1
|
Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
Collapse
Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
| |
Collapse
|
2
|
Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
Collapse
Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| |
Collapse
|
3
|
Evolution of dynamical networks enhances catalysis in a designer enzyme. Nat Chem 2021; 13:1017-1022. [PMID: 34413499 DOI: 10.1038/s41557-021-00763-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/30/2021] [Indexed: 02/08/2023]
Abstract
Activation heat capacity is emerging as a crucial factor in enzyme thermoadaptation, as shown by the non-Arrhenius behaviour of many natural enzymes. However, its physical origin and relationship to the evolution of catalytic activity remain uncertain. Here we show that directed evolution of a computationally designed Kemp eliminase reshapes protein dynamics, which gives rise to an activation heat capacity absent in the original design. These changes buttress transition-state stabilization. Extensive molecular dynamics simulations show that evolution results in the closure of solvent-exposed loops and a better packing of the active site. Remarkably, this gives rise to a correlated dynamical network that involves the transition state and large parts of the protein. This network tightens the transition-state ensemble, which induces a negative activation heat capacity and non-linearity in the activity-temperature dependence. Our results have implications for understanding enzyme evolution and suggest that selectively targeting the conformational dynamics of the transition-state ensemble by design and evolution will expedite the creation of novel enzymes.
Collapse
|
4
|
Serapian SA, Moroni E, Ferraro M, Colombo G. Atomistic Simulations of the Mechanisms of the Poorly Catalytic Mitochondrial Chaperone Trap1: Insights into the Effects of Structural Asymmetry on Reactivity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Stefano A. Serapian
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100 Pavia, Italy
| | - Elisabetta Moroni
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
| | - Mariarosaria Ferraro
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100 Pavia, Italy
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
| |
Collapse
|
5
|
Römer RA, Römer NS, Wallis AK. Flexibility and mobility of SARS-CoV-2-related protein structures. Sci Rep 2021; 11:4257. [PMID: 33608565 PMCID: PMC7896093 DOI: 10.1038/s41598-021-82849-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/22/2021] [Indexed: 12/22/2022] Open
Abstract
The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein-using its complete homo-trimer configuration with 2905 residues-our method identifies a large-scale opening and closing of the S1 subunit through movement of the S[Formula: see text] domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.
Collapse
Affiliation(s)
- Rudolf A Römer
- CY Advanced Studies and LPTM (UMR8089 of CNRS), CY Cergy-Paris Université, 95302, Cergy-Pontoise, France.
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.
| | - Navodya S Römer
- School of Life Sciences, University of Lincoln, Brayford Pool Campus, Lincoln, LN6 7TS, UK
| | - A Katrine Wallis
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| |
Collapse
|
6
|
Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-1163. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
Collapse
|
7
|
Contreras S, Bertolani SJ, Siegel JB. A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry. ACS OMEGA 2019; 4:22356-22362. [PMID: 31909318 PMCID: PMC6941179 DOI: 10.1021/acsomega.9b02636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/04/2019] [Indexed: 05/15/2023]
Abstract
Accurate prediction and modeling of an enzyme's active site are critical for engineering efforts as well as providing insight into an enzyme's naturally occurring function. Previous efforts demonstrated that the integration of constraints enforcing strict geometric orientations between catalytic residues significantly improved the modeling accuracy for the active sites of monomeric enzymes. In this study, a similar approach was explored to evaluate the effect on the active sites of homomeric enzymes. A benchmark of 17 homomeric enzymes with known structures and a bound ligand relevant to the established chemistry were identified from the protein data bank. The enzymes identified span multiple classes as well as symmetries. Unlike what was observed for the monomeric enzymes, upon the application of catalytic geometric constraints, there was no significant improvement observed in modeling accuracy for either the active site of the protein structure or the accuracy of the subsequently docked ligand. Upon further analysis, it is apparent that the symmetric interface being modeled is inaccurate and prevented the active sites from being modeled at atomic-level accuracy. This is consistent with the challenge others have identified in being able to predict de novo protein symmetry. To further improve the accuracy of active site modeling for homomeric proteins, new methodologies to accurately model the symmetric interfaces of these complexes are needed.
Collapse
Affiliation(s)
- Stephanie
C. Contreras
- Department
of Chemistry, Department of Biochemistry and Molecular Medicine, and Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Steve J. Bertolani
- Department
of Chemistry, Department of Biochemistry and Molecular Medicine, and Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Department
of Chemistry, Department of Biochemistry and Molecular Medicine, and Genome Center, University of California, Davis, Davis, California 95616, United States
- E-mail:
| |
Collapse
|
8
|
McManus TJ, Wells SA, Walker AB. Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase. Phys Biol 2019; 17:016002. [PMID: 31220825 DOI: 10.1088/1478-3975/ab2b5c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
It has been suggested that structural rigidity is connected to thermostability, e.g. in enzymes from thermophilic microorganisms. We examine the importance of correctly handling salt bridges, and interactions which we term 'strong polars', when constructing the constraint network for global rigidity analysis in these systems. Through a comparison of rigidity in citrate synthases, we clarify the relationship between rigidity and thermostability. In particular, with our corrected handling of strong polar interactions, the difference in rigidity between mesophilic and thermophilic structures is detected more clearly than in previous studies. The increase in rigidity did not detract from the functional flexibility of the active site in all systems once their respective temperature range had been reached. We then examine the distribution of salt bridges in thermophiles that were previously unaccounted for in flexibility studies. We show that in hyperthermophiles these have stabilising roles in the active site; occuring in close proximity to key residues involved in catalysis and binding of the protein.
Collapse
Affiliation(s)
- T J McManus
- Department of Physics, University of Bath, Bath, BA2 7AY, United Kingdom
| | | | | |
Collapse
|
9
|
Oliveira ASF, Shoemark DK, Campello HR, Wonnacott S, Gallagher T, Sessions RB, Mulholland AJ. Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations. Structure 2019; 27:1171-1183.e3. [PMID: 31130483 DOI: 10.1016/j.str.2019.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/28/2019] [Accepted: 04/10/2019] [Indexed: 02/02/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) modulate synaptic transmission in the nervous system. These receptors have emerged as therapeutic targets in drug discovery for treating several conditions, including Alzheimer's disease, pain, and nicotine addiction. In this in silico study, we use a combination of equilibrium and nonequilibrium molecular dynamics simulations to map dynamic and structural changes induced by nicotine in the human α4β2 nAChR. They reveal a striking pattern of communication between the extracellular binding pockets and the transmembrane domains (TMDs) and show the sequence of conformational changes associated with the initial steps in this process. We propose a general mechanism for signal transduction for Cys-loop receptors: the mechanistic steps for communication proceed firstly through loop C in the principal subunit, and are subsequently transmitted, gradually and cumulatively, to loop F of the complementary subunit, and then to the TMDs through the M2-M3 linker.
Collapse
Affiliation(s)
- A Sofia F Oliveira
- School of Biochemistry, University of Bristol, Bristol BS8 1DT, UK; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Hugo Rego Campello
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Susan Wonnacott
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Timothy Gallagher
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| |
Collapse
|
10
|
Schlee S, Straub K, Schwab T, Kinateder T, Merkl R, Sterner R. Prediction of quaternary structure by analysis of hot spot residues in protein-protein interfaces: the case of anthranilate phosphoribosyltransferases. Proteins 2019; 87:815-825. [PMID: 31134642 DOI: 10.1002/prot.25744] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/06/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022]
Abstract
It is an important goal of computational biology to correctly predict the association state of a protein based on its amino acid sequence and the structures of known homologues. We have pursued this goal on the example of anthranilate phosphoribosyltransferase (AnPRT), an enzyme that is involved in the biosynthesis of the amino acid tryptophan. Firstly, known crystal structures of naturally occurring homodimeric AnPRTs were analyzed using the Protein Interfaces, Surfaces, and Assemblies (PISA) service of the European Bioinformatics Institute (EBI). This led to the identification of two hydrophobic "hot spot" amino acids in the protein-protein interface that were predicted to be essential for self-association. Next, in a comprehensive multiple sequence alignment (MSA), naturally occurring AnPRT variants with hydrophilic or charged amino acids in place of hydrophobic residues in the two hot spot positions were identified. Representative variants were characterized in terms of thermal stability, enzymatic activity, and quaternary structure. We found that AnPRT variants with charged residues in both hot spot positions exist exclusively as monomers in solution. Variants with hydrophilic amino acids in one hot spot position occur in both forms, monomer and dimer. The results of the present study provide a detailed characterization of the determinants of the AnPRT monomer-dimer equilibrium and show that analysis of hot spots in combination with MSAs can be a valuable tool in prediction of protein quaternary structures.
Collapse
Affiliation(s)
- Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Schwab
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| |
Collapse
|
11
|
Curado‐Carballada C, Feixas F, Osuna S. Molecular Dynamics Simulations on
Aspergillus niger
Monoamine Oxidase: Conformational Dynamics and Inter‐monomer Communication Essential for Its Efficient Catalysis. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Christian Curado‐Carballada
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona, Catalonia Spain
| | - Ferran Feixas
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona, Catalonia Spain
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona, Catalonia Spain
- ICREAPg. Lluís Companys 23 08010 Barcelona Spain
| |
Collapse
|
12
|
Roccatano D, Hayward S. Free Energy Profile of Domain Movement in Ligand-Free Citrate Synthase. J Phys Chem B 2019; 123:1998-2004. [PMID: 30744380 DOI: 10.1021/acs.jpcb.8b12001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Citrate synthase plays a fundamental role in the metabolic cycle of the cell. Its catalytic mechanism is complex involving the binding of two substrates that cause a domain movement. In this paper, we used classical molecular dynamics simulations and umbrella-sampling simulations to determine the potential of mean force along a reaction coordinate for the domain movement in ligand-free citrate synthase from pig ( Sus scrofa). The results show that, at 293 K, the closed-domain conformation has a ∼4 kb T higher energy than the open-domain conformation. In a simple two-state model, this difference means that the enzyme spends 98% of the time in the open-domain conformation ready to receive the substrate, oxaloacetate, rather than the closed-domain conformation where the binding site would be inaccessible to the substrate. Given that experimental evidence indicates that the binding of oxaloacetate induces at least partial closure, this would imply an induced-fit mechanism which we argue is applicable to all enzymes with a functional domain movement for reasons of catalytic efficiency. A barrier of 4 kb T gives an estimation of the mean first passage time in the range 1-10 μs.
Collapse
Affiliation(s)
- Danilo Roccatano
- School of Mathematics and Physics , University of Lincoln , Brayford Pool, Lincoln LN6 7TS , United Kingdom
| | - Steven Hayward
- Computational Biology Laboratory, School of Computing Sciences , University of East Anglia , Norwich NR4 7TJ , United Kingdom
| |
Collapse
|
13
|
Adjogatse E, Erskine P, Wells SA, Kelly JM, Wilden JD, Chan AWE, Selwood D, Coker A, Wood S, Cooper JB. Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:861-876. [DOI: 10.1107/s2059798318009208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/25/2018] [Indexed: 12/24/2022]
Abstract
Two of the world's most neglected tropical diseases, human African trypanosomiasis (HAT) and Chagas disease, are caused by protozoan parasites of the genus Trypanosoma. These organisms possess specialized metabolic pathways, frequently distinct from those in humans, which have potential to be exploited as novel drug targets. This study elucidates the structure and function of L-threonine-3-dehydrogenase (TDH) from T. brucei, the causative pathogen of HAT. TDH is a key enzyme in the metabolism of L-threonine, and an inhibitor of TDH has been shown to have trypanocidal activity in the procyclic form of T. brucei. TDH is a nonfunctional pseudogene in humans, suggesting that it may be possible to rationally design safe and specific therapies for trypanosomiasis by targeting this parasite enzyme. As an initial step, the TDH gene from T. brucei was expressed and the three-dimensional structure of the enzyme was solved by X-ray crystallography. In multiple crystallographic structures, T. brucei TDH is revealed to be a dimeric short-chain dehydrogenase that displays a considerable degree of conformational variation in its ligand-binding regions. Geometric simulations of the structure have provided insight into the dynamic behaviour of this enzyme. Furthermore, structures of TDH bound to its natural substrates and known inhibitors have been determined, giving an indication of the mechanism of catalysis of the enzyme. Collectively, these results provide vital details for future drug design to target TDH or related enzymes.
Collapse
|
14
|
Holland CJ, MacLachlan BJ, Bianchi V, Hesketh SJ, Morgan R, Vickery O, Bulek AM, Fuller A, Godkin A, Sewell AK, Rizkallah PJ, Wells S, Cole DK. In Silico and Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility. Front Immunol 2018; 9:674. [PMID: 29696015 PMCID: PMC5904202 DOI: 10.3389/fimmu.2018.00674] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
T-cell immunity is controlled by T cell receptor (TCR) binding to peptide major histocompatibility complexes (pMHCs). The nature of the interaction between these two proteins has been the subject of many investigations because of its central role in immunity against pathogens, cancer, in autoimmunity, and during organ transplant rejection. Crystal structures comparing unbound and pMHC-bound TCRs have revealed flexibility at the interaction interface, particularly from the perspective of the TCR. However, crystal structures represent only a snapshot of protein conformation that could be influenced through biologically irrelevant crystal lattice contacts and other factors. Here, we solved the structures of three unbound TCRs from multiple crystals. Superposition of identical TCR structures from different crystals revealed some conformation differences of up to 5 Å in individual complementarity determining region (CDR) loops that are similar to those that have previously been attributed to antigen engagement. We then used a combination of rigidity analysis and simulations of protein motion to reveal the theoretical potential of TCR CDR loop flexibility in unbound state. These simulations of protein motion support the notion that crystal structures may only offer an artifactual indication of TCR flexibility, influenced by crystallization conditions and crystal packing that is inconsistent with the theoretical potential of intrinsic TCR motions.
Collapse
Affiliation(s)
- Christopher J Holland
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Immunocore, Abingdon, United Kingdom
| | - Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Valentina Bianchi
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Sophie J Hesketh
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Richard Morgan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Owen Vickery
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anna M Bulek
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Andrew Godkin
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Pierre J Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Stephen Wells
- Department of Chemistry, University of Bath, Bath, United Kingdom
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Immunocore, Abingdon, United Kingdom
| |
Collapse
|
15
|
Raza S, Sanober G, Rungrotmongkol T, Azam SS. The Vitality of Swivel Domain Motion in Performance of Enzyme I of Phosphotransferase System; A Comprehensive Molecular Dynamic Study. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.07.086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
16
|
Jones HBL, Wells SA, Prentice EJ, Kwok A, Liang LL, Arcus VL, Pudney CR. A complete thermodynamic analysis of enzyme turnover links the free energy landscape to enzyme catalysis. FEBS J 2017. [PMID: 28650586 DOI: 10.1111/febs.14152] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Our understanding of how enzymes work is coloured by static structure depictions where the enzyme scaffold is presented as either immobile, or in equilibrium between well-defined static conformations. Proteins, however, exhibit a large degree of motion over a broad range of timescales and magnitudes and this is defined thermodynamically by the enzyme free energy landscape (FEL). The role and importance of enzyme motion is extremely contentious. Much of the challenge is in the experimental detection of so called 'conformational sampling' involved in enzyme turnover. Herein we apply combined pressure and temperature kinetics studies to elucidate the full suite of thermodynamic parameters defining an enzyme FEL as it relates to enzyme turnover. We find that the key thermodynamic parameters governing vibrational modes related to enzyme turnover are the isobaric expansivity term and the change in heat capacity for enzyme catalysis. Variation in the enzyme FEL affects these terms. Our analysis is supported by a range of biophysical and computational approaches that specifically capture information on protein vibrational modes and the FEL (all atom flexibility calculations, red edge excitation shift spectroscopy and viscosity studies) that provide independent evidence for our findings. Our data suggest that restricting the enzyme FEL may be a powerful strategy when attempting to rationally engineer enzymes, particularly to alter thermal activity. Moreover, we demonstrate how rational predictions can be made with a rapid computational approach.
Collapse
Affiliation(s)
- Hannah B L Jones
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Stephen A Wells
- Department of Chemical Engineering, Faculty of Science, University of Bath, UK
| | - Erica J Prentice
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - Anthony Kwok
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Liyin L Liang
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - Vickery L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - Christopher R Pudney
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| |
Collapse
|
17
|
Fokas AS, Cole DJ, Hine NDM, Wells SA, Payne MC, Chin AW. Evidence of Correlated Static Disorder in the Fenna-Matthews-Olson Complex. J Phys Chem Lett 2017; 8:2350-2356. [PMID: 28485971 DOI: 10.1021/acs.jpclett.7b00669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Observation of excitonic quantum beats in photosynthetic antennae has prompted wide debate regarding the function of excitonic coherence in pigment-protein complexes. Much of this work focuses on the interactions of excitons with the femto-to-picosecond dynamical fluctuations of their environment. However, in experiments these effects can be masked by static disorder of the excited-state energies across ensembles, whose microscopic origins are challenging to predict. Here the excited-state properties of ∼2000 atom clusters of the Fenna-Matthews-Olson complex are simulated using a unique combination of linear-scaling density functional theory and constrained geometric dynamics. While slow, large amplitude protein motion leads to large variations in the Qy transitions of two pigments, we identify pigment-protein correlations that greatly reduce variations in the energy gap across the ensemble, which is consistent with experimental observations of suppressed inhomogeneous dephasing of quantum beats.
Collapse
Affiliation(s)
- Alexander S Fokas
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J Cole
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
- School of Chemistry, Newcastle University , Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick , Coventry CV4 7AL, United Kingdom
| | - Stephen A Wells
- Department of Chemistry, University of Bath , Claverton Down BA2 7AY, United Kingdom
| | - Michael C Payne
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Alex W Chin
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| |
Collapse
|
18
|
Römer RA, Wells SA, Emilio Jimenez‐Roldan J, Bhattacharyya M, Vishweshwara S, Freedman RB. The flexibility and dynamics of protein disulfide isomerase. Proteins 2016; 84:1776-1785. [PMID: 27616289 PMCID: PMC5111589 DOI: 10.1002/prot.25159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/29/2016] [Accepted: 08/24/2016] [Indexed: 01/01/2023]
Abstract
We have studied the mobility of the multidomain folding catalyst, protein disulfide isomerase (PDI), by a coarse‐graining approach based on flexibility. We analyze our simulations of yeast PDI (yPDI) using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. We find that there is interdomain flexibility at every interdomain junction but these show very different characteristics. The extent of interdomain flexibility is such that yPDI's two active sites can approach much more closely than is found in crystal structures—and indeed hinge motion to bring these sites into proximity is the lowest energy normal mode of motion of the protein. The flexibility predicted for yPDI (based on one structure) includes the other known conformation of yPDI and is consistent with (i) the mobility observed experimentally for mammalian PDI and (ii) molecular dynamics. We also observe intradomain flexibility and clear differences between the domains in their propensity for internal motion. Our results suggest that PDI flexibility enables it to interact with many different partner molecules of widely different sizes and shapes, and highlights considerable similarities of yPDI and mammalian PDI. Proteins 2016; 84:1776–1785. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Rudolf A. Römer
- Department of Physics and Centre for Scientific ComputingThe University of WarwickCoventryCV4 7ALUnited Kingdom
| | - Stephen A. Wells
- Department of Chemical EngineeringUniversity of BathBathBA2 7AYUnited Kingdom
| | - J. Emilio Jimenez‐Roldan
- Department of Physics and Centre for Scientific ComputingThe University of WarwickCoventryCV4 7ALUnited Kingdom
| | - Moitrayee Bhattacharyya
- Molecular Biophysics Unit, Indian Institute of ScienceBangalore560012India
- Present address: Moitrayee Bhattacharyya's current address is Department of Molecular and Cell BiologyUniversity of California BerkeleyCalifornia94720.
| | | | - Robert B. Freedman
- School of Life SciencesThe University of WarwickCoventryCV4 7ALUnited Kingdom
| |
Collapse
|
19
|
Neti SS, Eckert DM, Poulter CD. Construction of Functional Monomeric Type 2 Isopentenyl Diphosphate:Dimethylallyl Diphosphate Isomerase. Biochemistry 2016; 55:4229-38. [PMID: 27379573 DOI: 10.1021/acs.biochem.6b00564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the isoprenoid biosynthetic pathway. The enzyme from Streptomyces pneumoniae (spIDI-2) is a homotetramer in solution with behavior, including a substantial increase in the rate of FMN reduction by NADPH in the presence of IPP, suggesting that substrate binding at one subunit alters the kinetic and binding properties of another. We now report the construction of catalytically active monomeric spIDI-2. The monomeric enzyme contains a single-point mutation (N37A) and a six-residue C-terminal deletion that preserves the secondary structure of the subunits in the wild-type (wt) homotetramer. UV-vis spectra of the enzyme-bound flavin mononucleotide (FMN) cofactor in FMNox, FMNred, and FMNred·IPP/DMAPP states are the same for monomeric and wt homotetrameric spIDI-2. The mutations in monomeric IDI-2 lower the melting temperature of the protein by 20 °C and reduce the binding affinities of FMN and IDI by 40-fold but have a minimal effect on kcat. Stopped-flow kinetic studies of monomeric spIDI-2 showed that the rate of reduction of FMN by NADH (k = 1.64 × 10(-3) s(-1)) is substantially faster when IPP is added to the monomeric enzyme (k = 0.57 s(-1)), similar to behavior seen for wt-spIDI-2. Our results indicate that cooperative interactions among subunits in the wt homotetramer are not responsible for the increased rate of reduction of spIDI-2·FMN by NADH, and two possible scenarios for the enhancement are suggested.
Collapse
Affiliation(s)
- Syam Sundar Neti
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Debra M Eckert
- Department of Biochemistry, University of Utah School of Medicine , Salt Lake City, Utah 84112, United States
| | - C Dale Poulter
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
| |
Collapse
|