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Lester A, Sandman M, Herring C, Girard C, Dixon B, Ramsdell H, Reber C, Poulos J, Mitchell A, Spinney A, Henager ME, Evans CN, Turlington M, Johnson QR. Computational Exploration of Potential CFTR Binding Sites for Type I Corrector Drugs. Biochemistry 2023; 62:2503-2515. [PMID: 37437308 PMCID: PMC10433520 DOI: 10.1021/acs.biochem.3c00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/22/2023] [Indexed: 07/14/2023]
Abstract
Cystic fibrosis (CF) is a recessive genetic disease that is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The recent development of a class of drugs called "correctors", which repair the structure and function of mutant CFTR, has greatly enhanced the life expectancy of CF patients. These correctors target the most common disease causing CFTR mutant F508del and are exemplified by the FDA-approved VX-809. While one binding site of VX-809 to CFTR was recently elucidated by cryo-electron microscopy, four additional binding sites have been proposed in the literature and it has been theorized that VX-809 and structurally similar correctors may engage multiple CFTR binding sites. To explore these five binding sites, ensemble docking was performed on wild-type CFTR and the F508del mutant using a large library of structurally similar corrector drugs, including VX-809 (lumacaftor), VX-661 (tezacaftor), ABBV-2222 (galicaftor), and a host of other structurally related molecules. For wild-type CFTR, we find that only one site, located in membrane spanning domain 1 (MSD1), binds favorably to our ligand library. While this MSD1 site also binds our ligand library for F508del-CFTR, the F508del mutation also opens a binding site in nucleotide binding domain 1 (NBD1), which enables strong binding of our ligand library to this site. This NBD1 site in F508del-CFTR exhibits the strongest overall binding affinity for our library of corrector drugs. This data may serve to better understand the structural changes induced by mutation of CFTR and how correctors bind to the protein. Additionally, it may aid in the design of new, more effective CFTR corrector drugs.
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Affiliation(s)
- Anna Lester
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Madeline Sandman
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Caitlin Herring
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Christian Girard
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Brandon Dixon
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Havanna Ramsdell
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Callista Reber
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Jack Poulos
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Alexis Mitchell
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Allison Spinney
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Marissa E. Henager
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Claudia N. Evans
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Mark Turlington
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Quentin R. Johnson
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
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2
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Foutch D, Pham B, Shen T. Protein conformational switch discerned via network centrality properties. Comput Struct Biotechnol J 2021; 19:3599-3608. [PMID: 34257839 PMCID: PMC8246261 DOI: 10.1016/j.csbj.2021.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensemble-informed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.
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Affiliation(s)
- David Foutch
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bill Pham
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.,UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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Surpeta B, Sequeiros-Borja CE, Brezovsky J. Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering. Int J Mol Sci 2020; 21:E2713. [PMID: 32295283 PMCID: PMC7215530 DOI: 10.3390/ijms21082713] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022] Open
Abstract
Computational prediction has become an indispensable aid in the processes of engineering and designing proteins for various biotechnological applications. With the tremendous progress in more powerful computer hardware and more efficient algorithms, some of in silico tools and methods have started to apply the more realistic description of proteins as their conformational ensembles, making protein dynamics an integral part of their prediction workflows. To help protein engineers to harness benefits of considering dynamics in their designs, we surveyed new tools developed for analyses of conformational ensembles in order to select engineering hotspots and design mutations. Next, we discussed the collective evolution towards more flexible protein design methods, including ensemble-based approaches, knowledge-assisted methods, and provable algorithms. Finally, we highlighted apparent challenges that current approaches are facing and provided our perspectives on their further development.
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Affiliation(s)
- Bartłomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Carlos Eduardo Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
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Das P, Golloshi R, McCord RP, Shen T. Using contact statistics to characterize structure transformation of biopolymer ensembles. Phys Rev E 2020; 101:012419. [PMID: 32069653 PMCID: PMC7329163 DOI: 10.1103/physreve.101.012419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Indexed: 12/20/2022]
Abstract
As a unique subset of functional polymers, many biopolymers have a set of well-defined three-dimensional (3D) structural characteristics that can be described by spatial contacts between monomers. Statistical analysis of the contacts has been extremely productive in characterizing the biopolymer structural ensemble, such as for 3D chromosome structures. Often, native contacts and compartment structures are the focus of the studies, while the generic polymer aspect, such as the overall decaying of contacts with increasing sequence distance, is analyzed separately or preemptively removed. Here, we explore insights that can be gained by performing "compartment analysis" that keeps the distance decay, which we believe is particularly useful for characterizing the structure transformation of biopolymers. We tested contact analysis on several such transformations under physical perturbation or biological processes, including (1) unfolding of proteins induced by thermal denaturation, (2) chromosome conformation transition during the cell cycle, and (3) chromosome unpacking by physicochemical perturbations. Useful score functions were developed to further quantitatively characterize the transformation judging from the contact analysis. We also find that the sinusoidal undertone of eigenvector patterns (the "unwanted," low frequency signal, in contrast to the detailed A/B compartment) that had previously been attributed to biological effects of centromere proximal and distal interactions may in fact reflect a universal feature of polymers that have relatively weaker long-range contacts.
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Affiliation(s)
- Priyojit Das
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville, Tennessee 37996, USA
| | - Rosela Golloshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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Roche J, Potoyan DA. Disorder Mediated Oligomerization of DISC1 Proteins Revealed by Coarse-Grained Molecular Dynamics Simulations. J Phys Chem B 2019; 123:9567-9575. [PMID: 31614085 DOI: 10.1021/acs.jpcb.9b07467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Disrupted-in-schizophrenia-1 (DISC1) is a scaffold protein of significant importance for neuro-development and a prominent candidate protein in the etiology of mental disorders. In this work, we investigate the role of conformational heterogeneity and local structural disorder in the oligomerization pathway of the full-length DISC1 and of two truncation variants. Through extensive coarse-grained molecular dynamics simulations with a predictive energy landscape-based model, we shed light on the interplay of local and global disorder which lead to different oligomerization pathways. We found that both global conformational heterogeneity and local structural disorder play an important role in shaping distinct oligomerization trends of DISC1. This study also sheds light on the differences in oligomerization pathways of the full-length protein compared to the truncated variants produced by a chromosomal translocation associated with schizophrenia. We report that oligomerization of full-length DISC1 sequence works in a nonadditive manner with respect to truncated fragments that do not mirror the conformational landscape or binding affinities of the full-length unit.
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Affiliation(s)
- Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology , Iowa State University , Ames , Iowa 50011 , United States
| | - Davit A Potoyan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology , Iowa State University , Ames , Iowa 50011 , United States.,Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States.,Bioinformatics and Computational Biology Program , Iowa State University , Ames , Iowa 50011 , United States
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Lindsay RJ, Pham B, Shen T, McCord RP. Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework. Nucleic Acids Res 2019; 46:8143-8152. [PMID: 29992238 PMCID: PMC6144818 DOI: 10.1093/nar/gky604] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/25/2018] [Indexed: 11/13/2022] Open
Abstract
Conformational ensembles of biopolymers, whether proteins or chromosomes, can be described using contact matrices. Principal component analysis (PCA) on the contact data has been used to interrogate both protein and chromosome structures and/or dynamics. However, as these fields have developed separately, variants of PCA have emerged. Previously, a variant we hereby term Implicit-PCA (I-PCA) has been applied to chromosome contact matrices and revealed the spatial segregation of active and inactive chromatin. Separately, Explicit-PCA (E-PCA) has previously been applied to proteins and characterized their correlated structure fluctuations. Here, we swapped analysis methods (I-PCA and E-PCA), applying each to a different biopolymer type (chromosome or protein) than the one for which they were initially developed. We find that applying E-PCA to chromosome distance matrices derived from microscopy data can reveal the dominant motion (concerted fluctuation) of these chromosomes. Further, by applying E-PCA to Hi-C data across the human blood cell lineage, we isolated the aspects of chromosome structure that most strongly differentiate cell types. Conversely, when we applied I-PCA to simulation snapshots of proteins, the major component reported the consensus features of the structure, making this a promising approach for future analysis of semi-structured proteins.
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Affiliation(s)
- Richard J Lindsay
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Bill Pham
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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Pham B, Lindsay RJ, Shen T. Effector-Binding-Directed Dimerization and Dynamic Communication between Allosteric Sites of Ribonucleotide Reductase. Biochemistry 2019; 58:697-705. [PMID: 30571104 DOI: 10.1021/acs.biochem.8b01131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Proteins forming dimers or larger complexes can be strongly influenced by their effector-binding status. We investigated how the effector-binding event is coupled with interface formation via computer simulations, and we quantified the correlation of two types of contact interactions: between the effector and its binding pocket and between protein monomers. This was achieved by connecting the protein dynamics at the monomeric level with the oligomer interface information. We applied this method to ribonucleotide reductase (RNR), an essential enzyme for de novo DNA synthesis. RNR contains two important allosteric sites, the s-site (specificity site) and the a-site (activity site), which bind different effectors. We studied these different binding states with atomistic simulation and used their coarse-grained contact information to analyze the protein dynamics. The results reveal that the effector-protein dynamics at the s-site and dimer interface formation are positively coupled. We further quantify the resonance level between these two events, which can be applied to other similar systems. At the a-site, different effector-binding states (ATP vs dATP) drastically alter the protein dynamics and affect the activity of the enzyme. On the basis of these results, we propose a new mechanism of how the a-site regulates enzyme activation.
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Affiliation(s)
- Bill Pham
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Richard J Lindsay
- UT-ORNL Graduate School of Genome Science and Technology , Knoxville , Tennessee 37996 , United States
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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Johnson QR, Lindsay RJ, Shen T. CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations. J Comput Chem 2018; 39:1568-1578. [PMID: 29464733 DOI: 10.1002/jcc.25192] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/04/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022]
Abstract
A computational method which extracts the dominant motions from an ensemble of biomolecular conformations via a correlation analysis of residue-residue contacts is presented. The algorithm first renders the structural information into contact matrices, then constructs the collective modes based on the correlated dynamics of a selected set of dynamic contacts. Associated programs can bridge the results for further visualization using graphics software. The aim of this method is to provide an analysis of conformations of biopolymers from the contact viewpoint. It may assist a systematical uncovering of conformational switching mechanisms existing in proteins and biopolymer systems in general by statistical analysis of simulation snapshots. In contrast to conventional correlation analyses of Cartesian coordinates (such as distance covariance analysis and Cartesian principal component analysis), this program also provides an alternative way to locate essential collective motions in general. Herein, we detail the algorithm in a stepwise manner and comment on the importance of the method as applied to decoding allosteric mechanisms. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Quentin R Johnson
- National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee, 37996.,Oak Ridge National Laboratory, UT-ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee, 37830
| | - Richard J Lindsay
- Oak Ridge National Laboratory, UT-ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee, 37830.,UT-ORNL Graduate School of Genome Science and Technology, Knoxville, Tennessee, 37996
| | - Tongye Shen
- Oak Ridge National Laboratory, UT-ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee, 37830.,Department of Biochemistry Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
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