1
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Kao TY, Chiang YW. DEERefiner-assisted structural refinement using pulsed dipolar spectroscopy: a study on multidrug transporter LmrP. Phys Chem Chem Phys 2023; 25:24508-24517. [PMID: 37656008 DOI: 10.1039/d3cp02569a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Pulsed dipolar spectroscopy, such as double electron-electron resonance (DEER), has been underutilized in protein structure determination, despite its ability to provide valuable spatial information. In this study, we present DEERefiner, a user-friendly MATLAB-based GUI program that enables the modeling of protein structures by combining an initial structure and DEER distance restraints. We illustrate the effectiveness of DEERefiner by successfully modeling the ligand-dependent conformational changes of the proton-drug antiporter LmrP to an extracellular-open-like conformation with an impressive precision of 0.76 Å. Additionally, DEERefiner was able to uncover a previously hypothesized but experimentally unresolved proton-dependent conformation of LmrP, characterized as an extracellular-closed/partially intracellular-open conformation, with a precision of 1.16 Å. Our work not only highlights the ability of DEER spectroscopy to model protein structures but also reveals the potential of DEERefiner to advance the field by providing an accessible and applicable tool for precise protein structure modeling, thereby paving the way for deeper insights into protein function.
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Affiliation(s)
- Te-Yu Kao
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan.
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan.
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2
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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3
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NMR Analysis of the Interactions and Conformational Plasticity of Dynein Intermediate Chain. Methods Mol Biol 2023; 2623:241-256. [PMID: 36602690 DOI: 10.1007/978-1-0716-2958-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cytoplasmic dynein complexes play crucial roles in intracellular transport of cellular organelles. While the motor domain of dynein is well characterized by techniques such as X-ray crystallography and cryo-electron microscopy (Cryo-EM), structural representations of dynein usually include only the more packed and easily resolved regions and omit the long flexible and poorly structured regions. One such flexible region is the N-terminal half of the intermediate chain (IC), which contains almost 300 amino acids that are predicted to be disordered. This level of disorder makes IC impossible to study by X-ray crystallography and Cryo-EM, but amenable to study by solution nuclear magnetic resonance (NMR), a powerful technique that can elucidate residue-specific information in a dynamic ensemble of structures, and transient binding interactions of associated proteins. Here, we describe the methods we use to characterize flexible and disordered proteins including protein expression, purification, sample preparation, and NMR data acquisition and analysis.
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4
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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5
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Tugarinov V, Ceccon A, Clore GM. NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:1-24. [PMID: 35282867 PMCID: PMC8921508 DOI: 10.1016/j.pnmrs.2021.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 05/24/2023]
Abstract
A survey, primarily based on work in the authors' laboratory during the last 10 years, is provided of recent developments in NMR studies of exchange processes involving protein-ligand and protein-protein interactions. We start with a brief overview of the theoretical background of Dark state Exchange Saturation Transfer (DEST) and lifetime line-broadening (ΔR2) NMR methodology. Some limitations of the DEST/ΔR2 methodology in applications to molecular systems with intermediate molecular weights are discussed, along with the means of overcoming these limitations with the help of closely related exchange NMR techniques, such as the measurements of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion, exchange-induced chemical shifts or rapidly-relaxing components of relaxation decays. Some theoretical underpinnings of the quantitative description of global dynamics of proteins on the surface of very high molecular weight particles (nanoparticles) are discussed. Subsequently, several applications of DEST/ΔR2 methodology are described from a methodological perspective with an emphasis on providing examples of how kinetic and relaxation parameters for exchanging systems can be reliably extracted from NMR data for each particular model of exchange. Among exchanging systems that are not associated with high molecular weight species, we describe several exchange NMR-based studies that focus on kinetic modelling of transient pre-nucleation oligomerization of huntingtin peptides that precedes aggregation and fibril formation.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
| | - Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
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6
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Villani G. A Time-Dependent Quantum Approach to Allostery and a Comparison With Light-Harvesting in Photosynthetic Phenomenon. Front Mol Biosci 2020; 7:156. [PMID: 33005625 PMCID: PMC7483663 DOI: 10.3389/fmolb.2020.00156] [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] [Received: 02/28/2020] [Accepted: 06/19/2020] [Indexed: 11/26/2022] Open
Abstract
The allosteric effect is one of the most important processes in regulating the function of proteins, and the elucidation of this phenomenon plays a significant role in understanding emergent behaviors in biological regulation. In this process, a perturbation, generated by a ligand in a part of the macromolecule (the allosteric site), moves along this system and reaches a specific (active) site, dozens of Ångströms away, with a great efficiency. The dynamics of this perturbation in the macromolecule can model precisely the allosteric process. In this article, we will be studying the general characteristics of allostery, using a time-dependent quantum approach to obtain rules that apply to this kind of process. Considering the perturbation as a wave that moves within the molecular system, we will characterize the allosteric process with three of the properties of this wave in the active site: (1) ta, the characteristic time for reaching that site, (2) Aa, the amplitude of the wave in this site, and (3) Ba, its corresponding spectral broadening. These three parameters, together with the process mechanism and the perturbation efficiency in the process, can describe the phenomenon. One of the main purposes of this paper is to link the parameters ta, Aa, and Ba and the perturbation efficiency to the characteristics of the system. There is another fundamental process for life that has some characteristics similar to allostery: the light-harvesting (LH) process in photosynthesis. Here, as in allostery, two distant macromolecular sites are involved—two sites dozens of Ångströms away. In both processes, it is particularly important that the perturbation is distributed efficiently without dissipating in the infinite degrees of freedom within the macromolecule. The importance of considering quantum effects in the LH process is well documented in literature, and the quantum coherences are experimentally proven by time-dependent spectroscopic techniques. Given the existing similarities between these two processes in macromolecules, in this work, we suggest using Quantum Mechanics (QM) to study allostery.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici (UOS Pisa) - CNR, Area della Ricerca di Pisa, Pisa, Italy
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7
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Liebau J, Tersa M, Trastoy B, Patrick J, Rodrigo-Unzueta A, Corzana F, Sparrman T, Guerin ME, Mäler L. Unveiling the activation dynamics of a fold-switch bacterial glycosyltransferase by 19F NMR. J Biol Chem 2020; 295:9868-9878. [PMID: 32434931 PMCID: PMC7380196 DOI: 10.1074/jbc.ra120.014162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/19/2020] [Indexed: 11/06/2022] Open
Abstract
Fold-switch pathways remodel the secondary structure topology of proteins in response to the cellular environment. It is a major challenge to understand the dynamics of these folding processes. Here, we conducted an in-depth analysis of the α-helix–to–β-strand and β-strand–to–α-helix transitions and domain motions displayed by the essential mannosyltransferase PimA from mycobacteria. Using 19F NMR, we identified four functionally relevant states of PimA that coexist in dynamic equilibria on millisecond-to-second timescales in solution. We discovered that fold-switching is a slow process, on the order of seconds, whereas domain motions occur simultaneously but are substantially faster, on the order of milliseconds. Strikingly, the addition of substrate accelerated the fold-switching dynamics of PimA. We propose a model in which the fold-switching dynamics constitute a mechanism for PimA activation.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Montse Tersa
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Beatriz Trastoy
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Joan Patrick
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ane Rodrigo-Unzueta
- Departamento de Bioquímica and Instituto Biofisika, Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Bizkaia, Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, Logroño, Spain
| | | | - Marcelo E Guerin
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain .,Departamento de Bioquímica and Instituto Biofisika, Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden .,Department of Chemistry, Umeå University, Umeå, Sweden
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8
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Miao Q, Liu WM, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019; 58:13093-13100. [PMID: 31314159 PMCID: PMC6771572 DOI: 10.1002/anie.201906049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/15/2019] [Indexed: 01/20/2023]
Abstract
Synthetic metal complexes can be used as paramagnetic probes for the study of proteins and protein complexes. Herein, two transition metal NMR probes (TraNPs) are reported. TraNPs are attached through two arms to a protein to generate a pseudocontact shift (PCS) using cobalt(II), or paramagnetic relaxation enhancement (PRE) with manganese(II). The PCS analysis of TraNPs attached to three different proteins shows that the size of the anisotropic component of the magnetic susceptibility depends on the probe surroundings at the surface of the protein, contrary to what is observed for lanthanoid‐based probes. The observed PCS are relatively small, making cobalt‐based probes suitable for localized studies, such as of an active site. The obtained PREs are stronger than those obtained with nitroxide spin labels and the possibility to generate both PCS and PRE offers advantages. The properties of TraNPs in comparison with other cobalt‐based probes are discussed.
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Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wei-Min Liu
- Department of Chemistry, Fu Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New, Taipei City, 24205, Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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9
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Miao Q, Liu W, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double‐Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Wei‐Min Liu
- Department of Chemistry Fu Jen Catholic University No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205 Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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10
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Zarbafian S, Moghadasi M, Roshandelpoor A, Nan F, Li K, Vakli P, Vajda S, Kozakov D, Paschalidis IC. Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes. Sci Rep 2018; 8:5896. [PMID: 29650980 PMCID: PMC5955889 DOI: 10.1038/s41598-018-23982-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/21/2018] [Indexed: 01/18/2023] Open
Abstract
We propose a novel stochastic global optimization algorithm with applications to the refinement stage of protein docking prediction methods. Our approach can process conformations sampled from multiple clusters, each roughly corresponding to a different binding energy funnel. These clusters are obtained using a density-based clustering method. In each cluster, we identify a smooth “permissive” subspace which avoids high-energy barriers and then underestimate the binding energy function using general convex polynomials in this subspace. We use the underestimator to bias sampling towards its global minimum. Sampling and subspace underestimation are repeated several times and the conformations sampled at the last iteration form a refined ensemble. We report computational results on a comprehensive benchmark of 224 protein complexes, establishing that our refined ensemble significantly improves the quality of the conformations of the original set given to the algorithm. We also devise a method to enhance the ensemble from which near-native models are selected.
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Affiliation(s)
- Shahrooz Zarbafian
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Mohammad Moghadasi
- Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Athar Roshandelpoor
- Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Feng Nan
- Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Keyong Li
- Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Pirooz Vakli
- Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America.,Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America.
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America.
| | - Ioannis Ch Paschalidis
- Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America. .,Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America. .,Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America. .,8 Saint Mary's St., Boston, MA, 02215, United States of America.
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11
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Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations. Int J Mol Sci 2018; 19:ijms19030916. [PMID: 29558421 PMCID: PMC5877777 DOI: 10.3390/ijms19030916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/15/2018] [Accepted: 03/17/2018] [Indexed: 12/17/2022] Open
Abstract
A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.
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12
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Olivieri C, Subrahmanian MV, Xia Y, Kim J, Porcelli F, Veglia G. Simultaneous detection of intra- and inter-molecular paramagnetic relaxation enhancements in protein complexes. JOURNAL OF BIOMOLECULAR NMR 2018; 70:133-140. [PMID: 29396770 PMCID: PMC6029865 DOI: 10.1007/s10858-018-0165-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/19/2018] [Indexed: 05/16/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) measurements constitute a powerful approach for detecting both permanent and transient protein-protein interactions. Typical PRE experiments require an intrinsic or engineered paramagnetic site on one of the two interacting partners; while a second, diamagnetic binding partner is labeled with stable isotopes (15N or 13C). Multiple paramagnetic labeled centers or reversed labeling schemes are often necessary to obtain sufficient distance restraints to model protein-protein complexes, making this approach time consuming and expensive. Here, we show a new strategy that combines a modified pulse sequence (1HN-Γ2-CCLS) with an asymmetric labeling scheme to enable the detection of both intra- and inter-molecular PREs simultaneously using only one sample preparation. We applied this strategy to the non-covalent dimer of ubiquitin. Our method confirmed the previously identified binding interface for the transient di-ubiquitin complex, and at the same time, unveiled the internal structural dynamics rearrangements of ubiquitin upon interaction. In addition to reducing the cost of sample preparation and speed up PRE measurements, by detecting the intra-molecular PRE this new strategy will make it possible to measure and calibrate inter-molecular distances more accurately for both symmetric and asymmetric protein-protein complexes.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- DIBAF - University of Tuscia - Largo dell'Università, Blocco D, 01100, Viterbo, Italy
| | - Manu Veliparambil Subrahmanian
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
| | - Youlin Xia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jonggul Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- Department of Chemistry, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
| | - Fernando Porcelli
- DIBAF - University of Tuscia - Largo dell'Università, Blocco D, 01100, Viterbo, Italy
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA.
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13
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Identification of productive and futile encounters in an electron transfer protein complex. Proc Natl Acad Sci U S A 2017; 114:E1840-E1847. [PMID: 28223532 DOI: 10.1073/pnas.1616813114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Well-defined, stereospecific states in protein complexes are often in exchange with an ensemble of more dynamic orientations: the encounter states. The structure of the stereospecific complex between cytochrome P450cam and putidaredoxin was solved recently by X-ray diffraction as well as paramagnetic NMR spectroscopy. Other than the stereospecific complex, the NMR data clearly show the presence of additional states in the complex in solution. In these encounter states, populated for a small percentage of the time, putidaredoxin assumes multiple orientations and samples a large part of the surface of cytochrome P450cam. To characterize the nature of the encounter states, an extensive paramagnetic NMR dataset has been analyzed using the Maximum Occurrence of Regions methodology. The analysis reveals the location and maximal spatial extent of the additional states needed to fully explain the NMR data. Under the assumption of sparsity of the size of the conformational ensemble, several minor states can be located quite precisely. The distribution of these minor states correlates with the electrostatic potential map around cytochrome P450cam. Whereas some minor states are on isolated positively charged patches, others are connected to the stereospecific site via positively charged paths. The existence of electrostatically favorable pathways between the stereospecific interaction site and the different minor states or lack thereof suggests a means to discriminate between productive and futile encounter states.
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14
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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15
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Schueler-Furman O, Wodak SJ. Computational approaches to investigating allostery. Curr Opin Struct Biol 2016; 41:159-171. [PMID: 27607077 DOI: 10.1016/j.sbi.2016.06.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 06/23/2016] [Indexed: 01/01/2023]
Abstract
Allosteric regulation plays a key role in many biological processes, such as signal transduction, transcriptional regulation, and many more. It is rooted in fundamental thermodynamic and dynamic properties of macromolecular systems that are still poorly understood and are moreover modulated by the cellular context. Here we review the computational approaches used in the investigation of allosteric processes in protein systems. We outline how the models of allostery have evolved from their initial formulation in the sixties to the current views, which more fully account for the roles of the thermodynamic and dynamic properties of the system. We then describe the major classes of computational approaches employed to elucidate the mechanisms of allostery, the insights they have provided, as well as their limitations. We complement this analysis by highlighting the role of computational approaches in promising practical applications, such as the engineering of regulatory modules and identifying allosteric binding sites.
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Affiliation(s)
- Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University, Hadassah Medical School, POB 12272, Jerusalem 91120, Israel
| | - Shoshana J Wodak
- VIB Structural Biology Research Center, VUB, Pleinlaan 2, 1050 Brussels, Belgium.
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16
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Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. J Mol Biol 2016; 428:2943-64. [PMID: 27255863 PMCID: PMC4976022 DOI: 10.1016/j.jmb.2016.05.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 05/19/2016] [Accepted: 05/24/2016] [Indexed: 11/17/2022]
Abstract
Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field.
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Affiliation(s)
- Wonpil Im
- Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66047, United States.
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, United States.
| | - Arthur Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, United States.
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States.
| | - Ilya A Vakser
- Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66047, United States.
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17
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Venditti V, Egner TK, Clore GM. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering. Chem Rev 2016; 116:6305-22. [PMID: 26739383 PMCID: PMC5590664 DOI: 10.1021/acs.chemrev.5b00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Solving structures or structural ensembles of large macromolecular systems in solution poses a challenging problem. While NMR provides structural information at atomic resolution, increased spectral complexity, chemical shift overlap, and short transverse relaxation times (associated with slow tumbling) render application of the usual techniques that have been so successful for medium sized systems (<50 kDa) difficult. Solution X-ray scattering, on the other hand, is not limited by molecular weight but only provides low resolution structural information related to the overall shape and size of the system under investigation. Here we review how combining atomic resolution structures of smaller domains with sparse experimental data afforded by NMR residual dipolar couplings (which yield both orientational and shape information) and solution X-ray scattering data in rigid-body simulated annealing calculations provides a powerful approach for investigating the structural aspects of conformational dynamics in large multidomain proteins. The application of this hybrid methodology is illustrated for the 128 kDa dimer of bacterial Enzyme I which exists in a variety of open and closed states that are sampled at various points in the catalytic cycles, and for the capsid protein of the human immunodeficiency virus.
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Affiliation(s)
- Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Timothy K. Egner
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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18
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Tuncbag N, Gursoy A, Keskin O, Nussinov R. The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology. Expert Rev Proteomics 2016; 13:447-9. [PMID: 27104235 PMCID: PMC4938151 DOI: 10.1080/14789450.2016.1182023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nurcan Tuncbag
- Middle East Technical University, Graduate School of Informatics, Department of Health Informatics, Ankara, Turkey
| | - Attila Gursoy
- Koc University, Center for Computational Biology and Bioinformatics, Istanbul, Turkey
- Koc University, Computer Engineering, College of Engineering, Istanbul, Turkey
| | - Ozlem Keskin
- Koc University, Center for Computational Biology and Bioinformatics, Istanbul, Turkey
- Koc University, Computer Engineering, College of Engineering, Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, Maryland, United States
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, Israel
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19
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Liu Z, Casey TM, Blackburn ME, Huang X, Pham L, de Vera IMS, Carter JD, Kear-Scott JL, Veloro AM, Galiano L, Fanucci GE. Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts. Phys Chem Chem Phys 2016; 18:5819-31. [PMID: 26489725 PMCID: PMC4758878 DOI: 10.1039/c5cp04556h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The conformational landscape of HIV-1 protease (PR) can be experimentally characterized by pulsed-EPR double electron-electron resonance (DEER). For this characterization, nitroxide spin labels are attached to an engineered cysteine residue in the flap region of HIV-1 PR. DEER distance measurements from spin-labels contained within each flap of the homodimer provide a detailed description of the conformational sampling of apo-enzyme as well as induced conformational shifts as a function of inhibitor binding. The distance distribution profiles are further interpreted in terms of a conformational ensemble scheme that consists of four unique states termed "curled/tucked", "closed", "semi-open" and "wide-open" conformations. Reported here are the DEER results for a drug-resistant variant clinical isolate sequence, V6, in the presence of FDA approved protease inhibitors (PIs) as well as a non-hydrolyzable substrate mimic, CaP2. Results are interpreted in the context of the current understanding of the relationship between conformational sampling, drug resistance, and kinetic efficiency of HIV-1PR as derived from previous DEER and kinetic data for a series of HIV-1PR constructs that contain drug-pressure selected mutations or natural polymorphisms. Specifically, these collective results support the notion that inhibitor-induced closure of the flaps correlates with inhibitor efficiency and drug resistance. This body of work also suggests DEER as a tool for studying conformational sampling in flexible enzymes as it relates to function.
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Affiliation(s)
- Zhanglong Liu
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Thomas M Casey
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Mandy E Blackburn
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Xi Huang
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Linh Pham
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Ian Mitchelle S de Vera
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Jeffrey D Carter
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Jamie L Kear-Scott
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Angelo M Veloro
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Luis Galiano
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
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20
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Zhang L, Jiang H, Sheong F, Pardo-Avila F, Cheung PH, Huang X. Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands. Methods Enzymol 2016; 578:343-71. [DOI: 10.1016/bs.mie.2016.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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Chen JL, Yang Y, Zhang LL, Liang H, Huber T, Su XC, Otting G. Analysis of the solution conformations of T4 lysozyme by paramagnetic NMR spectroscopy. Phys Chem Chem Phys 2016; 18:5850-9. [DOI: 10.1039/c5cp07196h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paramagnetic data show that the average structure of T4-lysozyme in solution is more open than its crystal structure.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry
- The Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry
- The Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Lin-Lin Zhang
- State Key Laboratory of Elemento-organic Chemistry
- The Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Haobo Liang
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Thomas Huber
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry
- The Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Gottfried Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
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22
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The low-affinity complex of cytochrome c and its peroxidase. Nat Commun 2015; 6:7073. [PMID: 25944250 PMCID: PMC4432590 DOI: 10.1038/ncomms8073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/30/2015] [Indexed: 01/07/2023] Open
Abstract
The complex of yeast cytochrome c peroxidase and cytochrome c is a paradigm of the biological electron transfer (ET). Building on seven decades of research, two different models have been proposed to explain its functional redox activity. One postulates that the intermolecular ET occurs only in the dominant, high-affinity protein–protein orientation, while the other posits formation of an additional, low-affinity complex, which is much more active than the dominant one. Unlike the high-affinity interaction—extensively studied by X-ray crystallography and NMR spectroscopy—until now the binding of cytochrome c to the low-affinity site has not been observed directly, but inferred mainly from kinetics experiments. Here we report the structure of this elusive, weak protein complex and show that it consists of a dominant, inactive bound species and an ensemble of minor, ET-competent protein–protein orientations, which summarily account for the experimentally determined value of the ET rate constant. The redox activity of cytochrome c in complex with its peroxidase has been rationalized by two possible models; a readily observable high-affinity complex and a more elusive but potentially more active low-affinity complex. Here, the authors provide an NMR-based structural mapping of this low-affinity complex.
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Abstract
Myriad biological processes proceed through states that defy characterization by conventional atomic-resolution structural biological methods. The invisibility of these 'dark' states can arise from their transient nature, low equilibrium population, large molecular weight, and/or heterogeneity. Although they are invisible, these dark states underlie a range of processes, acting as encounter complexes between proteins and as intermediates in protein folding and aggregation. New methods have made these states accessible to high-resolution analysis by nuclear magnetic resonance (NMR) spectroscopy, as long as the dark state is in dynamic equilibrium with an NMR-visible species. These methods - paramagnetic NMR, relaxation dispersion, saturation transfer, lifetime line broadening, and hydrogen exchange - allow the exploration of otherwise invisible states in exchange with a visible species over a range of timescales, each taking advantage of some unique property of the dark state to amplify its effect on a particular NMR observable. In this review, we introduce these methods and explore two specific techniques - paramagnetic relaxation enhancement and dark state exchange saturation transfer - in greater detail.
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Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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24
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Nussinov R, Tsai CJ, Liu J. Principles of allosteric interactions in cell signaling. J Am Chem Soc 2014; 136:17692-701. [PMID: 25474128 PMCID: PMC4291754 DOI: 10.1021/ja510028c] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 02/07/2023]
Abstract
Linking cell signaling events to the fundamental physicochemical basis of the conformational behavior of single molecules and ultimately to cellular function is a key challenge facing the life sciences. Here we outline the emerging principles of allosteric interactions in cell signaling, with emphasis on the following points. (1) Allosteric efficacy is not a function of the chemical composition of the allosteric pocket but reflects the extent of the population shift between the inactive and active states. That is, the allosteric effect is determined by the extent of preferred binding, not by the overall binding affinity. (2) Coupling between the allosteric and active sites does not decide the allosteric effect; however, it does define the propagation pathways, the allosteric binding sites, and key on-path residues. (3) Atoms of allosteric effectors can act as "driver" or "anchor" and create attractive "pulling" or repulsive "pushing" interactions. Deciphering, quantifying, and integrating the multiple co-occurring events present daunting challenges to our scientific community.
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Affiliation(s)
- Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler
Institute of Molecular Medicine, Department of Human Genetics and
Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jin Liu
- Department
of Biophysics, University of Texas Southwestern
Medical Center, 5323
Harry Hines Boulevard, Dallas, Texas 75390, United
States
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
and Center for Scientific Computation, Southern
Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275, United
States
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25
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Bashir Q, Meulenbroek EM, Pannu NS, Ubbink M. Engineering specificity in a dynamic protein complex with a single conserved mutation. FEBS J 2014; 281:4892-905. [DOI: 10.1111/febs.13028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Qamar Bashir
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | | | - Navraj S. Pannu
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
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26
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Carter JD, Mathias JD, Gomez EF, Ran Y, Xu F, Galiano L, Tran NQ, D'Amore PW, Wright CS, Chakravorty DK, Fanucci GE. Characterizing solution surface loop conformational flexibility of the GM2 activator protein. J Phys Chem B 2014; 118:10607-17. [PMID: 25127419 PMCID: PMC4161144 DOI: 10.1021/jp505938t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
GM2AP
has a β-cup topology with numerous X-ray structures
showing multiple conformations for some of the surface loops, revealing
conformational flexibility that may be related to function, where
function is defined as either membrane binding associated with ligand
binding and extraction or interaction with other proteins. Here, site-directed
spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy
and molecular dynamic (MD) simulations are used to characterize the
mobility and conformational flexibility of various structural regions
of GM2AP. A series of 10 single cysteine amino acid substitutions
were generated, and the constructs were chemically modified with the
methanethiosulfonate spin label. Continuous wave (CW) EPR line shapes
were obtained and subsequently simulated using the microscopic order
macroscopic disorder (MOMD) program. Line shapes for sites that have
multiple conformations in the X-ray structures required two spectral
components, whereas spectra of the remaining sites were adequately
fit with single-component parameters. For spin labeled sites L126C
and I66C, spectra were acquired as a function of temperature, and
simulations provided for the determination of thermodynamic parameters
associated with conformational change. Binding to GM2 ligand did not
alter the conformational flexibility of the loops, as evaluated by
EPR and NMR spectroscopies. These results confirm that the conformational
flexibility observed in the surface loops of GM2AP crystals is present
in solution and that the exchange is slow on the EPR time scale (>ns).
Furthermore, MD simulation results are presented and agree well with
the conformational heterogeneity revealed by SDSL.
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Affiliation(s)
- Jeffery D Carter
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
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Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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29
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The ensemble nature of allostery. Nature 2014; 508:331-9. [PMID: 24740064 DOI: 10.1038/nature13001] [Citation(s) in RCA: 881] [Impact Index Per Article: 88.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/03/2014] [Indexed: 02/07/2023]
Abstract
Allostery is the process by which biological macromolecules (mostly proteins) transmit the effect of binding at one site to another, often distal, functional site, allowing for regulation of activity. Recent experimental observations demonstrating that allostery can be facilitated by dynamic and intrinsically disordered proteins have resulted in a new paradigm for understanding allosteric mechanisms, which focuses on the conformational ensemble and the statistical nature of the interactions responsible for the transmission of information. Analysis of allosteric ensembles reveals a rich spectrum of regulatory strategies, as well as a framework to unify the description of allosteric mechanisms from different systems.
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30
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Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis IC, Clore GM, Vajda S. Encounter complexes and dimensionality reduction in protein-protein association. eLife 2014; 3:e01370. [PMID: 24714491 PMCID: PMC3978769 DOI: 10.7554/elife.01370] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein–protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition. DOI:http://dx.doi.org/10.7554/eLife.01370.001 Proteins rarely act alone. Instead, they tend to bind to other proteins to form structures known as complexes. When two proteins come together to form a complex, they twist and turn through a series of intermediate states before they form the actual complex. These intermediate states are difficult to study because they don’t last for very long, which means that our knowledge of how complexes are formed remains incomplete. One promising approach for studying the formation of complexes is called paramagnetic relaxation enhancement. In this technique certain areas in one of the proteins are labelled with magnetic particles, which produce signals when the two proteins are close to each other. Repeating the measurement several times with the magnetic particles in different positions provides information about the overall structure of the complex. Computational modelling can then be used to work out the fine details of the structure, including the shapes of the intermediate structures made by the proteins as they interact. A computer method called docking can be used to predict the most favourable positions that the proteins can take, relative to one another, in a complex. This involves calculating the energy contained in the system, with the correct structure having the lowest energy. Docking methods also predict protein models with slightly higher energies, but with structures that are radically different. Modellers usually ignore these structures, but comparing the docking results to paramagnetic relaxation enhancement data, Kozakov et al. found that these structures actually represent the intermediate states. Analysing the structure of the intermediate states revealed that the movement of the two proteins relative to one another is severely restricted as they form the final complex. Kozakov et al. found that proteins associate along preferred pathways, similar to the way a protein slides along DNA in the process of protein-DNA recognition. Knowing that the movement of the proteins is restricted in this way will enable researchers to improve the efficiency of docking calculations. DOI:http://dx.doi.org/10.7554/eLife.01370.002
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Affiliation(s)
- Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston, United States
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31
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Van de Water K, van Nuland NAJ, Volkov AN. Transient protein encounters characterized by paramagnetic NMR. Chem Sci 2014. [DOI: 10.1039/c4sc01232a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multiple encounters, sampled by interacting proteins in search of the dominant, functionally active orientation, are visualized by paramagnetic NMR.
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Affiliation(s)
- K. Van de Water
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
| | - N. A. J. van Nuland
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
| | - A. N. Volkov
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
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Lian LY. NMR studies of weak protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:59-72. [PMID: 23611315 DOI: 10.1016/j.pnmrs.2012.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Accepted: 11/22/2012] [Indexed: 06/02/2023]
Affiliation(s)
- Lu-Yun Lian
- NMR Centre for Structural Biology, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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33
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NMR as a tool to identify and characterize protein folding intermediates. Arch Biochem Biophys 2013; 531:90-9. [DOI: 10.1016/j.abb.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/20/2022]
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Duzdevich D, Greene EC. Towards physiological complexity with in vitro single-molecule biophysics. Philos Trans R Soc Lond B Biol Sci 2012; 368:20120271. [PMID: 23267187 DOI: 10.1098/rstb.2012.0271] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single-molecule biology has matured in recent years, driven to greater sophistication by the development of increasingly advanced experimental techniques. A progressive appreciation for its unique strengths is attracting research that spans an exceptionally broad swath of physiological phenomena--from the function of nucleosomes to protein diffusion in the cell membrane. Newfound enthusiasm notwithstanding, the single-molecule approach is limited to an intrinsically defined set of biological questions; such limitation applies to all experimental approaches, and an explicit statement of the boundaries delineating each set offers a guide to most fruitfully orienting in vitro single-molecule research in the future. Here, we briefly describe a simple conceptual framework to categorize how submolecular, molecular and intracellular processes are studied. We highlight the domain of single-molecule biology in this scheme, with an emphasis on its ability to probe various forms of heterogeneity inherent to populations of discrete biological macromolecules. We then give a general overview of our high-throughput DNA curtain methodology for studying protein-nucleic acid interactions, and by contextualizing it within this framework, we explore what might be the most enticing avenues of future research. We anticipate that a focus on single-molecule biology's unique strengths will suggest a new generation of experiments with greater complexity and more immediately translatable physiological relevance.
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Affiliation(s)
- Daniel Duzdevich
- Department of Biological Sciences, Columbia University, 650 West 168th Street, New York, NY 10032, USA
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Griesinger C, Bennati M, Vieth HM, Luchinat C, Parigi G, Höfer P, Engelke F, Glaser SJ, Denysenkov V, Prisner TF. Dynamic nuclear polarization at high magnetic fields in liquids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 64:4-28. [PMID: 22578315 DOI: 10.1016/j.pnmrs.2011.10.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 10/11/2011] [Indexed: 05/03/2023]
Affiliation(s)
- C Griesinger
- MPI for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
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36
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The binding process of a nonspecific enzyme with DNA. Biophys J 2011; 101:1139-47. [PMID: 21889451 DOI: 10.1016/j.bpj.2011.07.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/20/2011] [Accepted: 07/05/2011] [Indexed: 11/22/2022] Open
Abstract
Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states. We consider the structural and energetic features and the role of water in the DNA grooves in the process of protein-DNA recognition. Here we have used the nuclease domain of colicin E7 (N-ColE7) from Escherichia coli in complex with a 12-bp DNA duplex as the model system to consider how a protein approaches, encounters, and associates with DNA. Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales. We define the encounter states and identified the spatial and orientational aspects. For the molecular length-scales, we used molecular-dynamics simulations. Several intermediate binding states were found, which have different positions and orientations of protein around DNA including major and minor groove orientations. The results show that the contact number and the hydrated interfacial area are measures that facilitate better understanding of sequence-independent protein-DNA binding landscapes and pathways.
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37
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Volkov AN, Nicholls P, Worrall JA. The complex of cytochrome c and cytochrome c peroxidase: The end of the road? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1482-503. [DOI: 10.1016/j.bbabio.2011.07.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 11/25/2022]
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Clore GM. Exploring translocation of proteins on DNA by NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:209-19. [PMID: 21847629 PMCID: PMC3207612 DOI: 10.1007/s10858-011-9555-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
While an extensive body of knowledge has accumulated on the structures of transcription factors, DNA and their complexes from both NMR and crystallography, much less is known at a molecular level regarding the mechanisms whereby transcription factors locate their specific DNA target site within an overwhelming sea of non-specific DNA sites. Indirect kinetic data suggested that three processes are involved in the search procedure: jumping by dissociation of the protein from the DNA followed by re-association at another site, direct transfer from one DNA molecule or segment to another, and one-dimensional sliding. In this brief perspective I summarize recent NMR developments from our laboratory that have permitted direct characterization of the species and molecular mechanisms involved in the target search process, including the detection of highly transient sparsely-populated states. The main tool in these studies involves the application of paramagnetic relaxation enhancement, supplemented by z-exchange spectroscopy, lineshape analysis and residual dipolar couplings. These studies led to the first direct demonstration of rotation-coupled sliding of a protein along the DNA and the direct transfer of a protein from one DNA molecule to another without dissociating into free solution.
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Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 02892-0520, USA.
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39
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Fawzi NL, Fleissner MR, Anthis NJ, Kálai T, Hideg K, Hubbell WL, Clore GM. A rigid disulfide-linked nitroxide side chain simplifies the quantitative analysis of PRE data. JOURNAL OF BIOMOLECULAR NMR 2011; 51:105-14. [PMID: 21947919 PMCID: PMC3489005 DOI: 10.1007/s10858-011-9545-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/22/2011] [Indexed: 05/03/2023]
Abstract
The measurement of (1)H transverse paramagnetic relaxation enhancement (PRE) has been used in biomolecular systems to determine long-range distance restraints and to visualize sparsely-populated transient states. The intrinsic flexibility of most nitroxide and metal-chelating paramagnetic spin-labels, however, complicates the quantitative interpretation of PREs due to delocalization of the paramagnetic center. Here, we present a novel, disulfide-linked nitroxide spin label, R1p, as an alternative to these flexible labels for PRE studies. When introduced at solvent-exposed α-helical positions in two model proteins, calmodulin (CaM) and T4 lysozyme (T4L), EPR measurements show that the R1p side chain exhibits dramatically reduced internal motion compared to the commonly used R1 spin label (generated by reacting cysteine with the spin labeling compound often referred to as MTSL). Further, only a single nitroxide position is necessary to account for the PREs arising from CaM S17R1p, while an ensemble comprising multiple conformations is necessary for those observed for CaM S17R1. Together, these observations suggest that the nitroxide adopts a single, fixed position when R1p is placed at solvent-exposed α-helical positions, greatly simplifying the interpretation of PRE data by removing the need to account for the intrinsic flexibility of the spin label.
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Affiliation(s)
- Nicolas L. Fawzi
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MA 20892-0520, USA
| | - Mark R. Fleissner
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MA 20892-0520, USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, University of Pécs, Szigeti str. 12, 7624 Pécs, Hungary
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, Szigeti str. 12, 7624 Pécs, Hungary
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MA 20892-0520, USA
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40
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Clore GM. Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation. Protein Sci 2011; 20:229-46. [PMID: 21280116 DOI: 10.1002/pro.576] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sparsely populated states of macromolecules, characterized by short lifetimes and high free-energies relative to the predominant ground state, often play a key role in many biological, chemical, and biophysical processes. In this review, we briefly summarize various new developments in NMR spectroscopy that permit these heretofore invisible, sparsely populated states to be detected, characterized, and in some instances visualized. Relaxation dispersion spectroscopy yields detailed kinetic information on processes involving species characterized by distinct chemical shifts with lifetimes in the ∼50 μs-10 ms range and populations as low as 0.5%. In the fast exchange regime (time scale less than ∼250-500 μs), the footprint of sparsely populated states can be observed on paramagnetic relaxation enhancement profiles measured on the resonances of the major species, thereby yielding structural information that is directly related to paramagnetic center-nuclei distances from which it is possible, under suitable circumstances, to compute a structure or ensemble of structures for the minor species. Finally, differential transverse relaxation measurements can be used to detect lifetime broadening effects that directly reflect the unidirectional rates for the conversion of NMR-visible into high-molecular weight NMR-invisible species. Examples of these various approaches are presented.
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Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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41
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Religa TL, Ruschak AM, Rosenzweig R, Kay LE. Site-Directed Methyl Group Labeling as an NMR Probe of Structure and Dynamics in Supramolecular Protein Systems: Applications to the Proteasome and to the ClpP Protease. J Am Chem Soc 2011; 133:9063-8. [DOI: 10.1021/ja202259a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Tomasz L. Religa
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Amy M. Ruschak
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Rina Rosenzweig
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
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42
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Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations. J Am Chem Soc 2010; 132:11487-95. [PMID: 20672804 DOI: 10.1021/ja100867c] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent experimental studies have confirmed a long-held view that protein complex formation proceeds via a short-lived encounter state. The population of this transient intermediate, stabilized mainly by long-range electrostatic interactions, varies among different complexes. Here we show that the occupancy of the encounter state can be modulated across a broad range by single point mutations of interfacial residues. Using a combination of Monte Carlo simulations and paramagnetic relaxation enhancement NMR spectroscopy, we illustrate that it is possible to both enhance and diminish the binding specificity in an electron transfer complex of yeast cytochrome c (Cc) and cytochrome c peroxidase. The Cc T12A mutation decreases the population of the encounter to 10% as compared with 30% in the wild-type complex. More dramatically, the Cc R13A substitution reverses the relative occupancies of the stereospecific and the encounter forms, with the latter now being the dominant species with the population of 80%. This finding indicates that the encounter state can make a large contribution to the stability of a protein complex. Also, it appears that by adjusting the amount of the encounter through a judicious choice of point mutations, we can remodel the energy landscape of a protein complex and tune its binding specificity.
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44
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Volkov AN, Ubbink M, van Nuland NAJ. Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2010; 48:225-36. [PMID: 21049303 PMCID: PMC3235994 DOI: 10.1007/s10858-010-9452-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 09/28/2010] [Indexed: 05/20/2023]
Abstract
Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such transient intermediates in a number of protein-protein and protein-DNA complexes. Here we present an analysis of the recently published PRE NMR data for a protein complex of yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). First, we describe a simple, general method to map out the spatial and temporal distributions of binding geometries constituting the Cc-CcP encounter state. We show that the spatiotemporal mapping provides a reliable estimate of the experimental coverage and, at higher coverage levels, allows to delineate the conformational space sampled by the minor species. To further refine the encounter state, we performed PRE-based ensemble simulations. The generated solutions reproduce well the experimental data and lie within the allowed regions of the encounter maps, confirming the validity of the mapping approach. The refined encounter ensembles are distributed predominantly in a region encompassing the dominant form of the complex, providing experimental proof for the results of classical theoretical simulations.
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Affiliation(s)
- Alexander N Volkov
- Department of Molecular and Cellular Interactions, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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45
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Madl T, Gabel F, Sattler M. NMR and small-angle scattering-based structural analysis of protein complexes in solution. J Struct Biol 2010; 173:472-82. [PMID: 21074620 DOI: 10.1016/j.jsb.2010.11.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 11/01/2010] [Accepted: 11/04/2010] [Indexed: 01/14/2023]
Abstract
Structural analysis of multi-domain protein complexes is a key challenge in current biology and a prerequisite for understanding the molecular basis of essential cellular processes. The use of solution techniques is important for characterizing the quaternary arrangements and dynamics of domains and subunits of these complexes. In this respect solution NMR is the only technique that allows atomic- or residue-resolution structure determination and investigation of dynamic properties of multi-domain proteins and their complexes. As experimental NMR data for large protein complexes are sparse, it is advantageous to combine these data with additional information from other solution techniques. Here, the utility and computational approaches of combining solution state NMR with small-angle X-ray and Neutron scattering (SAXS/SANS) experiments for structural analysis of large protein complexes is reviewed. Recent progress in experimental and computational approaches of combining NMR and SAS are discussed and illustrated with recent examples from the literature. The complementary aspects of combining NMR and SAS data for studying multi-domain proteins, i.e. where weakly interacting domains are connected by flexible linkers, are illustrated with the structural analysis of the tandem RNA recognition motif (RRM) domains (RRM1-RRM2) of the human splicing factor U2AF65 bound to a nine-uridine (U9) RNA oligonucleotide.
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Affiliation(s)
- Tobias Madl
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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46
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Schwieters CD, Suh JY, Grishaev A, Ghirlando R, Takayama Y, Clore GM. Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering. J Am Chem Soc 2010; 132:13026-45. [PMID: 20731394 PMCID: PMC2955445 DOI: 10.1021/ja105485b] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution structures of free Enzyme I (EI, ∼128 kDa, 575 × 2 residues), the first enzyme in the bacterial phosphotransferase system, and its complex with HPr (∼146 kDa) have been solved using novel methodology that makes use of prior structural knowledge (namely, the structures of the dimeric EIC domain and the isolated EIN domain both free and complexed to HPr), combined with residual dipolar coupling (RDC), small- (SAXS) and wide- (WAXS) angle X-ray scattering and small-angle neutron scattering (SANS) data. The calculational strategy employs conjoined rigid body/torsion/Cartesian simulated annealing, and incorporates improvements in calculating and refining against SAXS/WAXS data that take into account complex molecular shapes in the description of the solvent layer resulting in a better representation of the SAXS/WAXS data. The RDC data orient the symmetrically related EIN domains relative to the C(2) symmetry axis of the EIC dimer, while translational, shape, and size information is provided by SAXS/WAXS. The resulting structures are independently validated by SANS. Comparison of the structures of the free EI and the EI-HPr complex with that of the crystal structure of a trapped phosphorylated EI intermediate reveals large (∼70-90°) hinge body rotations of the two subdomains comprising the EIN domain, as well as of the EIN domain relative to the dimeric EIC domain. These large-scale interdomain motions shed light on the structural transitions that accompany the catalytic cycle of EI.
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Affiliation(s)
- Charles D. Schwieters
- Division of Computational Biosciences, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624
| | - Jeong-Yong Suh
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - Alexander Grishaev
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of health, Bethesda, MD 20892-0530, U.S.A
| | - Yuki Takayama
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - G. Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
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47
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Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Q Rev Biophys 2010; 43:295-332. [DOI: 10.1017/s0033583510000119] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractEnergy landscape theories have provided a common ground for understanding the protein folding problem, which once seemed to be overwhelmingly complicated. At the same time, the native state was found to be an ensemble of interconverting states with frustration playing a more important role compared to the folding problem. The landscape of the folded protein – the native landscape – is glassier than the folding landscape; hence, a general description analogous to the folding theories is difficult to achieve. On the other hand, the native basin phase volume is much smaller, allowing a protein to fully sample its native energy landscape on the biological timescales. Current computational resources may also be used to perform this sampling for smaller proteins, to build a ‘topographical map’ of the native landscape that can be used for subsequent analysis. Several major approaches to representing this topographical map are highlighted in this review, including the construction of kinetic networks, hierarchical trees and free energy surfaces with subsequent structural and kinetic analyses. In this review, we extensively discuss the important question of choosing proper collective coordinates characterizing functional motions. In many cases, the substates on the native energy landscape, which represent different functional states, can be used to obtain variables that are well suited for building free energy surfaces and analyzing the protein's functional dynamics. Normal mode analysis can provide such variables in cases where functional motions are dictated by the molecule's architecture. Principal component analysis is a more expensive way of inferring the essential variables from the protein's motions, one that requires a long molecular dynamics simulation. Finally, the two popular models for the allosteric switching mechanism, ‘preexisting equilibrium’ and ‘induced fit’, are interpreted within the energy landscape paradigm as extreme points of a continuum of transition mechanisms. Some experimental evidence illustrating each of these two models, as well as intermediate mechanisms, is presented and discussed.
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48
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Pan Y, Nussinov R. Lysine120 interactions with p53 response elements can allosterically direct p53 organization. PLoS Comput Biol 2010; 6:e1000878. [PMID: 20700496 PMCID: PMC2916859 DOI: 10.1371/journal.pcbi.1000878] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 07/08/2010] [Indexed: 01/02/2023] Open
Abstract
p53 can serve as a paradigm in studies aiming to figure out how allosteric perturbations in transcription factors (TFs) triggered by small changes in DNA response element (RE) sequences, can spell selectivity in co-factor recruitment. p53-REs are 20-base pair (bp) DNA segments specifying diverse functions. They may be located near the transcription start sites or thousands of bps away in the genome. Their number has been estimated to be in the thousands, and they all share a common motif. A key question is then how does the p53 protein recognize a particular p53-RE sequence among all the similar ones? Here, representative p53-REs regulating diverse functions including cell cycle arrest, DNA repair, and apoptosis were simulated in explicit solvent. Among the major interactions between p53 and its REs involving Lys120, Arg280 and Arg248, the bps interacting with Lys120 vary while the interacting partners of other residues are less so. We observe that each p53-RE quarter site sequence has a unique pattern of interactions with p53 Lys120. The allosteric, DNA sequence-induced conformational and dynamic changes of the altered Lys120 interactions are amplified by the perturbation of other p53-DNA interactions. The combined subtle RE sequence-specific allosteric effects propagate in the p53 and in the DNA. The resulting amplified allosteric effects far away are reflected in changes in the overall p53 organization and in the p53 surface topology and residue fluctuations which play key roles in selective co-factor recruitment. As such, these observations suggest how similar p53-RE sequences can spell the preferred co-factor binding, which is the key to the selective gene transactivation and consequently different functional effects.
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Affiliation(s)
- Yongping Pan
- Basic Science Program, Science Applications International Corporation-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Science Applications International Corporation-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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49
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Nocek JM, Knutson AK, Xiong P, Co NP, Hoffman BM. Photoinitiated singlet and triplet electron transfer across a redesigned [myoglobin, cytochrome b5] interface. J Am Chem Soc 2010; 132:6165-75. [PMID: 20392066 PMCID: PMC2868514 DOI: 10.1021/ja100499j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a strategy by which reactive binding of a weakly bound, 'dynamically docked (DD)' complex without a known structure can be strengthened electrostatically through optimized placement of surface charges, and discuss its use in modulating complex formation between myoglobin (Mb) and cytochrome b(5) (b(5)). The strategy employs paired Brownian dynamics (BD) simulations, one which monitors overall binding, the other reactive binding, to examine [X --> K] mutations on the surface of the partners, with a focus on single and multiple [D/E --> K] charge reversal mutations. This procedure has been applied to the [Mb, b(5)] complex, indicating mutations of Mb residues D44, D60, and E85 to be the most promising, with combinations of these showing a nonlinear enhancement of reactive binding. A novel method of displaying BD profiles shows that the 'hits' of b(5) on the surfaces of Mb(WT), Mb(D44K/D60K), and Mb(D44K/D60K/E85K) progressively coalesce into two 'clusters': a 'diffuse' cluster of hits that are distributed over the Mb surface and have negligible electrostatic binding energy and a 'reactive' cluster of hits with considerable stability that are localized near its heme edge, with short Fe-Fe distances favorable to electron transfer (ET). Thus, binding and reactivity progressively become correlated by the mutations. This finding relates to recent proposals that complex formation is a two-step process, proceeding through the formation of a weakly bound encounter complex to a well-defined bound complex. The design procedure has been tested through measurements of photoinitiated ET between the Zn-substituted forms of Mb(WT), Mb(D44K/D60K), and Mb(D44K/D60K/E85K) and Fe(3+)b(5). Both mutants convert the complex from the DD regime exhibited by Mb(WT), in which the transient complex is in fast kinetic exchange with its partners, k(off) >> k(et), to the slow-exchange regime, k(et) >> k(off), and both mutants exhibit rapid intracomplex ET from the triplet excited state to Fe(3+)b(5) (rate constant, k(et) approximately 10(6) s(-1)). The affinity constants of the mutant Mbs cannot be derived through conventional analysis procedures because intracomplex singlet ET quenching causes the triplet-ground absorbance difference to progressively decrease during a titration, but this effect has been incorporated into a new procedure for computing binding constants. Most importantly, these measurements reveal the presence of fast photoinduced singlet ET across the protein-protein interface, (1)k(et) approximately 2 x 10(8) s(-1).
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50
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Religa TL, Sprangers R, Kay LE. Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR. Science 2010; 328:98-102. [PMID: 20360109 DOI: 10.1126/science.1184991] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The proteasome catalyzes the majority of protein degradation in the cell and plays an integral role in cellular homeostasis. Control over proteolysis by the 20S core-particle (CP) proteasome is achieved by gated access of substrate; thus, an understanding of the molecular mechanism by which these gates regulate substrate entry is critical. We used methyl-transverse relaxation optimized nuclear magnetic resonance spectroscopy to show that the amino-terminal residues that compose the gates of the alpha subunits of the Thermoplasma acidophilum proteasome are highly dynamic over a broad spectrum of time scales and that gating termini are in conformations that extend either well inside (closed gate) or outside (open gate) of the antechamber. Interconversion between these conformers on a time scale of seconds leads to a dynamic regulation of 20S CP proteolysis activity.
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Affiliation(s)
- Tomasz L Religa
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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