona 08034, Spain
- Joint BSC-IRB Research Programme
in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona,
Spain
| | - Xavier Salvatella
- Joint BSC-IRB Research Programme
in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona,
Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain
| | - Juan Fernandez-Recio
- Joint BSC-IRB research programme
in Computational Biology, Barcelona Supercomputing Center (BSC), Jordi Girona 29, Barcelona 08034, Spain
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47
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Case DA. Chemical shifts in biomolecules. Curr Opin Struct Biol 2013; 23:172-6. [PMID: 23422068 DOI: 10.1016/j.sbi.2013.01.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/14/2013] [Accepted: 01/22/2013] [Indexed: 11/30/2022]
Abstract
NMR chemical shifts are sensitive probes of structure and dynamics in proteins. Empirical models, based on a large database of measured shifts, take an input structure and provide increasingly accurate estimates of the corresponding shifts. Quantum chemical calculations can provide the same information, with greater generality but (currently) with less accuracy. These methods are now providing new ways to approach NMR structure determination, and new insights into the conformational dynamics of proteins.
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Affiliation(s)
- David A Case
- Department of Chemistry & Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA.
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48
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Malovichko MV, Sabo TM, Maurer MC. Ligand binding to anion-binding exosites regulates conformational properties of thrombin. J Biol Chem 2013; 288:8667-8678. [PMID: 23378535 DOI: 10.1074/jbc.m112.410829] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thrombin participates in coagulation, anticoagulation, and initiation of platelet activation. To fulfill its diverse roles and maintain hemostasis, this serine protease is regulated via the extended active site region and anion-binding exosites (ABEs) I and II. For the current project, amide proton hydrogen-deuterium exchange coupled with MALDI-TOF mass spectrometry was used to characterize ligand binding to individual exosites and to investigate the presence of exosite-active site and exosite-exosite interactions. PAR3(44-56) and PAR1(49-62) were observed to bind to thrombin ABE I and then to exhibit long range effects over to ABE II. By contrast, Hirudin(54-65) focused more on ABE I and did not transmit influences over to ABE II. Although these three ligands were each directed to ABE I, they did not promote the same conformational consequences. D-Phe-Pro-Arg-chloromethyl ketone inhibition at the thrombin active site led to further local and long range consequences to thrombin-ABE I ligand complexes with the autolysis loop often most affected. When Hirudin(54-65) was bound to ABE I, it was still possible to bind GpIbα(269-286) or fibrinogen γ'(410-427) to ABE II. Each ligand exerted its predominant influences on thrombin and also allowed interexosite communication. The results obtained support the proposal that thrombin is a highly dynamic protein. The transmission of ligand-specific local and long range conformational events is proposed to help regulate this multifunctional enzyme.
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Affiliation(s)
| | - T Michael Sabo
- Chemistry Department, University of Louisville, Louisville, Kentucky 40292
| | - Muriel C Maurer
- Chemistry Department, University of Louisville, Louisville, Kentucky 40292.
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49
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Tollinger M, Sivertsen A, Meier BH, Ernst M, Schanda P. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. J Am Chem Soc 2012; 134:14800-7. [PMID: 22908968 PMCID: PMC3557925 DOI: 10.1021/ja303591y] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Indexed: 02/04/2023]
Abstract
We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr-Purcell-Meiboom-Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers.
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Affiliation(s)
- Martin Tollinger
- Institut für Organische
Chemie, Universität Innsbruck, 6020
Innsbruck, Austria
| | - Astrid
C. Sivertsen
- CEA, Institut de Biologie Structurale
Jean-Pierre Ebel, 41 rue Jules
Horowitz, 38027 Grenoble Cedex 1, France
- CNRS, Institut
de Biologie Structurale Jean-Pierre Ebel, Grenoble, 41 rue Jules Horowitz,
38027 Grenoble Cedex 1, France
- Université
Joseph Fourier−Grenoble 1, Institut de Biologie
Structurale Jean-Pierre Ebel, Grenoble, 41 rue Jules Horowitz, 38027
Grenoble Cedex 1, France
| | - Beat H. Meier
- Physical
Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093
Zürich, Switzerland
| | - Matthias Ernst
- Physical
Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093
Zürich, Switzerland
| | - Paul Schanda
- CEA, Institut de Biologie Structurale
Jean-Pierre Ebel, 41 rue Jules
Horowitz, 38027 Grenoble Cedex 1, France
- CNRS, Institut
de Biologie Structurale Jean-Pierre Ebel, Grenoble, 41 rue Jules Horowitz,
38027 Grenoble Cedex 1, France
- Université
Joseph Fourier−Grenoble 1, Institut de Biologie
Structurale Jean-Pierre Ebel, Grenoble, 41 rue Jules Horowitz, 38027
Grenoble Cedex 1, France
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50
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Sfriso P, Emperador A, Orellana L, Hospital A, Gelpí JL, Orozco M. Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations. J Chem Theory Comput 2012; 8:4707-18. [DOI: 10.1021/ct300494q] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pedro Sfriso
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
| | - Agusti Emperador
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
| | - Laura Orellana
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
| | - Adam Hospital
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
- Structural Bioinformatics Node,
Instituto Nacional De Bioinformática, Institute of Research
in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain
| | - Josep Lluis Gelpí
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
- Computational Bioinformatics Node,
Instituto Nacional De Bioinformática, Barcelona Supercomputing
Center, Jordi Girona 29, Barcelona, 08034, Spain
- Departament de Bioquímica,
Facultat de Biologia, Universtitat de Barcelona, Avgda Diagonal 647,
Barcelona, 08028, Spain
| | - Modesto Orozco
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
- Structural Bioinformatics Node,
Instituto Nacional De Bioinformática, Institute of Research
in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain
- Departament de Bioquímica,
Facultat de Biologia, Universtitat de Barcelona, Avgda Diagonal 647,
Barcelona, 08028, Spain
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