1
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Lin C, Mazor Y, Reppert M. Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis. J Phys Chem B 2024; 128:2266-2280. [PMID: 38442033 DOI: 10.1021/acs.jpcb.3c06488] [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: 03/07/2024]
Abstract
Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.
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Affiliation(s)
- Chientzu Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
| | - Yuval Mazor
- School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
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2
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Uppal S, Liu T, Galvan E, Gomez F, Tittley T, Poliakov E, Gentleman S, Redmond TM. An inducible amphipathic α-helix mediates subcellular targeting and membrane binding of RPE65. Life Sci Alliance 2022; 6:6/1/e202201546. [PMID: 36265895 PMCID: PMC9585964 DOI: 10.26508/lsa.202201546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
RPE65 retinol isomerase is an indispensable player in the visual cycle between the vertebrate retina and RPE. Although membrane association is critical for RPE65 function, its mechanism is not clear. Residues 107-125 are believed to interact with membranes but are unresolved in all RPE65 crystal structures, whereas palmitoylation at C112 also plays a role. We report the mechanism of membrane recognition and binding by RPE65. Binding of aa107-125 synthetic peptide with membrane-mimicking micellar surfaces induces transition from unstructured loop to amphipathic α-helical (AH) structure but this transition is automatic in the C112-palmitoylated peptide. We demonstrate that the AH significantly affects palmitoylation level, membrane association, and isomerization activity of RPE65. Furthermore, aa107-125 functions as a membrane sensor and the AH as a membrane-targeting motif. Molecular dynamic simulations clearly show AH-membrane insertion, supporting our experimental findings. Collectively, these studies allow us to propose a working model for RPE65-membrane binding, and to provide a novel role for cysteine palmitoylation.
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Affiliation(s)
| | | | | | | | | | | | | | - T Michael Redmond
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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3
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Rossi MA, Palzkill T, Almeida FCL, Vila AJ. Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions. Mol Biol Evol 2022; 39:6711538. [PMID: 36136729 PMCID: PMC9547502 DOI: 10.1093/molbev/msac194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein evolution depends on the adaptation of these molecules to different functional challenges. This occurs by tuning their biochemical, biophysical, and structural traits through the accumulation of mutations. While the role of protein dynamics in biochemistry is well recognized, there are limited examples providing experimental evidence of the optimization of protein dynamics during evolution. Here we report an NMR study of four variants of the CTX-M β-lactamases, in which the interplay of two mutations outside the active site enhances the activity against a cephalosporin substrate, ceftazidime. The crystal structures of these enzymes do not account for this activity enhancement. By using NMR, here we show that the combination of these two mutations increases the backbone dynamics in a slow timescale and the exposure to the solvent of an otherwise buried β-sheet. The two mutations located in this β-sheet trigger conformational changes in loops located at the opposite side of the active site. We postulate that the most active variant explores alternative conformations that enable binding of the more challenging substrate ceftazidime. The impact of the mutations in the dynamics is context-dependent, in line with the epistatic effect observed in the catalytic activity of the different variants. These results reveal the existence of a dynamic network in CTX-M β-lactamases that has been exploited in evolution to provide a net gain-of-function, highlighting the role of alternative conformations in protein evolution.
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Affiliation(s)
- Maria-Agustina Rossi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, Rosario, Argentina
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, USA,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, USA
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4
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Winston DS, Gorman SD, Boehr DD. Conformational transitions in yeast chorismate mutase important for allosteric regulation as identified by nuclear magnetic resonance spectroscopy. J Mol Biol 2022; 434:167531. [DOI: 10.1016/j.jmb.2022.167531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
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5
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Hou XN, Tochio H. Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints. Biophys Rev 2022; 14:55-66. [PMID: 35340613 PMCID: PMC8921464 DOI: 10.1007/s12551-021-00916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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6
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Di Savino A, Foerster JM, Ullmann GM, Ubbink M. Enhancing the population of the encounter complex affects protein complex formation efficiency. FEBS J 2021; 289:535-548. [PMID: 34403572 PMCID: PMC9293183 DOI: 10.1111/febs.16159] [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: 03/09/2021] [Revised: 07/08/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
Optimal charge distribution is considered to be important for efficient formation of protein complexes. Electrostatic interactions guide encounter complex formation that precedes the formation of an active protein complex. However, disturbing the optimized distribution by introduction of extra charged patches on cytochrome c peroxidase does not lead to a reduction in productive encounters with its partner cytochrome c. To test whether a complex with a high population of encounter complex is more easily affected by suboptimal charge distribution, the interactions of cytochrome c mutant R13A with wild‐type cytochrome c peroxidase and a variant with an additional negative patch were studied. The complex of the peroxidase and cytochrome c R13A was reported to have an encounter state population of 80%, compared to 30% for the wild‐type cytochrome c. NMR analysis confirms the dynamic nature of the interaction and demonstrates that the mutant cytochrome c samples the introduced negative patch. Kinetic experiments show that productive complex formation is fivefold to sevenfold slower at moderate and high ionic strength values for cytochrome c R13A but the association rate is not affected by the additional negative patch on cytochrome c peroxidase, showing that the total charge on the protein surface can compensate for less optimal charge distribution. At low ionic strength (44 mm), the association with the mutant cytochrome c reaches the same high rates as found for wild‐type cytochrome c, approaching the diffusion limit.
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7
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Intrinsically disordered proteins and membranes: a marriage of convenience for cell signalling? Biochem Soc Trans 2021; 48:2669-2689. [PMID: 33155649 PMCID: PMC7752083 DOI: 10.1042/bst20200467] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023]
Abstract
The structure-function paradigm has guided investigations into the molecules involved in cellular signalling for decades. The peripheries of this paradigm, however, start to unravel when considering the co-operation between proteins and the membrane in signalling processes. Intrinsically disordered regions hold distinct advantages over folded domains in terms of their binding promiscuity, sensitivity to their particular environment and their ease of modulation through post-translational modifications. Low sequence complexity and bias towards charged residues are also favourable for the multivalent electrostatic interactions that occur at the surfaces of lipid bilayers. This review looks at the principles behind the successful marriage between protein disorder and membranes in addition to the role of this partnership in modifying and regulating signalling in cellular processes. The HVR (hypervariable region) of small GTPases is highlighted as a well-studied example of the nuanced role a short intrinsically disordered region can play in the fine-tuning of signalling pathways.
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8
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Ren W, Dokainish HM, Shinobu A, Oshima H, Sugita Y. Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations. J Phys Chem B 2021; 125:2898-2909. [PMID: 33728914 PMCID: PMC10954230 DOI: 10.1021/acs.jpcb.0c11600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conformational changes of proteins upon ligand binding are usually explained in terms of several mechanisms including the induced fit, conformational selection, or their mixtures. Due to the slow time scales, conventional molecular dynamics (cMD) simulations based on the atomistic models cannot easily simulate the open-to-closed conformational transition in proteins. In our previous study, we have developed an enhanced sampling scheme (generalized replica exchange with solute tempering selected surface charged residues: gREST_SSCR) for multidomain proteins and applied it to ligand-mediated conformational changes in the G134R mutant of ribose-binding protein (RBPG134R) in solution. The free-energy landscape (FEL) of RBPG134R in the presence of a ribose at the binding site included the open and closed states and two intermediates, open-like and closed-like forms. Only the open and open-like forms existed in the FEL without a ribose. In the current study, the coupling between the conformational changes and ligand binding is further investigated using coarse-grained MD, multiple atomistic cMD, and free-energy calculations. The ribose is easily dissociated from the binding site of wild-type RBP and RBPG134R in the cMD simulations starting from the open and open-like forms. In contrast, it is stable at the binding site in the simulations from the closed and closed-like forms. The free-energy calculations provide the binding affinities of different structures, supporting the results of cMD simulations. Importantly, cMD simulations from the closed-like structures reveal transitions toward the closed one in the presence of a bound ribose. On the basis of the computational results, we propose a molecular mechanism in which conformational selection and induced fit happen in the first and second halves of the open-to-closed transition in RBP, respectively.
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Affiliation(s)
- Weitong Ren
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hisham M. Dokainish
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ai Shinobu
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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9
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Terrazas-López M, Lobo-Galo N, Aguirre-Reyes LG, Bustos-Jaimes I, Marcos-Víquez JÁ, González-Segura L, Díaz-Sánchez ÁG. Interaction of N-succinyl diaminopimelate desuccinylase with orphenadrine and disulfiram. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Di Cera E. Mechanisms of ligand binding. BIOPHYSICS REVIEWS 2020; 1:011303. [PMID: 33313600 PMCID: PMC7714259 DOI: 10.1063/5.0020997] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
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11
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Di Savino A, Foerster JM, La Haye T, Blok A, Timmer M, Ullmann GM, Ubbink M. Efficient Encounter Complex Formation and Electron Transfer to Cytochrome c Peroxidase with an Additional, Distant Electrostatic Binding Site. Angew Chem Int Ed Engl 2020; 59:23239-23243. [PMID: 32827196 PMCID: PMC7756542 DOI: 10.1002/anie.202010006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Indexed: 12/14/2022]
Abstract
Electrostatic interactions can strongly increase the efficiency of protein complex formation. The charge distribution in redox proteins is often optimized to steer a redox partner to the electron transfer active binding site. To test whether the optimized distribution is more important than the strength of the electrostatic interactions, an additional negative patch was introduced on the surface of cytochrome c peroxidase, away from the stereospecific binding site, and its effect on the encounter complex as well as the rate of complex formation was determined. Monte Carlo simulations and paramagnetic relaxation enhancement NMR experiments indicate that the partner, cytochrome c, interacts with the new patch. Unexpectedly, the rate of the active complex formation was not reduced, but rather slightly increased. The findings support the idea that for efficient protein complex formation the strength of the electrostatic interaction is more critical than an optimized charge distribution.
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Affiliation(s)
- Antonella Di Savino
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Johannes M Foerster
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447, Bayreuth, Germany
| | - Thijmen La Haye
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands.,Present address: University of Delft, TNW Applied Sciences, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Anneloes Blok
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Monika Timmer
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - G Matthias Ullmann
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447, Bayreuth, Germany
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
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12
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Di Savino A, Foerster JM, La Haye T, Blok A, Timmer M, Ullmann GM, Ubbink M. Efficient Encounter Complex Formation and Electron Transfer to Cytochrome
c
Peroxidase with an Additional, Distant Electrostatic Binding Site. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonella Di Savino
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - Johannes M. Foerster
- University of Bayreuth Computational Biochemistry Universitätsstraße 30, NW I 95447 Bayreuth Germany
| | - Thijmen La Haye
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
- Present address: University of Delft TNW Applied Sciences Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Anneloes Blok
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - Monika Timmer
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - G. Matthias Ullmann
- University of Bayreuth Computational Biochemistry Universitätsstraße 30, NW I 95447 Bayreuth Germany
| | - Marcellus Ubbink
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
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13
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Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities. Commun Biol 2020; 3:419. [PMID: 32747735 PMCID: PMC7400645 DOI: 10.1038/s42003-020-01149-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/14/2020] [Indexed: 11/08/2022] Open
Abstract
Protein dynamics plays key roles in ligand binding. However, the microscopic description of conformational dynamics-coupled ligand binding remains a challenge. In this study, we integrate molecular dynamics simulations, Markov state model (MSM) analysis and experimental methods to characterize the conformational dynamics of ligand-bound glutamine binding protein (GlnBP). We show that ligand-bound GlnBP has high conformational flexibility and additional metastable binding sites, presenting a more complex energy landscape than the scenario in the absence of ligand. The diverse conformations of GlnBP demonstrate different binding affinities and entail complex transition kinetics, implicating a concerted ligand binding mechanism. Single molecule fluorescence resonance energy transfer measurements and mutagenesis experiments are performed to validate our MSM-derived structure ensemble as well as the binding mechanism. Collectively, our study provides deeper insights into the protein dynamics-coupled ligand binding, revealing an intricate regulatory network underlying the apparent binding affinity. Zhang, Wu, Feng et al. show that ligand-bound glutamine binding protein assumes multiple metastable binding sites, presenting a more dynamic energy landscape than its ligand-free form. This study provides insights into the ligand-binding mechanisms coupled with protein dynamics that underly the apparent binding affinity.
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14
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Definition of functionally and structurally distinct repressive states in the nuclear receptor PPARγ. Nat Commun 2019; 10:5825. [PMID: 31862968 PMCID: PMC6925260 DOI: 10.1038/s41467-019-13768-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022] Open
Abstract
The repressive states of nuclear receptors (i.e., apo or bound to antagonists or inverse agonists) are poorly defined, despite the fact that nuclear receptors are a major drug target. Most ligand bound structures of nuclear receptors, including peroxisome proliferator-activated receptor γ (PPARγ), are similar to the apo structure. Here we use NMR, accelerated molecular dynamics and hydrogen-deuterium exchange mass spectrometry to define the PPARγ structural ensemble. We find that the helix 3 charge clamp positioning varies widely in apo and is stabilized by efficacious ligand binding. We also reveal a previously undescribed mechanism for inverse agonism involving an omega loop to helix switch which induces disruption of a tripartite salt-bridge network. We demonstrate that ligand binding can induce multiple structurally distinct repressive states. One state recruits peptides from two different corepressors, while another recruits just one, providing structural evidence of ligand bias in a nuclear receptor. The repressive states of peroxisome proliferator-activated receptor γ (PPARγ) are ill-defined, despite nuclear receptors being a major drug target. Here authors demonstrate multiple structurally distinct repressive states, providing a structural rationale for ligand bias in a nuclear receptor.
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15
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Das T, Eliezer D. Membrane interactions of intrinsically disordered proteins: The example of alpha-synuclein. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2019; 1867:879-889. [PMID: 31096049 PMCID: PMC6661188 DOI: 10.1016/j.bbapap.2019.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022]
Abstract
Peripheral membrane proteins associate reversibly with biological membranes that, compared to protein binding partners, are structurally labile and devoid of specific binding pockets. Membranes in different subcellular compartments vary primarily in their chemical composition and physical properties, and recognition of these features is therefore critical for allowing such proteins to engage their proper membrane targets. Intrinsically disordered proteins (IDPs) are well-suited to accomplish this task using highly specific and low- to moderate-affinity interactions governed by recognition principles that are both similar to and different from those that mediate the membrane interactions of rigid proteins. IDPs have also evolved multiple mechanisms to regulate membrane (and other) interactions and achieve their impressive functional diversity. Moreover, IDP-membrane interactions may have a kinetic advantage in fast processes requiring rapid control of such interactions, such as synaptic transmission or signaling. Herein we review the biophysics, regulation and functional implications of IDP-membrane interactions and include a brief overview of some of the methods that can be used to study such interactions. At each step, we use the example of alpha-synuclein, a protein involved in the pathogenesis of Parkinson's disease and one of the best characterized membrane-binding IDP, to illustrate some of the principles discussed.
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Affiliation(s)
- Tapojyoti Das
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States of America
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States of America.
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16
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de Paula VS, Valente AP. A Dynamic Overview of Antimicrobial Peptides and Their Complexes. Molecules 2018; 23:molecules23082040. [PMID: 30111717 PMCID: PMC6222744 DOI: 10.3390/molecules23082040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/05/2018] [Accepted: 08/09/2018] [Indexed: 01/06/2023] Open
Abstract
In this narrative review, we comprehensively review the available information about the recognition, structure, and dynamics of antimicrobial peptides (AMPs). Their complex behaviors occur across a wide range of time scales and have been challenging to portray. Recent advances in nuclear magnetic resonance and molecular dynamics simulations have revealed the importance of the molecular plasticity of AMPs and their abilities to recognize targets. We also highlight experimental data obtained using nuclear magnetic resonance methodologies, showing that conformational selection is a major mechanism of target interaction in AMP families.
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Affiliation(s)
- Viviane Silva de Paula
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Ana Paula Valente
- Centro de Biologia Estrutural e Bioimagem, Instituto de Bioquímica Médica, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
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17
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Nitsche C, Otting G. NMR studies of ligand binding. Curr Opin Struct Biol 2017; 48:16-22. [PMID: 29017071 DOI: 10.1016/j.sbi.2017.09.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
NMR spectroscopy is an established tool in drug discovery, but its strength is commonly regarded to be largely confined to the early stages of hit discovery and fragment based drug design, where NMR offers unique capabilities of characterizing the binding modes of ligand molecules that bind sufficiently weakly to be in rapid exchange between bound and free state. Here we, first, provide a meta-review of recent reviews on NMR studies of ligand binding and, second, review recent progress towards NMR characterization of the ligand binding mode in stable protein-ligand complexes, with particular emphasis on the global positioning system (GPS) approach enabled by paramagnetic lanthanide tags.
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Affiliation(s)
- Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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18
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Ye L, Van Eps N, Li X, Ernst OP, Prosser RS. Utilizing tagged paramagnetic shift reagents to monitor protein dynamics by NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1555-1563. [PMID: 28951313 DOI: 10.1016/j.bbapap.2017.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/11/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
Abstract
Calmodulin is a ubiquitous calcium sensor protein, known to serve as a critical interaction hub with a wide range of signaling partners. While the holo form of calmodulin (CaM-4Ca2+) has a well-defined ground state structure, it has been shown to undergo exchange, on a millisecond timescale, to a conformation resembling that of the peptide bound state. Tagged paramagnetic relaxation agents have been previously used to identify long-range dipolar interactions through relaxation effects on nuclear spins of interest. In the case of calmodulin, this lead to the determination of the relative orientation of the N- and C-terminal domains and the presence of a weakly populated peptide bound like state. Here, we make use of pseudocontact shifts from a tagged paramagnetic shift reagent which allows us to define minor states both in 13C and 15N NMR spectra and through 13C- and 15N-edited 1H-CPMG relaxation dispersion measurements. This is validated by pulsed EPR (DEER) spectroscopy which reveals an ensemble consisting of a compact peptide-bound like conformer, an intermediate peptide-bound like conformer, and a (dumbbell-like) extended ground state conformer of CaM-4Ca2+, where addition of the MLCK peptide increases the population of the peptide-bound conformers. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Libin Ye
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Xiang Li
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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19
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Prosser RS, Ye L, Pandey A, Orazietti A. Activation processes in ligand-activated G protein-coupled receptors: A case study of the adenosine A 2A receptor. Bioessays 2017; 39. [PMID: 28787091 DOI: 10.1002/bies.201700072] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here we review concepts related to an ensemble description of G-protein-coupled receptors (GPCRs). The ensemble is characterized by both inactive and active states, whose equilibrium populations and exchange rates depend sensitively on ligand, environment, and allosteric factors. This review focuses on the adenosine A2 receptor (A2A R), a prototypical class A GPCR. 19 F Nuclear Magnetic Resonance (NMR) studies show that apo A2A R is characterized by a broad ensemble of conformers, spanning inactive to active states, and resembling states defined earlier for rhodopsin. In keeping with ideas associated with a conformational selection mechanism, addition of agonist serves to allosterically restrict the overall degrees of freedom at the G protein binding interface and bias both states and functional dynamics to facilitate G protein binding and subsequent activation. While the ligand does not necessarily "induce" activation, it does bias sampling of states, increase the cooperativity of the activation process and thus, the lifetimes of functional activation intermediates, while restricting conformational dynamics to that needed for activation.
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Affiliation(s)
- R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Libin Ye
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada
| | - Aditya Pandey
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada
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20
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Abstract
Conformational selection (CS) and induced fit (IF) are two widely used interpretations of binding of a ligand to biological macromolecules. Both mechanisms envision a two-step reaction in which a conformational transition either precedes (CS) or follows (IF) the binding step. Under pseudo-first-order conditions where the ligand is in excess compared to the macromolecule, both mechanisms produce two relaxations. A fast one eventually increases linearly with ligand concentration and reflects the binding interaction. A slow one saturates to a constant value after decreasing or increasing hyperbolically with ligand concentration. This relaxation is the one most often accessible to experimental measurements and is potentially diagnostic of the mechanism involved. A relaxation that decreases unequivocally identifies CS, but a hyperbolic increase is compatible with both CS and IF. The potential ambiguity between the two mechanisms is more than qualitative. Here we show that the entire kinetic repertoire of IF is nothing but a mathematical special case of CS as revealed by a simple transformation of the rate constants, which emphasizes the need for independent support of either mechanism from additional experimental evidence. We discuss a simple strategy for distinguishing between IF and CS under the most common conditions encountered in practice, i.e., when the ligand is in excess compared to the macromolecule and a single relaxation is accessible to experimental measurements.
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Affiliation(s)
- Pradipta Chakraborty
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
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21
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Abstract
Whereas protein-ligand binding affinities have long-established prominence, binding rate constants and binding mechanisms have gained increasing attention in recent years. Both new computational methods and new experimental techniques have been developed to characterize the latter properties. It is now realized that binding mechanisms, like binding rate constants, can and should be quantitatively determined. In this review, we summarize studies and synthesize ideas on several topics in the hope of providing a coherent picture of and physical insight into binding kinetics. The topics include microscopic formulation of the kinetic problem and its reduction to simple rate equations; computation of binding rate constants; quantitative determination of binding mechanisms; and elucidation of physical factors that control binding rate constants and mechanisms.
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Affiliation(s)
- Xiaodong Pang
- Department of Physics, Florida State University, Tallahassee, Florida 32306; .,Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
| | - Huan-Xiang Zhou
- Department of Physics, Florida State University, Tallahassee, Florida 32306; .,Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
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22
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Ozgur B, Ozdemir ES, Gursoy A, Keskin O. Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations. J Phys Chem B 2017; 121:3686-3700. [DOI: 10.1021/acs.jpcb.6b10401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Beytullah Ozgur
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - E. Sila Ozdemir
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
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23
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High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments. Curr Opin Struct Biol 2017; 42:50-58. [DOI: 10.1016/j.sbi.2016.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/16/2016] [Accepted: 10/19/2016] [Indexed: 11/17/2022]
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24
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Liu X, Speckhard DC, Shepherd TR, Sun YJ, Hengel SR, Yu L, Fowler CA, Gakhar L, Fuentes EJ. Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions. Structure 2016; 24:2053-2066. [PMID: 27998539 DOI: 10.1016/j.str.2016.08.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 07/27/2016] [Accepted: 09/30/2016] [Indexed: 11/29/2022]
Abstract
Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to investigate the role of structure and conformational dynamics in molecular recognition. Crystal structures of the QM PDZ domain both free and bound to ligands showed structural features central to binding (enthalpy), while nuclear-magnetic-resonance-based methyl relaxation experiments and isothermal titration calorimetry revealed that conformational entropy contributes to affinity. In addition to motions relevant to thermodynamics, slower microsecond to millisecond switching was prevalent in the QM PDZ ligand-binding site consistent with a role in ligand specificity. Our data indicate that conformational dynamics plays distinct and fundamental roles in tuning the affinity (conformational entropy) and specificity (excited-state conformations) of molecular interactions. More broadly, our results have important implications for the evolution, regulation, and design of protein-ligand interactions.
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Affiliation(s)
- Xu Liu
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | | | - Tyson R Shepherd
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Young Joo Sun
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Sarah R Hengel
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Liping Yu
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Carver College of Medicine Medical Nuclear Magnetic Resonance Facility, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - C Andrew Fowler
- Carver College of Medicine Medical Nuclear Magnetic Resonance Facility, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Lokesh Gakhar
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Protein Crystallography Facility, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Ernesto J Fuentes
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
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25
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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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26
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Seetaha S, Yagi-Utsumi M, Yamaguchi T, Ishii K, Hannongbua S, Choowongkomon K, Kato K. Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase. ChemMedChem 2016; 11:363-6. [PMID: 26804978 DOI: 10.1002/cmdc.201500554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Indexed: 11/07/2022]
Abstract
Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques can provide long-range structural information complemented with local information derived from chemical-shift perturbation and nuclear Overhauser effect data. Here, we address the application of paramagnetic relaxation enhancement (PRE) to detect inhibitor-induced conformational change of a drug target protein using human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) as a model protein. Using a site-specific spin-labeled HIV-1 RT mutant with selective (13) C labeling, conformation-dependent PREs were successfully observed reflecting the stabilization of an open conformation of this enzyme caused by inhibitor binding. This study demonstrates that the paramagnetism-assisted NMR approach offers an alternative strategy in protein-based drug screening to identify allosteric inhibitors of a target protein.
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Affiliation(s)
- Supaporn Seetaha
- Graduate Program in Bioscience, Faculty of Science, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Maho Yagi-Utsumi
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Takumi Yamaguchi
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, 923-1292, Japan
| | - Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. .,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
| | - Koichi Kato
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan. .,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
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27
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Chakrabarti KS, Agafonov RV, Pontiggia F, Otten R, Higgins MK, Schertler GFX, Oprian DD, Kern D. Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis. Cell Rep 2015; 14:32-42. [PMID: 26725117 DOI: 10.1016/j.celrep.2015.12.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 10/17/2015] [Accepted: 11/20/2015] [Indexed: 11/28/2022] Open
Abstract
Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here, we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsin kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using nuclear magnetic resonance (NMR) spectroscopy, stopped-flow kinetics, and isothermal titration calorimetry, we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Protein dynamics in free recoverin limits the overall rate of binding.
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Affiliation(s)
- Kalyan S Chakrabarti
- Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454; Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454
| | - Roman V Agafonov
- Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454; Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454
| | - Francesco Pontiggia
- Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454; Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454
| | - Renee Otten
- Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454; Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Daniel D Oprian
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454.
| | - Dorothee Kern
- Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454; Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454.
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28
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Abstract
INTRODUCTION Molecular docking has become a popular method for virtual screening. Docking small molecules to a rigid biological receptor is fast but could produce many false negatives and identify less diverse compounds. Flexible receptor docking has alleviated this problem. AREAS COVERED This article focuses on reviewing ensemble docking as an approximate but inexpensive method to incorporate receptor flexibility in molecular docking. It outlines key features and recent advances of this method and points out problem areas that need to be addressed to make it even more useful in drug discovery. EXPERT OPINION Among the different methods introduced for flexible receptor docking, ensemble docking represents one of the most popular approaches, especially for high-throughput virtual screening. One can generate structural ensembles by using experimental structures, by structural modeling and by various types of molecular simulations. In building a structural ensemble, a judicious choice of the structures to be included can improve performance. Furthermore, reducing the size of the structural ensemble can cut computational costs, and removing the structures that can bind few ligands well could enrich the number of true actives identified by ensemble docking. The ability of ensemble docking to identify more true positives at the top of a rank-ordered list also depends on the choice of the methods to score and rank compounds, an area that needs further research.
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Affiliation(s)
- Chung F Wong
- a University of Missouri-St. Louis, Department of Chemistry and Biochemistry , 1 University Boulevard, St. Louis, MO 63121, USA +1 31 4516 5318 ;
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29
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Abstract
In this brief review, we summarize various aspects of NMR paramagnetic relaxation enhancement (PRE). We discuss the types of spin labels used in NMR studies, describe the relevant theory used to accurately calculate PREs from coordinates, including how to take into account the fact that paramagnetic labels tend to be highly mobile and sample a wide range of conformational space, and outline methods to refine structures or ensembles of structures directly against PRE data using simulated annealing. Finally, we show how the PRE can be used to detect, characterize, and visualize sparsely populated states of proteins and their complexes that are invisible to all other biophysical techniques.
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30
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Ueda T, Yoshiura C, Matsumoto M, Kofuku Y, Okude J, Kondo K, Shiraishi Y, Takeuchi K, Shimada I. Development of a method for reconstruction of crowded NMR spectra from undersampled time-domain data. JOURNAL OF BIOMOLECULAR NMR 2015; 62:31-41. [PMID: 25677224 PMCID: PMC4432090 DOI: 10.1007/s10858-015-9908-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/07/2015] [Indexed: 05/27/2023]
Abstract
NMR is a unique methodology for obtaining information about the conformational dynamics of proteins in heterogeneous biomolecular systems. In various NMR methods, such as transferred cross-saturation, relaxation dispersion, and paramagnetic relaxation enhancement experiments, fast determination of the signal intensity ratios in the NMR spectra with high accuracy is required for analyses of targets with low yields and stabilities. However, conventional methods for the reconstruction of spectra from undersampled time-domain data, such as linear prediction, spectroscopy with integration of frequency and time domain, and analysis of Fourier, and compressed sensing were not effective for the accurate determination of the signal intensity ratios of the crowded two-dimensional spectra of proteins. Here, we developed an NMR spectra reconstruction method, "conservation of experimental data in analysis of Fourier" (Co-ANAFOR), to reconstruct the crowded spectra from the undersampled time-domain data. The number of sampling points required for the transferred cross-saturation experiments between membrane proteins, photosystem I and cytochrome b 6 f, and their ligand, plastocyanin, with Co-ANAFOR was half of that needed for linear prediction, and the peak height reduction ratios of the spectra reconstructed from truncated time-domain data by Co-ANAFOR were more accurate than those reconstructed from non-uniformly sampled data by compressed sensing.
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Affiliation(s)
- Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0075 Japan
| | - Chie Yoshiura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masahiko Matsumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Japan Biological Informatics Consortium, Aomi, Koto-ku, Tokyo, 135-8073 Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Koh Takeuchi
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0075 Japan
- Molecular Profiling Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo, 135-0064 Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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31
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Li L, Wang L, Alexov E. On the energy components governing molecular recognition in the framework of continuum approaches. Front Mol Biosci 2015; 2:5. [PMID: 25988173 PMCID: PMC4429657 DOI: 10.3389/fmolb.2015.00005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/04/2015] [Indexed: 01/14/2023] Open
Abstract
Molecular recognition is a process that brings together several biological macromolecules to form a complex and one of the most important characteristics of the process is the binding free energy. Various approaches exist to model the binding free energy, provided the knowledge of the 3D structures of bound and unbound molecules. Among them, continuum approaches are quite appealing due to their computational efficiency while at the same time providing predictions with reasonable accuracy. Here we review recent developments in the field emphasizing on the importance of adopting adequate description of physical processes taking place upon the binding. In particular, we focus on the efforts aiming at capturing some of the atomistic details of the binding phenomena into the continuum framework. When possible, the energy components are reviewed independently of each other. However, it is pointed out that rigorous approaches should consider all energy contributions on the same footage. The two major schemes for utilizing the individual energy components to predict binding affinity are outlined as well.
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Affiliation(s)
- Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University Clemson, SC, USA
| | - Lin Wang
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University Clemson, SC, USA
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University Clemson, SC, USA
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32
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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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33
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Stafford KA, Trbovic N, Butterwick JA, Abel R, Friesner RA, Palmer AG. Conformational preferences underlying reduced activity of a thermophilic ribonuclease H. J Mol Biol 2014; 427:853-866. [PMID: 25550198 DOI: 10.1016/j.jmb.2014.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/14/2014] [Indexed: 11/30/2022]
Abstract
The conformational basis for reduced activity of the thermophilic ribonuclease HI enzyme from Thermus thermophilus, compared to its mesophilic homolog from Escherichia coli, is elucidated using a combination of NMR spectroscopy and molecular dynamics (MD) simulations. Explicit-solvent all-atom MD simulations of the two wild-type proteins and an E. coli mutant in which a glycine residue is inserted after position 80 to mimic the T. thermophilus protein reproduce the differences in conformational dynamics determined from (15)N spin-relaxation NMR spectroscopy of three loop regions that surround the active site and contain functionally important residues: the glycine-rich region, the handle region, and the β5/αE loop. Examination of the MD trajectories indicates that the thermophilic protein samples conformations productive for substrate binding and activity less frequently than the mesophilic enzyme, although these differences may manifest as either increased or decreased relative flexibility of the different regions. Additional MD simulations indicate that mutations increasing activity of the T. thermophilus enzyme at mesophilic temperatures do so by reconfiguring the local environments of the mutated sites to more closely resemble active conformations. Taken together, the results show that both locally increased and decreased flexibility contribute to an overall reduction in activity of T. thermophilus ribonuclease H compared to its mesophilic E. coli homolog.
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Affiliation(s)
- Kate A Stafford
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Nikola Trbovic
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Joel A Butterwick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Robert Abel
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | | | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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Gouridis G, Schuurman-Wolters GK, Ploetz E, Husada F, Vietrov R, de Boer M, Cordes T, Poolman B. Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ. Nat Struct Mol Biol 2014; 22:57-64. [DOI: 10.1038/nsmb.2929] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/06/2014] [Indexed: 11/09/2022]
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35
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Racca JD, Chen YS, Maloy JD, Wickramasinghe N, Phillips NB, Weiss MA. Structure-function relationships in human testis-determining factor SRY: an aromatic buttress underlies the specific DNA-bending surface of a high mobility group (HMG) box. J Biol Chem 2014; 289:32410-29. [PMID: 25258310 DOI: 10.1074/jbc.m114.597526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human testis determination is initiated by SRY, a Y-encoded architectural transcription factor. Mutations in SRY cause 46 XY gonadal dysgenesis with female somatic phenotype (Swyer syndrome) and confer a high risk of malignancy (gonadoblastoma). Such mutations cluster in the SRY high mobility group (HMG) box, a conserved motif of specific DNA binding and bending. To explore structure-function relationships, we constructed all possible substitutions at a site of clinical mutation (W70L). Our studies thus focused on a core aromatic residue (position 15 of the consensus HMG box) that is invariant among SRY-related HMG box transcription factors (the SOX family) and conserved as aromatic (Phe or Tyr) among other sequence-specific boxes. In a yeast one-hybrid system sensitive to specific SRY-DNA binding, the variant domains exhibited reduced (Phe and Tyr) or absent activity (the remaining 17 substitutions). Representative nonpolar variants with partial or absent activity (Tyr, Phe, Leu, and Ala in order of decreasing side-chain volume) were chosen for study in vitro and in mammalian cell culture. The clinical mutation (Leu) was found to markedly impair multiple biochemical and cellular activities as respectively probed through the following: (i) in vitro assays of specific DNA binding and protein stability, and (ii) cell culture-based assays of proteosomal degradation, nuclear import, enhancer DNA occupancy, and SRY-dependent transcriptional activation. Surprisingly, however, DNA bending is robust to this or the related Ala substitution that profoundly impairs box stability. Together, our findings demonstrate that the folding, trafficking, and gene-regulatory function of SRY requires an invariant aromatic "buttress" beneath its specific DNA-bending surface.
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Affiliation(s)
- Joseph D Racca
- From the Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Yen-Shan Chen
- From the Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - James D Maloy
- From the Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Nalinda Wickramasinghe
- From the Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Nelson B Phillips
- From the Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Michael A Weiss
- From the Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
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Gill ML, Palmer AG. Local isotropic diffusion approximation for coupled internal and overall molecular motions in NMR spin relaxation. J Phys Chem B 2014; 118:11120-8. [PMID: 25167331 PMCID: PMC4174990 DOI: 10.1021/jp506580c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The present work demonstrates that NMR spin relaxation rate constants for molecules interconverting between states with different diffusion tensors can be modeled theoretically by combining orientational correlation functions for exchanging spherical molecules with locally isotropic approximations for the diffusion anisotropic tensors. The resulting expressions are validated by comparison with correlation functions obtained by Monte Carlo simulations and are accurate for moderate degrees of diffusion anisotropy typically encountered in investigations of globular proteins. The results are complementary to an elegant, but more complex, formalism that is accurate for all degrees of diffusion anisotropy [Ryabov, Y.; Clore, G. M.; Schwieters, C. D. J. Chem. Phys. 2012, 136, 034108].
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Affiliation(s)
- Michelle L Gill
- Department of Biochemistry and Molecular Biophysics, Columbia University , 630 West 168th Street, New York, New York 10032, United States
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Hoang J, Prosser RS. Conformational Selection and Functional Dynamics of Calmodulin: A 19F Nuclear Magnetic Resonance Study. Biochemistry 2014; 53:5727-36. [DOI: 10.1021/bi500679c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joshua Hoang
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - R. Scott Prosser
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
- Department
of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S
1A8, Canada
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The Ever Changing Moods of Calmodulin: How Structural Plasticity Entails Transductional Adaptability. J Mol Biol 2014; 426:2717-35. [DOI: 10.1016/j.jmb.2014.05.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/14/2014] [Accepted: 05/16/2014] [Indexed: 11/20/2022]
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39
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Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit. Proc Natl Acad Sci U S A 2014; 111:10197-202. [PMID: 24982141 DOI: 10.1073/pnas.1407545111] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This study aimed to shed light on the long debate over whether conformational selection (CS) or induced fit (IF) is the governing mechanism for protein-ligand binding. The main difference between the two scenarios is whether the conformational transition of the protein from the unbound form to the bound form occurs before or after encountering the ligand. Here we introduce the IF fraction (i.e., the fraction of binding events achieved via IF), to quantify the binding mechanism. Using simulations of a model protein-ligand system, we demonstrate that both the rate of the conformational transition and the concentration of ligand molecules can affect the IF fraction. CS dominates at slow conformational transition and low ligand concentration. An increase in either quantity results in a higher IF fraction. Despite the many-body nature of the system and the involvement of multiple, disparate types of dynamics (i.e., ligand diffusion, protein conformational transition, and binding reaction), the overall binding kinetics over wide ranges of parameters can be fit to a single exponential, with the apparent rate constant exhibiting a linear dependence on ligand concentration. The present study may guide future kinetics experiments and dynamics simulations in determining the IF fraction.
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