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Dube N, Khan SH, Sasse R, Okafor CD. Identification of an Evolutionarily Conserved Allosteric Network in Steroid Receptors. J Chem Inf Model 2023; 63:571-582. [PMID: 36594606 PMCID: PMC9875803 DOI: 10.1021/acs.jcim.2c01096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Indexed: 01/04/2023]
Abstract
Allosteric pathways in proteins describe networks comprising amino acid residues which may facilitate the propagation of signals between distant sites. Through inter-residue interactions, dynamic and conformational changes can be transmitted from the site of perturbation to an allosteric site. While sophisticated computational methods have been developed to characterize such allosteric pathways linking specific sites on proteins, few attempts have been made to apply these approaches toward identifying new allosteric sites. Here, we use molecular dynamics simulations and suboptimal path analysis to discover new allosteric networks in steroid receptors with a focus on evolutionarily conserved pathways. Using modern receptors and a reconstructed ancestral receptor, we identify networks connecting several sites to the activation function surface 2 (AF-2), the site of coregulator recruitment. One of these networks is conserved across the entire family, connecting a predicted allosteric site located between helices 9 and 10 of the ligand-binding domain. We investigate the basis of this conserved network as well as the importance of this site, discovering that the site lies in a region of the ligand-binding domain characterized by conserved inter-residue contacts. This study suggests an evolutionarily importance of the helix 9-helix 10 site in steroid receptors and identifies an approach that may be applied to discover previously unknown allosteric sites in proteins.
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Affiliation(s)
- Namita Dube
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University Park, State College, Pennsylvania 16802, United States
| | - Sabab Hasan Khan
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University Park, State College, Pennsylvania 16802, United States
| | - Riley Sasse
- Department
of Chemistry, Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
| | - C. Denise Okafor
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University Park, State College, Pennsylvania 16802, United States
- Department
of Chemistry, Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
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2
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Khan SH, Braet SM, Koehler SJ, Elacqua E, Anand GS, Okafor CD. Ligand-induced shifts in conformational ensembles that describe transcriptional activation. eLife 2022; 11:e80140. [PMID: 36222302 PMCID: PMC9555869 DOI: 10.7554/elife.80140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/14/2022] [Indexed: 11/15/2022] Open
Abstract
Nuclear receptors function as ligand-regulated transcription factors whose ability to regulate diverse physiological processes is closely linked with conformational changes induced upon ligand binding. Understanding how conformational populations of nuclear receptors are shifted by various ligands could illuminate strategies for the design of synthetic modulators to regulate specific transcriptional programs. Here, we investigate ligand-induced conformational changes using a reconstructed, ancestral nuclear receptor. By making substitutions at a key position, we engineer receptor variants with altered ligand specificities. We combine cellular and biophysical experiments to characterize transcriptional activity, as well as elucidate mechanisms underlying altered transcription in receptor variants. We then use atomistic molecular dynamics (MD) simulations with enhanced sampling to generate ensembles of wildtype and engineered receptors in combination with multiple ligands, followed by conformational analysis and correlation of MD-based predictions with functional ligand profiles. We determine that conformational ensembles accurately describe ligand responses based on observed population shifts. These studies provide a platform which will allow structural characterization of physiologically-relevant conformational ensembles, as well as provide the ability to design and predict transcriptional responses in novel ligands.
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Affiliation(s)
- Sabab Hasan Khan
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityState CollegeUnited States
| | - Sean M Braet
- Department of Chemistry, Pennsylvania State UniversityState ParkUnited States
| | | | - Elizabeth Elacqua
- Department of Chemistry, Pennsylvania State UniversityState ParkUnited States
| | | | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityState CollegeUnited States
- Department of Chemistry, Pennsylvania State UniversityState ParkUnited States
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3
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Iorio A, Brochier-Armanet C, Mas C, Sterpone F, Madern D. Protein Conformational Space at the Edge of Allostery: Turning a Non-allosteric Malate Dehydrogenase into an "Allosterized" Enzyme using Evolution Guided Punctual Mutations. Mol Biol Evol 2022; 39:6691310. [PMID: 36056899 PMCID: PMC9486893 DOI: 10.1093/molbev/msac186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We unveil the intimate relationship between protein dynamics and allostery by following the trajectories of model proteins in their conformational and sequence spaces. Starting from a nonallosteric hyperthermophilic malate dehydrogenase, we have tracked the role of protein dynamics in the evolution of the allosteric capacity. Based on a large phylogenetic analysis of the malate (MalDH) and lactate dehydrogenase (LDH) superfamily, we identified two amino acid positions that could have had a major role for the emergence of allostery in LDHs, which we targeted for investigation by site-directed mutagenesis. Wild-type MalDH and the single and double mutants were tested with respect to their substrate recognition profiles. The double mutant displayed a sigmoid-shaped profile typical of homotropic activation in LDH. By using molecular dynamics simulations, we showed that the mutations induce a drastic change in the protein sampling of its conformational landscape, making transiently T-like (inactive) conformers, typical of allosteric LDHs, accessible. Our data fit well with the seminal key concept linking protein dynamics and evolvability. We showed that the selection of a new phenotype can be achieved by a few key dynamics-enhancing mutations causing the enrichment of low-populated conformational substates.
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Affiliation(s)
- Antonio Iorio
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Caroline Mas
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
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4
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Gonzalez NA, Li BA, McCully ME. The stability and dynamics of computationally designed proteins. Protein Eng Des Sel 2022; 35:gzac001. [PMID: 35174855 PMCID: PMC9214642 DOI: 10.1093/protein/gzac001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Protein stability, dynamics and function are intricately linked. Accordingly, protein designers leverage dynamics in their designs and gain insight to their successes and failures by analyzing their proteins' dynamics. Molecular dynamics (MD) simulations are a powerful computational tool for quantifying both local and global protein dynamics. This review highlights studies where MD simulations were applied to characterize the stability and dynamics of designed proteins and where dynamics were incorporated into computational protein design. First, we discuss the structural basis underlying the extreme stability and thermostability frequently observed in computationally designed proteins. Next, we discuss examples of designed proteins, where dynamics were not explicitly accounted for in the design process, whose coordinated motions or active site dynamics, as observed by MD simulation, enhanced or detracted from their function. Many protein functions depend on sizeable or subtle conformational changes, so we finally discuss the computational design of proteins to perform a specific function that requires consideration of motion by multi-state design.
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Affiliation(s)
- Natali A Gonzalez
- Department of Biology, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA
| | - Brigitte A Li
- Department of Biology, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA
| | - Michelle E McCully
- Department of Biology, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA
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5
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Modi T, Campitelli P, Kazan IC, Ozkan SB. Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective. Curr Opin Struct Biol 2020; 66:207-215. [PMID: 33388636 DOI: 10.1016/j.sbi.2020.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 01/06/2023]
Abstract
While the function of a protein depends heavily on its ability to fold into a correct 3D structure, billions of years of evolution have tailored proteins from highly stable objects to flexible molecules as they adapted to environmental changes. Nature maintains the fine balance of protein folding and stability while still evolving towards new function through generations of fine-tuning necessary interactions with other proteins and small molecules. Here we focus on recent computational and experimental studies that shed light onto how evolution molds protein folding and the functional landscape from a conformational dynamics' perspective. Particularly, we explore the importance of dynamic allostery throughout protein evolution and discuss how the protein anisotropic network can give rise to allosteric and epistatic interactions.
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Affiliation(s)
- Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Ismail Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
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6
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Disruption of a key ligand-H-bond network drives dissociative properties in vamorolone for Duchenne muscular dystrophy treatment. Proc Natl Acad Sci U S A 2020; 117:24285-24293. [PMID: 32917814 DOI: 10.1073/pnas.2006890117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Duchenne muscular dystrophy is a genetic disorder that shows chronic and progressive damage to skeletal and cardiac muscle leading to premature death. Antiinflammatory corticosteroids targeting the glucocorticoid receptor (GR) are the current standard of care but drive adverse side effects such as deleterious bone loss. Through subtle modification to a steroidal backbone, a recently developed drug, vamorolone, appears to preserve beneficial efficacy but with significantly reduced side effects. We use combined structural, biophysical, and biochemical approaches to show that loss of a receptor-ligand hydrogen bond drives these remarkable therapeutic effects. Moreover, vamorolone uniformly weakens coactivator associations but not corepressor associations, implicating partial agonism as the main driver of its dissociative properties. Additionally, we identify a critical and evolutionarily conserved intramolecular network connecting the ligand to the coregulator binding surface. Interruption of this allosteric network by vamorolone selectively reduces GR-driven transactivation while leaving transrepression intact. Our results establish a mechanistic understanding of how vamorolone reduces side effects, guiding the future design of partial agonists as selective GR modulators with an improved therapeutic index.
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7
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D'Amico RN, Murray AM, Boehr DD. Driving Protein Conformational Cycles in Physiology and Disease: "Frustrated" Amino Acid Interaction Networks Define Dynamic Energy Landscapes: Amino Acid Interaction Networks Change Progressively Along Alpha Tryptophan Synthase's Catalytic Cycle. Bioessays 2020; 42:e2000092. [PMID: 32720327 DOI: 10.1002/bies.202000092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/09/2020] [Indexed: 12/22/2022]
Abstract
A general framework by which dynamic interactions within a protein will promote the necessary series of structural changes, or "conformational cycle," required for function is proposed. It is suggested that the free-energy landscape of a protein is biased toward this conformational cycle. Fluctuations into higher energy, although thermally accessible, conformations drive the conformational cycle forward. The amino acid interaction network is defined as those intraprotein interactions that contribute most to the free-energy landscape. Some network connections are consistent in every structural state, while others periodically change their interaction strength according to the conformational cycle. It is reviewed here that structural transitions change these periodic network connections, which then predisposes the protein toward the next set of network changes, and hence the next structural change. These concepts are illustrated by recent work on tryptophan synthase. Disruption of these dynamic connections may lead to aberrant protein function and disease states.
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Affiliation(s)
- Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, 107 Chemistry Building, University Park, PA, 16802, USA
| | - Alec M Murray
- Department of Chemistry, The Pennsylvania State University, 107 Chemistry Building, University Park, PA, 16802, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, 107 Chemistry Building, University Park, PA, 16802, USA
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