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Maria-Solano MA, Choi S. Dynamic allosteric networks drive adenosine A 1 receptor activation and G-protein coupling. eLife 2023; 12:RP90773. [PMID: 37656635 PMCID: PMC10473838 DOI: 10.7554/elife.90773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023] Open
Abstract
G-protein coupled receptors (GPCRs) present specific activation pathways and signaling among receptor subtypes. Hence, an extensive knowledge of the structural dynamics of the receptor is critical for the development of therapeutics. Here, we target the adenosine A1 receptor (A1R), for which a negligible number of drugs have been approved. We combine molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection to decipher the activation pathway of A1R, decode the allosteric networks and identify transient pockets. The A1R activation pathway reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers and the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of transient pockets and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. By an in-depth analysis of the bridge between activation pathway, energy networks and transient pockets, we provide a further understanding of A1R. This information can be useful to ease the design of allosteric modulators for A1R.
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Affiliation(s)
- Miguel A Maria-Solano
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
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Maria-Solano MA, Choi S. Dynamic allosteric networks drive adenosine A 1 receptor activation and G-protein coupling. Biophys J 2023; 122:31a. [PMID: 36783608 DOI: 10.1016/j.bpj.2022.11.388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Miguel A Maria-Solano
- College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, Republic of Korea
| | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, Republic of Korea
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Calvó-Tusell C, Maria-Solano MA, Osuna S, Feixas F. Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase. J Am Chem Soc 2022; 144:7146-7159. [PMID: 35412310 PMCID: PMC9052757 DOI: 10.1021/jacs.1c12629] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Deciphering the molecular
mechanisms of enzymatic allosteric regulation
requires the structural characterization of functional states and
also their time evolution toward the formation of the allosterically
activated ternary complex. The transient nature and usually slow millisecond
time scale interconversion between these functional states hamper
their experimental and computational characterization. Here, we combine
extensive molecular dynamics simulations, enhanced sampling techniques,
and dynamical networks to describe the allosteric activation of imidazole
glycerol phosphate synthase (IGPS) from the substrate-free form to
the active ternary complex. IGPS is a heterodimeric bienzyme complex
whose HisH subunit is responsible for hydrolyzing glutamine and delivering
ammonia for the cyclase activity in HisF. Despite significant advances
in understanding the underlying allosteric mechanism, essential molecular
details of the long-range millisecond allosteric activation of IGPS
remain hidden. Without using a priori information
of the active state, our simulations uncover how IGPS, with the allosteric
effector bound in HisF, spontaneously captures glutamine in a catalytically
inactive HisH conformation, subsequently attains a closed HisF:HisH
interface, and finally forms the oxyanion hole in HisH for efficient
glutamine hydrolysis. We show that the combined effector and substrate
binding dramatically decreases the conformational barrier associated
with oxyanion hole formation, in line with the experimentally observed
4500-fold activity increase in glutamine hydrolysis. The allosteric
activation is controlled by correlated time-evolving dynamic networks
connecting the effector and substrate binding sites. This computational
strategy tailored to describe millisecond events can be used to rationalize
the effect of mutations on the allosteric regulation and guide IGPS
engineering efforts.
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Affiliation(s)
- Carla Calvó-Tusell
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, 03760 Seoul, Republic of Korea
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
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Maria-Solano MA, Kinateder T, Iglesias-Fernández J, Sterner R, Osuna S. In Silico Identification and Experimental Validation of Distal Activity-Enhancing Mutations in Tryptophan Synthase. ACS Catal 2021; 11:13733-13743. [PMID: 34777912 PMCID: PMC8576815 DOI: 10.1021/acscatal.1c03950] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Allostery is a central mechanism for the regulation of multi-enzyme complexes. The mechanistic basis that drives allosteric regulation is poorly understood but harbors key information for enzyme engineering. In the present study, we focus on the tryptophan synthase complex that is composed of TrpA and TrpB subunits, which allosterically activate each other. Specifically, we develop a rational approach for identifying key amino acid residues of TrpB distal from the active site. Those residues are predicted to be crucial for shifting the inefficient conformational ensemble of the isolated TrpB to a productive ensemble through intra-subunit allosteric effects. The experimental validation of the conformationally driven TrpB design demonstrates its superior stand-alone activity in the absence of TrpA, comparable to those enhancements obtained after multiple rounds of experimental laboratory evolution. Our work evidences that the current challenge of distal active site prediction for enhanced function in computational enzyme design has become within reach.
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Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Javier Iglesias-Fernández
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- Nostrum Biodiscovery, Carrer de Baldiri Reixac, 10-12, Barcelona 08028, Spain
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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5
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Maria-Solano MA, Iglesias-Fernández J, Osuna S. Deciphering the Allosterically Driven Conformational Ensemble in Tryptophan Synthase Evolution. J Am Chem Soc 2019; 141:13049-13056. [DOI: 10.1021/jacs.9b03646] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Javier Iglesias-Fernández
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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Maria-Solano MA, Serrano-Hervás E, Romero-Rivera A, Iglesias-Fernández J, Osuna S. Role of conformational dynamics in the evolution of novel enzyme function. Chem Commun (Camb) 2018; 54:6622-6634. [PMID: 29780987 PMCID: PMC6009289 DOI: 10.1039/c8cc02426j] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022]
Abstract
The free energy landscape concept that describes enzymes as an ensemble of differently populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme activity, enantioselectivity, and specificity. Mutations introduced in the enzyme sequence can alter the populations of the pre-existing conformational states, thus strongly modifying the enzyme ability to accommodate alternative substrates, revert its enantiopreferences, and even increase the activity for some residual promiscuous reactions. In this feature article, we present an overview of the current experimental and computational strategies to explore the conformational free energy landscape of enzymes. We provide a series of recent publications that highlight the key role of conformational dynamics for the enzyme evolution towards new functions and substrates, and provide some perspectives on how conformational dynamism should be considered in future computational enzyme design protocols.
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Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Eila Serrano-Hervás
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Adrian Romero-Rivera
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Javier Iglesias-Fernández
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Sílvia Osuna
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
- ICREA
,
Pg. Lluís Companys 23
, 08010 Barcelona
, Spain
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Abstract
Alcohol Dehydrogenase (ADH) enzymes catalyse the reversible reduction of prochiral ketones to the corresponding alcohols. These enzymes present two differently shaped active site pockets, which dictate their substrate scope and selectivity. In this study, we computationally evaluate the effect of two commonly reported active site mutations (I86A, and W110T) on a secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) through Molecular Dynamics simulations. Our results indicate that the introduced mutations induce dramatic changes in the shape of the active site, but most importantly they impact the substrate-enzyme interactions. We demonstrate that the combination of Molecular Dynamics simulations with the tools POVME and NCIplot corresponds to a powerful strategy for rationalising and engineering the stereoselectivity of ADH variants.
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Affiliation(s)
- Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Quimica, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, 17003 Girona, Spain.
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Li G, Maria-Solano MA, Romero-Rivera A, Osuna S, Reetz MT. Inducing high activity of a thermophilic enzyme at ambient temperatures by directed evolution. Chem Commun (Camb) 2018; 53:9454-9457. [PMID: 28795696 DOI: 10.1039/c7cc05377k] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The long-standing problem of achieving high activity of a thermophilic enzyme at low temperatures and short reaction times with little tradeoff in thermostability has been solved by directed evolution, an alcohol dehydrogenase found in hot springs serving as the catalyst in enantioselective ketone reductions.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany and Fachbereich Chemie der Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032, Marburg, Germany.
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany and Fachbereich Chemie der Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032, Marburg, Germany.
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