1
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Bonin JP, Sapienza PJ, Lee AL. Dynamic allostery in substrate binding by human thymidylate synthase. eLife 2022; 11:79915. [PMID: 36200982 PMCID: PMC9536839 DOI: 10.7554/elife.79915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Human thymidylate synthase (hTS) is essential for DNA replication and therefore a therapeutic target for cancer. Effective targeting requires knowledge of the mechanism(s) of regulation of this 72 kDa homodimeric enzyme. Here, we investigate the mechanism of binding cooperativity of the nucleotide substrate. We have employed exquisitely sensitive methyl-based CPMG and CEST NMR experiments enabling us to identify residues undergoing bifurcated linear 3-state exchange, including concerted switching between active and inactive conformations in the apo enzyme. The inactive state is populated to only ~1.3%, indicating that conformational selection contributes negligibly to the cooperativity. Instead, methyl rotation axis order parameters, determined by 2H transverse relaxation rates, suggest that rigidification of the enzyme upon substrate binding is responsible for the entropically-driven cooperativity. Lack of the rigidification in product binding and substrate binding to an N-terminally truncated enzyme, both non-cooperative, support this idea. In addition, the lack of this rigidification in the N-terminal truncation indicates that interactions between the flexible N-terminus and the rest of the protein, which are perturbed by substrate binding, play a significant role in the cooperativity—a novel mechanism of dynamic allostery. Together, these findings yield a rare depth of insight into the substrate binding cooperativity of an essential enzyme.
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Affiliation(s)
- Jeffrey P Bonin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
| | - Andrew L Lee
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
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2
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Chalopin Y, Sparfel J. Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins. Front Mol Biosci 2022; 8:736376. [PMID: 35004841 PMCID: PMC8733615 DOI: 10.3389/fmolb.2021.736376] [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: 07/05/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.
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Affiliation(s)
- Yann Chalopin
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Julien Sparfel
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
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3
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Naganathan AN, Kannan A. A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures. Curr Res Struct Biol 2021; 3:257-267. [PMID: 34704074 PMCID: PMC8526763 DOI: 10.1016/j.crstbi.2021.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/08/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022] Open
Abstract
Protein sequences and structures evolve by satisfying varied physical and biochemical constraints. This multi-level selection is enabled not just by the patterning of amino acids on the sequence, but also via coupling between residues in the native structure. Here, we employ an energetically detailed statistical mechanical model with millions of microstates to extract such long-range structural correlations, i.e. thermodynamic coupling free energies, from a diverse family of protein structures. We find that despite the intricate and anisotropic distribution of coupling patterns, the majority of residues (>70%) are only marginally coupled contributing to functional motions and catalysis. Physical origins of ‘sectors’, determinants of native ensemble heterogeneity in extant, ancient and designed proteins, and the basis for allostery emerge naturally from coupling free energies. The statistical framework highlights how evolutionary selection and optimization occur at the level of global interaction network for a given protein fold impacting folding, function, and allosteric outputs. Evolution of protein structures occurs at the level of global interaction network. More than 70% of the protein residues are weakly or marginally coupled. Functional ‘sector’ regions are a manifestation of marginal coupling. Coupling indices vary across the entire proteins in extant-ancient and natural-designed pairs. The proposed methodology can be used to understand allostery and epistasis.
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Affiliation(s)
- Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Adithi Kannan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
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4
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Wang J, Jain A, McDonald LR, Gambogi C, Lee AL, Dokholyan NV. Mapping allosteric communications within individual proteins. Nat Commun 2020; 11:3862. [PMID: 32737291 PMCID: PMC7395124 DOI: 10.1038/s41467-020-17618-2] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 06/30/2020] [Indexed: 02/05/2023] Open
Abstract
Allostery in proteins influences various biological processes such as regulation of gene transcription and activities of enzymes and cell signaling. Computational approaches for analysis of allosteric coupling provide inexpensive opportunities to predict mutations and to design small-molecule agents to control protein function and cellular activity. We develop a computationally efficient network-based method, Ohm, to identify and characterize allosteric communication networks within proteins. Unlike previously developed simulation-based approaches, Ohm relies solely on the structure of the protein of interest. We use Ohm to map allosteric networks in a dataset composed of 20 proteins experimentally identified to be allosterically regulated. Further, the Ohm allostery prediction for the protein CheY correlates well with NMR CHESCA studies. Our webserver, Ohm.dokhlab.org, automatically determines allosteric network architecture and identifies critical coupled residues within this network.
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Affiliation(s)
- Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, 17033-0850, USA
| | - Abha Jain
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7363, USA
| | - Leanna R McDonald
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7363, USA
| | - Craig Gambogi
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7363, USA
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7363, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, 17033-0850, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Departments of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033-0850, USA.
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5
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Mukherjee T, Elmas M, Vo L, Alexiades V, Hong T, Alexandre G. Multiple CheY Homologs Control Swimming Reversals and Transient Pauses in Azospirillum brasilense. Biophys J 2019; 116:1527-1537. [PMID: 30975454 DOI: 10.1016/j.bpj.2019.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Chemotaxis, together with motility, helps bacteria foraging in their habitat. Motile bacteria exhibit a variety of motility patterns, often controlled by chemotaxis, to promote dispersal. Motility in many bacteria is powered by a bidirectional flagellar motor. The flagellar motor has been known to briefly pause during rotation because of incomplete reversals or stator detachment. Transient pauses were previously observed in bacterial strains lacking CheY, and these events could not be explained by incomplete motor reversals or stator detachment. Here, we systematically analyzed swimming trajectories of various chemotaxis mutants of the monotrichous soil bacterium, Azospirillum brasilense. Like other polar flagellated bacterium, the main swimming pattern in A. brasilense is run and reverse. A. brasilense also uses run-pauses and putative run-reverse-flick-like swimming patterns, although these are rare events. A. brasilense mutant derivatives lacking the chemotaxis master histidine kinase, CheA4, or the central response regulator, CheY7, also showed transient pauses. Strikingly, the frequency of transient pauses increased dramatically in the absence of CheY4. Our findings collectively suggest that reversals and pauses are controlled through signaling by distinct CheY homologs, and thus are likely to be functionally important in the lifestyle of this soil organism.
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Affiliation(s)
- Tanmoy Mukherjee
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Mustafa Elmas
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee
| | - Lam Vo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Vasilios Alexiades
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee
| | - Tian Hong
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee; National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennessee
| | - Gladys Alexandre
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
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6
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Pandya MJ, Schiffers S, Hounslow AM, Baxter NJ, Williamson MP. Why the Energy Landscape of Barnase Is Hierarchical. Front Mol Biosci 2018; 5:115. [PMID: 30619881 PMCID: PMC6306431 DOI: 10.3389/fmolb.2018.00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/07/2018] [Indexed: 01/29/2023] Open
Abstract
We have used NMR and computational methods to characterize the dynamics of the ribonuclease barnase over a wide range of timescales in free and inhibitor-bound states. Using temperature- and denaturant-dependent measurements of chemical shift, we show that barnase undergoes frequent and highly populated hinge bending. Using relaxation dispersion, we characterize a slower and less populated motion with a rate of 750 ± 200 s−1, involving residues around the lip of the active site, which occurs in both free and bound states and therefore suggests conformational selection. Normal mode calculations characterize correlated hinge bending motions on a very rapid timescale. These three measurements are combined with previous measurements and molecular dynamics calculations on barnase to characterize its dynamic landscape on timescales from picoseconds to milliseconds and length scales from 0.1 to 2.5 nm. We show that barnase has two different large-scale fluctuations: one on a timescale of 10−9−10−6 s that has no free energy barrier and is a hinge bending that is determined by the architecture of the protein; and one on a timescale of milliseconds (i.e., 750 s−1) that has a significant free energy barrier and starts from a partially hinge-bent conformation. These two motions can be described as hierarchical, in that the more highly populated faster motion provides a platform for the slower (less probable) motion. The implications are discussed. The use of temperature and denaturant is suggested as a simple and general way to characterize motions on the intermediate ns-μs timescale.
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Affiliation(s)
- Maya J Pandya
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stefanie Schiffers
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
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7
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Russell MJ. Green Rust: The Simple Organizing 'Seed' of All Life? Life (Basel) 2018; 8:E35. [PMID: 30150570 PMCID: PMC6161180 DOI: 10.3390/life8030035] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/28/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023] Open
Abstract
Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence FeII/FeIII oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.
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Affiliation(s)
- Michael J Russell
- Planetary Chemistry and Astrobiology, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109-8099, USA.
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8
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Noguera ME, Aran M, Smal C, Vazquez DS, Herrera MG, Roman EA, Alaimo N, Gallo M, Santos J. Insights on the conformational dynamics of human frataxin through modifications of loop-1. Arch Biochem Biophys 2017; 636:123-137. [PMID: 29097312 DOI: 10.1016/j.abb.2017.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/20/2017] [Accepted: 10/28/2017] [Indexed: 02/07/2023]
Abstract
Human frataxin (FXN) is a highly conserved mitochondrial protein involved in iron homeostasis and activation of the iron-sulfur cluster assembly. FXN deficiency causes the neurodegenerative disease Friedreich's Ataxia. Here, we investigated the effect of alterations in loop-1, a stretch presumably essential for FXN function, on the conformational stability and dynamics of the native state. We generated four loop-1 variants, carrying substitutions, insertions and deletions. All of them were stable and well-folded proteins. Fast local motions (ps-ns) and slower long-range conformational dynamics (μs-ms) were altered in some mutants as judged by NMR. Particularly, loop-1 modifications impact on the dynamics of a distant region that includes residues from the β-sheet, helix α1 and the C-terminal. Remarkably, all the mutants retain the ability to activate cysteine desulfurase, even when two of them exhibit a strong decrease in iron binding, revealing a differential sensitivity of these functional features to loop-1 perturbation. Consequently, we found that even for a small and relatively rigid protein, engineering a loop segment enables to alter conformational dynamics through a long-range effect, preserving the native-state structure and important aspects of function.
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Affiliation(s)
- Martín E Noguera
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Martín Aran
- The Leloir Institute Foundation and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Clara Smal
- The Leloir Institute Foundation and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Diego S Vazquez
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - María Georgina Herrera
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Ernesto A Roman
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Nadine Alaimo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, 00133 Roma, Italy
| | - Mariana Gallo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, 00133 Roma, Italy; IRBM Science Park S.p.A., Via Pontina km 30,600., 00071 Pomezia (RM), Italy.
| | - Javier Santos
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina.
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9
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Conti Nibali V, Morra G, Havenith M, Colombo G. Role of Terahertz (THz) Fluctuations in the Allosteric Properties of the PDZ Domains. J Phys Chem B 2017; 121:10200-10208. [PMID: 28991478 PMCID: PMC6421520 DOI: 10.1021/acs.jpcb.7b06590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
With
the aim of investigating the relationship between the fast
fluctuations of proteins and their allosteric behavior, we perform
molecular dynamics simulations of two model PDZ domains with differential
allosteric responses. We focus on protein dynamics in the THz regime
(0.1–3 THz) as opposed to lower frequencies. By characterizing
the dynamic modulation of the protein backbone induced by ligand binding
in terms of single residue and pairwise distance fluctuations, we
identify a response nucleus modulated by the ligand that is visible
only at THz frequencies. The residues of this nucleus undergo a significant
stiffening and an increase in mutual coordination upon binding. Additionally,
we find that the dynamic modulation is significantly more intense
for the side chains, where it is also redistributed to distal regions
not immediately in contact with the ligand allowing us to better define
the response nucleus at THz frequencies. The overlap between the known
allosterically responding residues of the investigated PDZ domains
and the modulated region highlighted here suggests that fast THz dynamics
could play a role in allosteric mechanisms.
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Affiliation(s)
| | - Giulia Morra
- Istituto di Chimica del Riconoscimento Molecolare, CNR , Via Mario Bianco 9, 20131 Milano, Italy.,Department of Physiology and Biophysics, Weill Cornell Medical College , New York, New York 10065, United States
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr Universität , 44801 Bochum, Germany
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR , Via Mario Bianco 9, 20131 Milano, Italy.,Dipartimento di Chimica, Università di Pavia , V.le Taramelli 10, 27100 Pavia, Italy
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10
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Otrusinová O, Demo G, Padrta P, Jaseňáková Z, Pekárová B, Gelová Z, Szmitkowska A, Kadeřávek P, Jansen S, Zachrdla M, Klumpler T, Marek J, Hritz J, Janda L, Iwaï H, Wimmerová M, Hejátko J, Žídek L. Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. J Biol Chem 2017; 292:17525-17540. [PMID: 28860196 DOI: 10.1074/jbc.m117.790212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/28/2017] [Indexed: 11/06/2022] Open
Abstract
Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1RD) from Arabidopsis thaliana We observed that the crystal structures of free, Mg2+-bound, and beryllofluoridated CKI1RD (a stable analogue of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2+ binding and beryllofluoridation alter the conformational equilibrium of the β3-α3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the β3-α3 loop while keeping the active-site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the β3-α3 loop directly interacts with the ATP-binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the β3-α3 loop of CKI1RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic β3-α3 loop of CKI1RD, the corresponding loop of the ETR1 receiver domain (ETR1RD) exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1RD is involved in phosphorylation-independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MSP.
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Affiliation(s)
- Olga Otrusinová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Gabriel Demo
- From the Central European Institute of Technology and
| | - Petr Padrta
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Jaseňáková
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Blanka Pekárová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Gelová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Agnieszka Szmitkowska
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Pavel Kadeřávek
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Séverine Jansen
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Milan Zachrdla
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | | | - Jaromír Marek
- From the Central European Institute of Technology and
| | - Jozef Hritz
- From the Central European Institute of Technology and
| | - Lubomír Janda
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Hideo Iwaï
- the Institute of Biotechnology, University of Helsinki, Viikinkaari 1 (P. O. Box 65), 00014 Helsinki, Finland
| | - Michaela Wimmerová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Jan Hejátko
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Lukáš Žídek
- From the Central European Institute of Technology and .,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
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11
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Effect of Phosphorylation on a Human-like Osteopontin Peptide. Biophys J 2017; 112:1586-1596. [PMID: 28445750 PMCID: PMC5406370 DOI: 10.1016/j.bpj.2017.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/25/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022] Open
Abstract
The last decade established that the dynamic properties of the phosphoproteome are central to function and its modulation. The temporal dimension of phosphorylation effects remains nonetheless poorly understood, particularly for intrinsically disordered proteins. Osteopontin, selected for this study due to its key role in biomineralization, is expressed in many species and tissues to play a range of distinct roles. A notable property of highly phosphorylated isoforms of osteopontin is their ability to sequester nanoclusters of calcium phosphate to form a core-shell structure, in a fluid that is supersaturated but stable. In Biology, this process enables soft and hard tissues to coexist in the same organism with relative ease. Here, we extend our understanding of the effect of phosphorylation on a disordered protein, the recombinant human-like osteopontin rOPN. The solution structures of the phosphorylated and unphosphorylated rOPN were investigated by small-angle x-ray scattering and no significant changes were detected on the radius of gyration or maximum interatomic distance. The picosecond-to-nanosecond dynamics of the hydrated powders of the two rOPN forms were further compared by elastic and quasi-elastic incoherent neutron scattering. Phosphorylation was found to block some nanosecond side-chain motions while increasing the flexibility of other side chains on the faster timescale. Phosphorylation can thus selectively change the dynamic behavior of even a highly disordered protein such as osteopontin. Through such an effect on rOPN, phosphorylation can direct allosteric mechanisms, interactions with substrates, cofactors and, in this case, amorphous or crystalline biominerals.
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12
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A self-consistent structural perturbation approach for determining the magnitude and extent of allosteric coupling in proteins. Biochem J 2017; 474:2379-2388. [DOI: 10.1042/bcj20170304] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/12/2017] [Accepted: 05/17/2017] [Indexed: 11/17/2022]
Abstract
Elucidating the extent of energetic coupling between residues in single-domain proteins, which is a fundamental determinant of allostery, information transfer and folding cooperativity, has remained a grand challenge. While several sequence- and structure-based approaches have been proposed, a self-consistent description that is simultaneously compatible with unfolding thermodynamics is lacking. We recently developed a simple structural perturbation protocol that captures the changes in thermodynamic stabilities induced by point mutations within the protein interior. Here, we show that a fundamental residue-specific component of this perturbation approach, the coupling distance, is uniquely sensitive to the environment of a residue in the protein to a distance of ∼15 Å. With just the protein contact map as an input, we reproduce the extent of percolation of perturbations within the structure as observed in network analysis of intra-protein interactions, molecular dynamics simulations and NMR-observed changes in chemical shifts. Using this rapid protocol that relies on a single structure, we explain the results of statistical coupling analysis (SCA) that requires hundreds of sequences to identify functionally critical sectors, the propagation and dissipation of perturbations within proteins and the higher-order couplings deduced from detailed NMR experiments. Our results thus shed light on the possible mechanistic origins of signaling through the interaction network within proteins, the likely distance dependence of perturbations induced by ligands and post-translational modifications and the origins of folding cooperativity through many-body interactions.
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13
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Carlson GM, Fenton AW. What Mutagenesis Can and Cannot Reveal About Allostery. Biophys J 2017; 110:1912-23. [PMID: 27166800 DOI: 10.1016/j.bpj.2016.03.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/24/2016] [Accepted: 03/14/2016] [Indexed: 10/21/2022] Open
Abstract
Allosteric regulation of protein function is recognized to be widespread throughout biology; however, knowledge of allosteric mechanisms, the molecular changes within a protein that couple one binding site to another, is limited. Although mutagenesis is often used to probe allosteric mechanisms, we consider herein what the outcome of a mutagenesis study truly reveals about an allosteric mechanism. Arguably, the best way to evaluate the effects of a mutation on allostery is to monitor the allosteric coupling constant (Qax), a ratio of the substrate binding constants in the absence versus presence of an allosteric effector. A range of substitutions at a given residue position in a protein can reveal when a particular substitution causes gain-of-function, which addresses a key challenge in interpreting mutation-dependent changes in the magnitude of Qax. Thus, whole-protein mutagenesis studies offer an acceptable means of identifying residues that contribute to an allosteric mechanism. With this focus on monitoring Qax, and keeping in mind the equilibrium nature of allostery, we consider alternative possibilities for what an allosteric mechanism might be. We conclude that different possible mechanisms (rotation-of-solid-domains, movement of secondary structure, side-chain repacking, changes in dynamics, etc.) will result in different findings in whole-protein mutagenesis studies.
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Affiliation(s)
- Gerald M Carlson
- Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Aron W Fenton
- Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.
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14
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Mori T, Saito S. Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity. J Phys Chem B 2016; 120:11683-11691. [DOI: 10.1021/acs.jpcb.6b08066] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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15
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Seo JH, Park JH, Lee EJ, Vo TTL, Choi H, Kim JY, Jang JK, Wee HJ, Lee HS, Jang SH, Park ZY, Jeong J, Lee KJ, Seok SH, Park JY, Lee BJ, Lee MN, Oh GT, Kim KW. ARD1-mediated Hsp70 acetylation balances stress-induced protein refolding and degradation. Nat Commun 2016; 7:12882. [PMID: 27708256 PMCID: PMC5059642 DOI: 10.1038/ncomms12882] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 08/10/2016] [Indexed: 01/04/2023] Open
Abstract
Heat shock protein (Hsp)70 is a molecular chaperone that maintains protein homoeostasis during cellular stress through two opposing mechanisms: protein refolding and degradation. However, the mechanisms by which Hsp70 balances these opposing functions under stress conditions remain unknown. Here, we demonstrate that Hsp70 preferentially facilitates protein refolding after stress, gradually switching to protein degradation via a mechanism dependent on ARD1-mediated Hsp70 acetylation. During the early stress response, Hsp70 is immediately acetylated by ARD1 at K77, and the acetylated Hsp70 binds to the co-chaperone Hop to allow protein refolding. Thereafter, Hsp70 is deacetylated and binds to the ubiquitin ligase protein CHIP to complete protein degradation during later stages. This switch is required for the maintenance of protein homoeostasis and ultimately rescues cells from stress-induced cell death in vitro and in vivo. Therefore, ARD1-mediated Hsp70 acetylation is a regulatory mechanism that temporally balances protein refolding/degradation in response to stress. The chaperone Hsp70 has a dual role, promoting both protein refolding and protein degradation. Seo and Park et al. show that Hsp70 acetylation enhances protein refolding after stress, and that subsequent deacetylation progressively promotes ubiquitin ligase binding and protein degradation.
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Affiliation(s)
- Ji Hae Seo
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Ji-Hyeon Park
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Eun Ji Lee
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Tam Thuy Lu Vo
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Hoon Choi
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Jun Yong Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Korea
| | - Jae Kyung Jang
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Hee-Jun Wee
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Hye Shin Lee
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Se Hwan Jang
- School of Life Sciences, Gwangju Institute of Science &Technology, Gwangju 61005, Korea
| | - Zee Yong Park
- School of Life Sciences, Gwangju Institute of Science &Technology, Gwangju 61005, Korea
| | - Jaeho Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - Seung-Hyeon Seok
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Jin Young Park
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Bong Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Mi-Ni Lee
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Goo Taeg Oh
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Kyu-Won Kim
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul 08826, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Korea.,Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
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16
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Sapienza PJ, Lee AL. Widespread Perturbation of Function, Structure, and Dynamics by a Conservative Single-Atom Substitution in Thymidylate Synthase. Biochemistry 2016; 55:5702-5713. [PMID: 27649373 DOI: 10.1021/acs.biochem.6b00838] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TSase) is responsible for synthesizing the sole de novo source of dTMP in all organisms. TSase is a drug target, and as such, it has been well studied in terms of both structure and reaction mechanism. Cysteine 146 in Escherichia coli TSase is universally conserved because it serves as the nucleophile in the enzyme mechanism. Here we use the C146S mutation to probe the role of the sulfur atom in early events in the catalytic cycle beyond serving as the nucleophile. Surprisingly, the single-atom substitution severely decreases substrate binding affinity, and the unfavorable ΔΔG°bind is comprised of roughly equal enthalpic and entropic components at 25 °C. Chemical shifts in the free and dUMP-bound states show the mutation causes perturbations throughout TSase, including regions important for complex stability, in agreement with a less favorable enthalpy change. We measured the nuclear magnetic resonance methyl symmetry axis order parameter (S2axis), a proxy for conformational entropy, for TSase at all vertices of the dUMP binding/C146S mutation thermodynamic cycle and found that the calculated TΔΔS°conf is similar in sign and magnitude to the calorimetric TΔΔS°. Further, we ascribed minor resonances in wild-type-dUMP spectra to a state with a covalent bond between Sγ of C146 and C6 of dUMP and find S2axis values are unaffected by covalent bond formation, indicating this reaction step is neutral with respect to ΔS°conf. Lastly, the C146S mutation allowed us to measure cofactor analog binding by isothermal titration calorimetry without the confounding heat signature of covalent bond formation. Raltitrexed binds free and singly bound TSase with similar affinities, yet the two binding events have different enthalpy changes, providing further evidence of communication between the two active sites.
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Affiliation(s)
- Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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17
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Amor BRC, Schaub MT, Yaliraki SN, Barahona M. Prediction of allosteric sites and mediating interactions through bond-to-bond propensities. Nat Commun 2016; 7:12477. [PMID: 27561351 PMCID: PMC5007447 DOI: 10.1038/ncomms12477] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 07/05/2016] [Indexed: 11/09/2022] Open
Abstract
Allostery is a fundamental mechanism of biological regulation, in which binding of a molecule at a distant location affects the active site of a protein. Allosteric sites provide targets to fine-tune protein activity, yet we lack computational methodologies to predict them. Here we present an efficient graph-theoretical framework to reveal allosteric interactions (atoms and communication pathways strongly coupled to the active site) without a priori information of their location. Using an atomistic graph with energy-weighted covalent and weak bonds, we define a bond-to-bond propensity quantifying the non-local effect of instantaneous bond fluctuations propagating through the protein. Significant interactions are then identified using quantile regression. We exemplify our method with three biologically important proteins: caspase-1, CheY, and h-Ras, correctly predicting key allosteric interactions, whose significance is additionally confirmed against a reference set of 100 proteins. The almost-linear scaling of our method renders it suitable for high-throughput searches for candidate allosteric sites.
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Affiliation(s)
- B R C Amor
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK.,Institute of Chemical Biology, Imperial College London, London SW7 2AZ, UK
| | - M T Schaub
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK
| | - S N Yaliraki
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK.,Institute of Chemical Biology, Imperial College London, London SW7 2AZ, UK
| | - M Barahona
- Institute of Chemical Biology, Imperial College London, London SW7 2AZ, UK.,Department of Mathematics, Imperial College London, London SW7 2AZ, UK
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18
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Peters J, Martinez N, Trovaslet M, Scannapieco K, Koza MM, Masson P, Nachon F. Dynamics of human acetylcholinesterase bound to non-covalent and covalent inhibitors shedding light on changes to the water network structure. Phys Chem Chem Phys 2016; 18:12992-3001. [PMID: 27109895 DOI: 10.1039/c6cp00280c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the effects of non-covalent reversible and covalent irreversible inhibitors on human acetylcholinesterase and human butyrylcholinesterase. Remarkably a non-covalent inhibitor, Huperzine A, has almost no effect on the molecular dynamics of the protein, whereas the covalently binding nerve agent soman renders the molecular structure stiffer in its aged form. The modified movements were studied by incoherent neutron scattering on different time scales and they indicate a stabilization and stiffening of aged human acetylcholinesterase. It is not straightforward to understand the forces leading to this strong effect. In addition to the specific interactions of the adduct within the protein, some indications point towards an extensive water structure change for the aged conjugate as water Bragg peaks appeared at cryogenic temperature despite an identical initial hydration state for all samples. Such a change associated to an apparent increase in free water volume upon aging suggests higher ordering of the hydration shell that leads to the stiffening of protein. Thus, several additive contributions seem responsible for the improved flexibility or stiffening effect of the inhibitors rather than a single interaction.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, LiPhy, F-38044 Grenoble, France
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19
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Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
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Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
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20
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Ahmad A, Cai Y, Chen X, Shuai J, Han A. Conformational Dynamics of Response Regulator RegX3 from Mycobacterium tuberculosis. PLoS One 2015. [PMID: 26201027 PMCID: PMC4511772 DOI: 10.1371/journal.pone.0133389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Two-component signal transduction systems (TCS) are vital for adaptive responses to various environmental stresses in bacteria, fungi and even plants. A TCS typically comprises of a sensor histidine kinase (SK) with its cognate response regulator (RR), which often has two domains—N terminal receiver domain (RD) and C terminal effector domain (ED). The histidine kinase phosphorylates the RD to activate the ED by promoting dimerization. However, despite significant progress on structural studies, how RR transmits activation signal from RD to ED remains elusive. Here we analyzed active to inactive transition process of OmpR/PhoB family using an active conformation of RegX3 from Mycobacterium tuberculosis as a model system by computational approaches. An inactive state of RegX3 generated from 150 ns molecular dynamic simulation has rotameric conformations of Thr79 and Tyr98 that are generally conserved in inactive RRs. Arg81 in loop β4α4 acts synergistically with loop β1α1 to change its interaction partners during active to inactive transition, potentially leading to the N-terminal movement of RegX3 helix α1. Global conformational dynamics of RegX3 is mainly dependent on α4β5 region, in particular seven ‘hot-spot’ residues (Tyr98 to Ser104), adjacent to which several coevolved residues at dimeric interface, including Ile76-Asp96, Asp97-Arg111 and Glu24-Arg113 pairs, are critical for signal transduction. Taken together, our computational analyses suggest a molecular linkage between Asp phosphorylation, proximal loops and α4β5α5 dimeric interface during RR active to inactive state transition, which is not often evidently defined from static crystal structures.
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Affiliation(s)
- Ashfaq Ahmad
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Xingqiang Chen
- Department of Physics, Xiamen University, Siming, Xiamen, China
| | - Jianwei Shuai
- Department of Physics, Xiamen University, Siming, Xiamen, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
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21
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Guo J, Zhou HX. Dynamically Driven Protein Allostery Exhibits Disparate Responses for Fast and Slow Motions. Biophys J 2015; 108:2771-4. [DOI: 10.1016/j.bpj.2015.04.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 12/29/2022] Open
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22
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Ocasio VJ, Corrêa F, Gardner KH. Ligand-induced folding of a two-component signaling receiver domain. Biochemistry 2015; 54:1353-63. [PMID: 25629646 DOI: 10.1021/bi501143b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To survive and adapt to environmental changes, bacteria commonly use two-component signaling systems. Minimally, these pathways use histidine kinases (HKs) to detect environmental signals, harnessing these to control phosphorylation levels of receiver (REC) domains of downstream response regulators that convert this signal into physiological responses. Studies of several prototypical REC domains suggest that phosphorylation shifts these proteins between inactive and active structures that are globally similar and well-folded. However, it is unclear how globally these findings hold within REC domains in general, particularly when they are considered within full-length proteins. Here, we present EL_LovR, a full-length REC-only protein that is phosphorylated in response to blue light in the marine α-proteobacterium, Erythrobacter litoralis HTCC2594. Notably, EL_LovR is similar to comparable REC-only proteins used in bacterial general stress responses, where genetic evidence suggests that their potent phosphatase activity is important to shut off such systems. Size exclusion chromatography, light scattering, and solution NMR experiments show that EL_LovR is monomeric and unfolded in solution under conditions routinely used for other REC structure determinations. Addition of Mg(2+) and phosphorylation induce progressively greater degrees of tertiary structure stabilization, with the solution structure of the fully activated EL_LovR adopting the canonical receiver domain fold. Parallel functional assays show that EL_LovR has a fast dephosphorylation rate, consistent with its proposed function as a phosphate sink that depletes the HK phosphoryl group, promoting the phosphatase activity of this enzyme. Our findings demonstrate that EL_LovR undergoes substantial ligand-dependent conformational changes that have not been reported for other RRs, expanding the scope of conformational changes and regulation used by REC domains, critical components of bacterial signaling systems.
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Affiliation(s)
- Victor J Ocasio
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center , Dallas, Texas 75390-8816, United States
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23
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Sgrignani J, Bon M, Colombo G, Magistrato A. Computational approaches elucidate the allosteric mechanism of human aromatase inhibition: a novel possible route to Small-molecule regulation of CYP450s activities? J Chem Inf Model 2014; 54:2856-68. [PMID: 25178092 DOI: 10.1021/ci500425y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Human aromatase (HA) is a P450 cytochrome (CYP) with an essential role in estrogen biosynthesis. Since more than 70% of breast cancers are positive for estrogenic receptor (ER), the reduction of estrogen physiological concentrations through HA inhibition is one of most important therapeutic strategies against this cancer type. Recently, experimental evidence showed that selected taxmoxifen metabolites, which are typically used as estrogen receptor modulators (SERMs), inhibit HA through an allosteric mechanism. In this work, we present a computational protocol to (i) characterize the structural framework and (ii) define the atomistic details of the determinants for the noncompetitive inhibition mechanism. Our calculations identify two putative binding sites able to efficiently bind all tamoxifen metabolites. Analysis of long-scale molecular dynamics simulations reveal that endoxifen, the most effective noncompetitive inhibitor, induces significant enzyme rigidity by binding in one of the possible peripheral sites. The consequence of this binding event is the suppression of one of the functional enzymatic collective motions associated with breathing of the substrate access channel. Moreover, an internal dynamics-based alignment of HA with six other human cytochromes shows that this collective motion is common to other members of the CYP450 protein family. On this basis, our findings may thus be of help for the development of new (pan)inhibitors for the therapeutic treatment of cancer, targeting and modulating the activity of HA and of estrogen receptor, and may also stimulate the development of new drug design strategies for chemoprevention and chemoprotection via allosteric inhibition of CYP450 proteins.
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Affiliation(s)
- Jacopo Sgrignani
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Milano, Italy
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24
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Hultqvist G, Haq SR, Punekar AS, Chi CN, Engström Å, Bach A, Strømgaard K, Selmer M, Gianni S, Jemth P. Energetic pathway sampling in a protein interaction domain. Structure 2014; 21:1193-1202. [PMID: 23810696 DOI: 10.1016/j.str.2013.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/24/2013] [Accepted: 05/29/2013] [Indexed: 01/10/2023]
Abstract
The affinity and specificity of protein-ligand interactions are influenced by energetic crosstalk within the protein domain. However, the molecular details of such intradomain allostery are still unclear. Here, we have experimentally detected and computationally predicted interaction pathways in the postsynaptic density 95/discs large/zonula occludens 1 (PDZ)-peptide ligand model system using wild-type and circularly permuted PDZ proteins. The circular permutant introduced small perturbations in the tertiary structure and a concomitant rewiring of allosteric pathways, allowing us to describe how subtle changes may reshape energetic signaling. The results were analyzed in the context of other members of the PDZ family, which were found to contain distinct interaction pathways for different peptide ligands. The data reveal a fascinating scenario whereby several energetic pathways are sampled within one single domain and distinct pathways are activated by specific protein ligands.
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Affiliation(s)
- Greta Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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25
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Villali J, Pontiggia F, Clarkson MW, Hagan MF, Kern D. Evidence against the "Y-T coupling" mechanism of activation in the response regulator NtrC. J Mol Biol 2014; 426:1554-67. [PMID: 24406745 DOI: 10.1016/j.jmb.2013.12.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/18/2013] [Accepted: 12/24/2013] [Indexed: 01/17/2023]
Abstract
The dominant theory on the mechanism of response regulators activation in two-component bacterial signaling systems is the "Y-T coupling" mechanism, wherein the χ1 rotameric state of a highly conserved aromatic residue correlates with the activation of the protein via structural rearrangements coupled to a conserved tyrosine. In this paper, we present evidence that, in the receiver domain of the response regulator nitrogen regulatory protein C (NtrC(R)), the interconversion of this tyrosine (Y101) between its rotameric states is actually faster than the rate of inactive/active conversion and is not correlated to the activation process. Data gathered from NMR relaxation dispersion experiments show that a subset of residues surrounding the conserved tyrosine sense a process that is occurring at a faster rate than the inactive/active conformational transition. We show that this process is related to χ1 rotamer exchange of Y101 and that mutation of this aromatic residue to a leucine eliminated this second faster process without affecting activation. Computational simulations of NtrC(R) in its active conformation further demonstrate that the rotameric state of Y101 is uncorrelated with the global conformational transition during activation. Moreover, the tyrosine does not appear to be involved in the stabilization of the active form upon phosphorylation and is not essential in propagating the signal downstream for ATPase activity of the central domain. Our data provide experimental evidence against the generally accepted "Y-T coupling" mechanism of activation in NtrC(R).
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Affiliation(s)
- Janice Villali
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Francesco Pontiggia
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Michael W Clarkson
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, MA 02452, USA
| | - Dorothee Kern
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA.
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26
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Dasgupta B, Nakamura H, Kinjo AR. Rigid-body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape-dependent manner. Proteins 2013; 82:77-89. [PMID: 23873626 DOI: 10.1002/prot.24371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/01/2013] [Accepted: 07/09/2013] [Indexed: 01/30/2023]
Abstract
To understand the dynamic aspects of multispecificity of ubiquitin, we studied nine ubiquitin-ligand (partner protein) complexes by normal mode analysis based on an elastic network model. The coupling between ubiquitin and ligand motions was analyzed by decomposing it into rigid-body (external) and vibrational (internal) motions of each subunit. We observed that in total the external motions in one of the subunits largely dominated the coupling. The combination of external motions of ubiquitin and the ligands showed general trends of rotations and translations. Moreover, we observed that the rotational motions of ubiquitin were correlated to the ligand orientations. We also identified ubiquitin atomic vibrations that differentiated the orientation of the ligand molecule. We observed that the extents of coupling were correlated to the shapes of the ligands, and this trend was more pronounced when the coupling involved vibrational motions of the ligand. In conclusion, an intricate interplay between internal and external motions of ubiquitin and the ligands help understand the dynamics of multispecificity, which is mostly guided by the shapes of the ligands and the complex.
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Affiliation(s)
- Bhaskar Dasgupta
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Kalodimos C. Regulation of Biological Function by Allosteric Interactions. J Mol Biol 2013; 425:2277-8. [DOI: 10.1016/j.jmb.2013.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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