1
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Sun J, Boyle AL, Brünle S, Ubbink M. A low-barrier proton shared between two aspartates acts as a conformational switch that changes the substrate specificity of the β-lactamase BlaC. Int J Biol Macromol 2024; 278:134665. [PMID: 39134195 DOI: 10.1016/j.ijbiomac.2024.134665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
Serine β-lactamases inactivate β-lactam antibiotics in a two-step mechanism comprising acylation and deacylation. For the deacylation step, a water molecule is activated by a conserved glutamate residue to release the adduct from the enzyme. The third-generation cephalosporin ceftazidime is a poor substrate for the class A β-lactamase BlaC from Mycobacterium tuberculosis but it can be hydrolyzed faster when the active site pocket is enlarged, as was reported for mutant BlaC P167S. The conformational change in the Ω-loop of the P167S mutant displaces the conserved glutamate (Glu166), suggesting it is not required for deacylation of the ceftazidime adduct. Here, we report the characterization of wild type BlaC and BlaC E166A at various pH values. The presence of Glu166 strongly enhances activity against nitrocefin but not ceftazidime, indicating it is indeed not required for deacylation of the adduct of the latter substrate. At high pH wild type BlaC was found to exist in two states, one of which converts ceftazidime much faster, resembling the open state previously reported for the BlaC mutant P167S. The pH-dependent switch between the closed and open states is caused by the loss at high pH of a low-barrier hydrogen bond, a proton shared between Asp172 and Asp179. These results illustrate how readily shifts in substrate specificity can occur as a consequence of subtle changes in protein structure.
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Affiliation(s)
- Jing Sun
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Aimee L Boyle
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Steffen Brünle
- Biophysical Structure Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Marcellus Ubbink
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
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2
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Mallimadugula UL, Cruz MA, Vithani N, Zimmerman MI, Bowman GR. The probability of cryptic pocket opening controls functional tradeoffs in filovirus immune evasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.22.609218. [PMID: 39229186 PMCID: PMC11370563 DOI: 10.1101/2024.08.22.609218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Cryptic pockets are of growing interest as potential drug targets. However, it remains unclear whether they contribute to protein function or if they are merely happenstantial features that can easily be evolved away to achieve drug resistance. Here, we explore whether a cryptic pocket in the Interferon Inhibitory Domain (IID) of viral protein 35 (VP35) of Zaire ebolavirus has a functional role. We use simulations and experiments to study the relationship between cryptic pocket opening and double-stranded RNA (dsRNA) binding of the IIDs of two other filoviruses, Reston and Marburg. These homologs have structures nearly identical to Zaire but block different interferon pathways because Marburg IID only binds the backbone, while Zaire and Reston IIDs bind both backbone and blunt ends of dsRNA. We hypothesized that these differences arise from alterations in their pocket dynamics. Simulations and thiol-labeling experiments demonstrate that Reston has a lower probability of opening the cryptic pocket while Marburg has a higher probability than Zaire. Subsequent dsRNA-binding assays with different length substrates suggest that closed conformations preferentially bind dsRNA blunt ends while open conformations prefer binding the backbone. Further, a point mutation that increases the probability of cryptic pocket opening in Reston shows that the open states prefer backbone binding, while a substitution that lowers the probability of pocket opening in Zaire improves binding to blunt ends. These results demonstrate the cryptic pocket controls a functional tradeoff, suggesting cryptic pockets are under selective pressure and may be difficult to evolve away to achieve drug resistance.
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Affiliation(s)
- Upasana L Mallimadugula
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew A Cruz
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Neha Vithani
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maxwell I Zimmerman
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gregory R Bowman
- Department of Biochemistry & Biophysics and Bioengineering, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Miller JJ, Mallimadugula UL, Zimmerman MI, Stuchell-Brereton MD, Soranno A, Bowman GR. Accounting for fast vs slow exchange in single molecule FRET experiments reveals hidden conformational states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597137. [PMID: 38895430 PMCID: PMC11185552 DOI: 10.1101/2024.06.03.597137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Proteins are dynamic systems whose structural preferences determine their function. Unfortunately, building atomically detailed models of protein structural ensembles remains challenging, limiting our understanding of the relationships between sequence, structure, and function. Combining single molecule Förster resonance energy transfer (smFRET) experiments with molecular dynamics simulations could provide experimentally grounded, all-atom models of a protein's structural ensemble. However, agreement between the two techniques is often insufficient to achieve this goal. Here, we explore whether accounting for important experimental details like averaging across structures sampled during a given smFRET measurement is responsible for this apparent discrepancy. We present an approach to account for this time-averaging by leveraging the kinetic information available from Markov state models of a protein's dynamics. This allows us to accurately assess which timescales are averaged during an experiment. We find this approach significantly improves agreement between simulations and experiments in proteins with varying degrees of dynamics, including the well-ordered protein T4 lysozyme, the partially disordered protein apolipoprotein E (ApoE), and a disordered amyloid protein (Aβ40). We find evidence for hidden states that are not apparent in smFRET experiments because of time averaging with other structures, akin to states in fast exchange in NMR, and evaluate different force fields. Finally, we show how remaining discrepancies between computations and experiments can be used to guide additional simulations and build structural models for states that were previously unaccounted for. We expect our approach will enable combining simulations and experiments to understand the link between sequence, structure, and function in many settings.
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Affiliation(s)
- Justin J. Miller
- Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Upasana L. Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Maxwell I. Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Melissa D. Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Gregory R. Bowman
- Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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4
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Borsatto A, Gianquinto E, Rizzi V, Gervasio FL. SWISH-X, an Expanded Approach to Detect Cryptic Pockets in Proteins and at Protein-Protein Interfaces. J Chem Theory Comput 2024; 20:3335-3348. [PMID: 38563746 PMCID: PMC11044271 DOI: 10.1021/acs.jctc.3c01318] [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: 12/01/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024]
Abstract
Protein-protein interactions mediate most molecular processes in the cell, offering a significant opportunity to expand the set of known druggable targets. Unfortunately, targeting these interactions can be challenging due to their typically flat and featureless interaction surfaces, which often change as the complex forms. Such surface changes may reveal hidden (cryptic) druggable pockets. Here, we analyze a set of well-characterized protein-protein interactions harboring cryptic pockets and investigate the predictive power of current computational methods. Based on our observations, we developed a new computational strategy, SWISH-X (SWISH Expanded), which combines the established cryptic pocket identification capabilities of SWISH with the rapid temperature range exploration of OPES MultiThermal. SWISH-X is able to reliably identify cryptic pockets at protein-protein interfaces while retaining its predictive power for revealing cryptic pockets in isolated proteins, such as TEM-1 β-lactamase.
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Affiliation(s)
- Alberto Borsatto
- School
of Pharmaceutical Sciences, University of
Geneva, 1205 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1205 Geneva, Switzerland
- Swiss
Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Eleonora Gianquinto
- Department
of Drug Science and Technology, University
of Turin, 10125 Turin, Italy
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, 1205 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1205 Geneva, Switzerland
- Swiss
Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Francesco Luigi Gervasio
- School
of Pharmaceutical Sciences, University of
Geneva, 1205 Geneva, Switzerland
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1205 Geneva, Switzerland
- Swiss
Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department
of Chemistry, University College London, WC1 H0AJ London, United Kingdom
- Institute
of Structural and Molecular Biology, University
College London, WC1E7JE London, United Kingdom
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5
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Amisaki T. Multilevel superposition for deciphering the conformational variability of protein ensembles. Brief Bioinform 2024; 25:bbae137. [PMID: 38557679 PMCID: PMC10983786 DOI: 10.1093/bib/bbae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
The dynamics and variability of protein conformations are directly linked to their functions. Many comparative studies of X-ray protein structures have been conducted to elucidate the relevant conformational changes, dynamics and heterogeneity. The rapid increase in the number of experimentally determined structures has made comparison an effective tool for investigating protein structures. For example, it is now possible to compare structural ensembles formed by enzyme species, variants or the type of ligands bound to them. In this study, the author developed a multilevel model for estimating two covariance matrices that represent inter- and intra-ensemble variability in the Cartesian coordinate space. Principal component analysis using the two estimated covariance matrices identified the inter-/intra-enzyme variabilities, which seemed to be important for the enzyme functions, with the illustrative examples of cytochrome P450 family 2 enzymes and class A $\beta$-lactamases. In P450, in which each enzyme has its own active site of a distinct size, an active-site motion shared universally between the enzymes was captured as the first principal mode of the intra-enzyme covariance matrix. In this case, the method was useful for understanding the conformational variability after adjusting for the differences between enzyme sizes. The developed method is advantageous in small ensemble-size problems and hence promising for use in comparative studies on experimentally determined structures where ensemble sizes are smaller than those generated, for example, by molecular dynamics simulations.
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Affiliation(s)
- Takashi Amisaki
- Department of Biological Regulation, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan
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6
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Meller A, Kelly D, Smith LG, Bowman GR. Toward physics-based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants. Protein Sci 2024; 33:e4902. [PMID: 38358129 PMCID: PMC10868452 DOI: 10.1002/pro.4902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/01/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
The goal of precision medicine is to utilize our knowledge of the molecular causes of disease to better diagnose and treat patients. However, there is a substantial mismatch between the small number of food and drug administration (FDA)-approved drugs and annotated coding variants compared to the needs of precision medicine. This review introduces the concept of physics-based precision medicine, a scalable framework that promises to improve our understanding of sequence-function relationships and accelerate drug discovery. We show that accounting for the ensemble of structures a protein adopts in solution with computer simulations overcomes many of the limitations imposed by assuming a single protein structure. We highlight studies of protein dynamics and recent methods for the analysis of structural ensembles. These studies demonstrate that differences in conformational distributions predict functional differences within protein families and between variants. Thanks to new computational tools that are providing unprecedented access to protein structural ensembles, this insight may enable accurate predictions of variant pathogenicity for entire libraries of variants. We further show that explicitly accounting for protein ensembles, with methods like alchemical free energy calculations or docking to Markov state models, can uncover novel lead compounds. To conclude, we demonstrate that cryptic pockets, or cavities absent in experimental structures, provide an avenue to target proteins that are currently considered undruggable. Taken together, our review provides a roadmap for the field of protein science to accelerate precision medicine.
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Affiliation(s)
- Artur Meller
- Department of Biochemistry and Molecular BiophysicsWashington University in St. LouisSt. LouisMissouriUSA
- Medical Scientist Training ProgramWashington University in St. LouisSt. LouisMissouriUSA
- Departments of Biochemistry & Biophysics and BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Devin Kelly
- Departments of Biochemistry & Biophysics and BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Louis G. Smith
- Departments of Biochemistry & Biophysics and BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Gregory R. Bowman
- Departments of Biochemistry & Biophysics and BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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7
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Singh K, Reddy G. Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms. J Chem Theory Comput 2024; 20:421-435. [PMID: 38134376 DOI: 10.1021/acs.jctc.3c00999] [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: 12/24/2023]
Abstract
Riboswitches are mRNA segments that regulate gene expression through conformational changes driven by their cognate ligand binding. The ykkC motif forms a riboswitch class that selectively senses a guanidinium ion (Gdm+) and regulates the downstream expression of proteins which aid in the efflux of excess Gdm+ from the cells. The aptamer domain (AD) of the guanidine-III riboswitch forms an H-type pseudoknot with a triple helical domain that binds a Gdm+. We studied the binding of Gdm+ to the AD of the guanidine (ykkC)-III riboswitch using computer simulations to probe the specificity of the riboswitch to Gdm+ binding. We show that Gdm+ binding is a fast process occurring on the nanosecond time scale, with minimal conformational changes to the AD. Using machine learning and Markov-state models, we identified the excited conformational states of the AD, which have a high Gdm+ binding propensity, making the Gdm+ binding landscape complex exhibiting both conformational selection and induced-fit mechanisms. The proposed apo-AD excited states and their role in the ligand-sensing mechanism are amenable to experimental verification. Further, targeting these excited-state conformations in discovering new antibiotics can be explored.
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Affiliation(s)
- Kushal Singh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012 Karnataka, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012 Karnataka, India
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8
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Colombo G. Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design. Curr Opin Struct Biol 2023; 83:102702. [PMID: 37716095 DOI: 10.1016/j.sbi.2023.102702] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The concept of allostery has become a central tenet in the study of biological systems. In parallel, the discovery of allosteric drugs is generating new opportunities to selectively modulate difficult targets involved in pathologic mechanisms. Molecular simulations can provide atomistically detailed insight into the processes involved in allosteric regulation and signaling, and at the same time, they have the potential to unveil regulatory hotspots or cryptic sites that are not immediately evident from the analysis of static structures. In this context, computational approaches should be able to connect the study of allosteric regulation at different scales to the possibility of leveraging this knowledge to expand the chemical space of new, active drugs. Here, we will discuss recent advances in the study of allosteric regulation via computational methods and connect the mechanistic knowledge generated to the possibility of designing new small molecules that can tweak the functions of their receptors.
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Affiliation(s)
- Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.
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9
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Sun J, Chikunova A, Boyle AL, Voskamp P, Timmer M, Ubbink M. Enhanced activity against a third-generation cephalosporin by destabilization of the active site of a class A beta-lactamase. Int J Biol Macromol 2023; 250:126160. [PMID: 37549761 DOI: 10.1016/j.ijbiomac.2023.126160] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The β-lactamase BlaC conveys resistance to a broad spectrum of β-lactam antibiotics to its host Mycobacterium tuberculosis but poorly hydrolyzes third-generation cephalosporins, such as ceftazidime. Variants of other β-lactamases have been reported to gain activity against ceftazidime at the cost of the native activity. To understand this trade-off, laboratory evolution was performed, screening for enhanced ceftazidime activity. The variant BlaC Pro167Ser shows faster breakdown of ceftazidime, poor hydrolysis of ampicillin and only moderately reduced activity against nitrocefin. NMR spectroscopy, crystallography and kinetic assays demonstrate that the resting state of BlaC P167S exists in an open and a closed state. The open state is more active in the hydrolysis of ceftazidime. In this state the catalytic residue Glu166, generally believed to be involved in the activation of the water molecule required for deacylation, is rotated away from the active site, suggesting it plays no role in the hydrolysis of ceftazidime. In the closed state, deacylation of the BlaC-ceftazidime adduct is slow, while hydrolysis of nitrocefin, which requires the presence of Glu166 in the active site, is barely affected, providing a structural explanation for the trade-off in activities.
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Affiliation(s)
- Jing Sun
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Aleksandra Chikunova
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Aimee L Boyle
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Patrick Voskamp
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Monika Timmer
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Marcellus Ubbink
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
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10
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Ridgway H, Orbell JD, Matsoukas MT, Kelaidonis K, Moore GJ, Tsiodras S, Gorgoulis VG, Chasapis CT, Apostolopoulos V, Matsoukas JM. W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics. Comput Struct Biotechnol J 2023; 21:4589-4612. [PMID: 37817778 PMCID: PMC10561063 DOI: 10.1016/j.csbj.2023.09.003] [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] [Indexed: 10/12/2023] Open
Abstract
Furins are serine endoproteases that process precursor proteins into their biologically active forms, and they play essential roles in normal metabolism and disease presentation, including promoting expression of bacterial virulence factors and viral pathogenesis. Thus, furins represent vital targets for development of antimicrobial and antiviral therapeutics. Recent experimental evidence indicated that dichlorophenyl (DCP)-pyridine "BOS" drugs (e.g., BOS-318) competitively inhibit human furin by an induced-fit mechanism in which tryptophan W254 in the furin catalytic cleft (FCC) functions as a molecular gate, rotating nearly 180o through a steep energy barrier about its chi-1 dihedral to an "open" orientation, exposing a buried (i.e., cryptic) hydrophobic pocket 1. Once exposed, the non-polar DCP group of BOS-318, and similar halo-phenyl groups of analogs, enter the cryptic pocket, stabilizing drug binding. Here, we demonstrate flexible-receptor docking of BOS-318 (and various analogs) was unable to emulate the induced-fit motif, even when tryptophan was replaced with less bulky phenylalanine or glycine. While either substitution allowed access to the hydrophobic pocket for most ligands tested, optimal binding was observed only for W254, inferring a stabilizing effect of the indole sidechain. Furthermore, non-equilibrium steered molecular dynamics (sMD) in which the bound drugs (or their fragments) were extracted from the FCC did not cause closure of the open W254 gate, consistent with the thermodynamic stability of the open or closed W254 orientations. Finally, interactive molecular dynamics (iMD) revealed two putative conduits of drug entry and binding into the FCC, each coupled with W254 dihedral rotation and opening of the cryptic pocket. The iMD simulations further revealed ligand entry and binding in the FCC is likely driven in part by energy fluxes stemming from disruption and re-formation of ligand and protein solvation shells during drug migration from the solution phase into the FCC.
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Affiliation(s)
- Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - John D. Orbell
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- College of Sport, Health & Engineering, Victoria University, Melbourne, VIC 8001, Australia
| | | | | | - Graham J. Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V8Y 3H4, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sotiris Tsiodras
- Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vasilis G. Gorgoulis
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, GR-11527 Athens, Greece
- Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, M20 4GJ Manchester, UK
- Biomedical Research Foundation, Academy of Athens, GR-11527 Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Surrey, UK
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne 3030, VIC, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne 3021, VIC, Australia
| | - John M. Matsoukas
- NewDrug/NeoFar PC, Patras Science Park, Patras 26504, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne 3030, VIC, Australia
- Department of Chemistry, University of Patras, 26504 Patras, Greece
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11
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Hommel U, Hurth K, Rondeau JM, Vulpetti A, Ostermeier D, Boettcher A, Brady JP, Hediger M, Lehmann S, Koch E, Blechschmidt A, Yamamoto R, Tundo Dottorello V, Haenni-Holzinger S, Kaiser C, Lehr P, Lingel A, Mureddu L, Schleberger C, Blank J, Ramage P, Freuler F, Eder J, Bornancin F. Discovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1β. Nat Commun 2023; 14:5497. [PMID: 37679328 PMCID: PMC10484922 DOI: 10.1038/s41467-023-41190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Human interleukin-1β (hIL-1β) is a pro-inflammatory cytokine involved in many diseases. While hIL-1β directed antibodies have shown clinical benefit, an orally available low-molecular weight antagonist is still elusive, limiting the applications of hIL-1β-directed therapies. Here we describe the discovery of a low-molecular weight hIL-1β antagonist that blocks the interaction with the IL-1R1 receptor. Starting from a low affinity fragment-based screening hit 1, structure-based optimization resulted in a compound (S)-2 that binds and antagonizes hIL-1β with single-digit micromolar activity in biophysical, biochemical, and cellular assays. X-ray analysis reveals an allosteric mode of action that involves a hitherto unknown binding site in hIL-1β encompassing two loops involved in hIL-1R1/hIL-1β interactions. We show that residues of this binding site are part of a conformationally excited state of the mature cytokine. The compound antagonizes hIL-1β function in cells, including primary human fibroblasts, demonstrating the relevance of this discovery for future development of hIL-1β directed therapeutics.
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Affiliation(s)
- Ulrich Hommel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
| | - Konstanze Hurth
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
| | - Jean-Michel Rondeau
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Anna Vulpetti
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Daniela Ostermeier
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Andreas Boettcher
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jacob Peter Brady
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Michael Hediger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Sylvie Lehmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Elke Koch
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Anke Blechschmidt
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Rina Yamamoto
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | | | | | - Christian Kaiser
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Philipp Lehr
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Luca Mureddu
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Christian Schleberger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jutta Blank
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Paul Ramage
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Felix Freuler
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Joerg Eder
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Frédéric Bornancin
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
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12
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Corbella M, Pinto GP, Kamerlin SCL. Loop dynamics and the evolution of enzyme activity. Nat Rev Chem 2023; 7:536-547. [PMID: 37225920 DOI: 10.1038/s41570-023-00495-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/26/2023]
Abstract
In the early 2000s, Tawfik presented his 'New View' on enzyme evolution, highlighting the role of conformational plasticity in expanding the functional diversity of limited repertoires of sequences. This view is gaining increasing traction with increasing evidence of the importance of conformational dynamics in both natural and laboratory evolution of enzymes. The past years have seen several elegant examples of harnessing conformational (particularly loop) dynamics to successfully manipulate protein function. This Review revisits flexible loops as critical participants in regulating enzyme activity. We showcase several systems of particular interest: triosephosphate isomerase barrel proteins, protein tyrosine phosphatases and β-lactamases, while briefly discussing other systems in which loop dynamics are important for selectivity and turnover. We then discuss the implications for engineering, presenting examples of successful loop manipulation in either improving catalytic efficiency, or changing selectivity completely. Overall, it is becoming clearer that mimicking nature by manipulating the conformational dynamics of key protein loops is a powerful method of tailoring enzyme activity, without needing to target active-site residues.
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Affiliation(s)
- Marina Corbella
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Gaspar P Pinto
- Department of Chemistry, Uppsala University, Uppsala, Sweden
- Cortex Discovery GmbH, Regensburg, Germany
| | - Shina C L Kamerlin
- Department of Chemistry, Uppsala University, Uppsala, Sweden.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
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13
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Voelz VA, Pande VS, Bowman GR. Folding@home: Achievements from over 20 years of citizen science herald the exascale era. Biophys J 2023; 122:2852-2863. [PMID: 36945779 PMCID: PMC10398258 DOI: 10.1016/j.bpj.2023.03.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/26/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over 20 years, the Folding@home distributed computing project has pioneered a massively parallel approach to biomolecular simulation, harnessing the resources of citizen scientists across the globe. Here, we summarize the scientific and technical advances this perspective has enabled. As the project's name implies, the early years of Folding@home focused on driving advances in our understanding of protein folding by developing statistical methods for capturing long-timescale processes and facilitating insight into complex dynamical processes. Success laid a foundation for broadening the scope of Folding@home to address other functionally relevant conformational changes, such as receptor signaling, enzyme dynamics, and ligand binding. Continued algorithmic advances, hardware developments such as graphics processing unit (GPU)-based computing, and the growing scale of Folding@home have enabled the project to focus on new areas where massively parallel sampling can be impactful. While previous work sought to expand toward larger proteins with slower conformational changes, new work focuses on large-scale comparative studies of different protein sequences and chemical compounds to better understand biology and inform the development of small-molecule drugs. Progress on these fronts enabled the community to pivot quickly in response to the COVID-19 pandemic, expanding to become the world's first exascale computer and deploying this massive resource to provide insight into the inner workings of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and aid the development of new antivirals. This success provides a glimpse of what is to come as exascale supercomputers come online and as Folding@home continues its work.
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Affiliation(s)
- Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania
| | | | - Gregory R Bowman
- Departments of Biochemistry & Biophysics and of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania.
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14
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He J, Dmochowski IJ. Local Xenon-Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme. Biochemistry 2023; 62:1659-1669. [PMID: 37192381 PMCID: PMC10821772 DOI: 10.1021/acs.biochem.3c00046] [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] [Indexed: 05/18/2023]
Abstract
Noble gases have well-established biological effects, yet their molecular mechanisms remain poorly understood. Here, we investigated, both experimentally and computationally, the molecular modes of xenon (Xe) action in bacteriophage T4 lysozyme (T4L). By combining indirect gassing methods with a colorimetric lysozyme activity assay, a reversible, Xe-specific (20 ± 3)% inhibition effect was observed. Accelerated molecular dynamic simulations revealed that Xe exerts allosteric inhibition on the protein by expanding a C-terminal hydrophobic cavity. Xe-induced cavity expansion results in global conformational changes, with long-range transduction distorting the active site where peptidoglycan binds. Interestingly, the peptide substrate binding site that enables lysozyme specificity does not change conformation. Two T4L mutants designed to reshape the C-terminal Xe cavity established a correlation between cavity expansion and enzyme inhibition. This work also highlights the use of Xe flooding simulations to identify new cryptic binding pockets. These results enrich our understanding of Xe-protein interactions at the molecular level and inspire further biochemical investigations with noble gases.
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Affiliation(s)
- Jiayi He
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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15
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Meller A, Bhakat S, Solieva S, Bowman GR. Accelerating Cryptic Pocket Discovery Using AlphaFold. J Chem Theory Comput 2023. [PMID: 36948209 PMCID: PMC10373493 DOI: 10.1021/acs.jctc.2c01189] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Cryptic pockets, or pockets absent in ligand-free, experimentally determined structures, hold great potential as drug targets. However, cryptic pocket openings are often beyond the reach of conventional biomolecular simulations because certain cryptic pocket openings involve slow motions. Here, we investigate whether AlphaFold can be used to accelerate cryptic pocket discovery either by generating structures with open pockets directly or generating structures with partially open pockets that can be used as starting points for simulations. We use AlphaFold to generate ensembles for 10 known cryptic pocket examples, including five that were deposited after AlphaFold's training data were extracted from the PDB. We find that in 6 out of 10 cases AlphaFold samples the open state. For plasmepsin II, an aspartic protease from the causative agent of malaria, AlphaFold only captures a partial pocket opening. As a result, we ran simulations from an ensemble of AlphaFold-generated structures and show that this strategy samples cryptic pocket opening, even though an equivalent amount of simulations launched from a ligand-free experimental structure fails to do so. Markov state models (MSMs) constructed from the AlphaFold-seeded simulations quickly yield a free energy landscape of cryptic pocket opening that is in good agreement with the same landscape generated with well-tempered metadynamics. Taken together, our results demonstrate that AlphaFold has a useful role to play in cryptic pocket discovery but that many cryptic pockets may remain difficult to sample using AlphaFold alone.
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Affiliation(s)
- Artur Meller
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
- Medical Scientist Training Program, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
| | - Soumendranath Bhakat
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Shahlo Solieva
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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16
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Liu J, Amaral LAN, Keten S. A new approach for extracting information from protein dynamics. Proteins 2023; 91:183-195. [PMID: 36094321 PMCID: PMC9844508 DOI: 10.1002/prot.26421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 01/19/2023]
Abstract
Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.
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Affiliation(s)
- Jenny Liu
- Department of Mechanical Engineering, Northwestern University
| | - Luís A. N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University
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17
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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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18
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Yuan Y, Deng J, Cui Q. Molecular Dynamics Simulations Establish the Molecular Basis for the Broad Allostery Hotspot Distributions in the Tetracycline Repressor. J Am Chem Soc 2022; 144:10870-10887. [PMID: 35675441 DOI: 10.1021/jacs.2c03275] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is imperative to identify the network of residues essential to the allosteric coupling for the purpose of rationally engineering allostery in proteins. Deep mutational scanning analysis has emerged as a function-centric approach for identifying such allostery hotspots in a comprehensive and unbiased fashion, leading to observations that challenge our understanding of allostery at the molecular level. Specifically, a recent deep mutational scanning study of the tetracycline repressor (TetR) revealed an unexpectedly broad distribution of allostery hotspots throughout the protein structure. Using extensive molecular dynamics simulations (up to 50 μs) and free energy computations, we establish the molecular and energetic basis for the strong anticooperativity between the ligand and DNA binding sites. The computed free energy landscapes in different ligation states illustrate that allostery in TetR is well described by a conformational selection model, in which the apo state samples a broad set of conformations, and specific ones are selectively stabilized by either ligand or DNA binding. By examining a range of structural and dynamic properties of residues at both local and global scales, we observe that various analyses capture different subsets of experimentally identified hotspots, suggesting that these residues modulate allostery in distinct ways. These results motivate the development of a thermodynamic model that qualitatively explains the broad distribution of hotspot residues and their distinct features in molecular dynamics simulations. The multifaceted strategy that we establish here for hotspot evaluations and our insights into their mechanistic contributions are useful for modulating protein allostery in mechanistic and engineering studies.
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Affiliation(s)
- Yuchen Yuan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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19
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Liu J, Amaral LAN, Keten S. A new approach for extracting information from protein dynamics. ARXIV 2022:arXiv:2203.08387v1. [PMID: 35313540 PMCID: PMC8936122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.
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Affiliation(s)
- Jenny Liu
- Department of Mechanical Engineering, Northwestern University
| | - Luís A N Amaral
- Department of Chemical and Biological Engineering, Northwestern University
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University
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