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Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024; 124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [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: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.
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Affiliation(s)
- Greta Grassmann
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Fausta Desantis
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- The
Open University Affiliated Research Centre at Istituto Italiano di
Tecnologia, Genoa 16163, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Gian Gaetano Tartaglia
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
- Center
for Human Technologies, Genoa 16152, Italy
| | - Annalisa Pastore
- Experiment
Division, European Synchrotron Radiation
Facility, Grenoble 38043, France
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| | - Michele Monti
- RNA
System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
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2
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Sabbir MG, Dar NJ, Bhat SA, Alanazi HH, Perry J. Editorial: Proteins and protein-complexes underlying mitochondrial structure-function and metabolism: implications in diseases. Front Cell Dev Biol 2024; 12:1386787. [PMID: 38505261 PMCID: PMC10949712 DOI: 10.3389/fcell.2024.1386787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Affiliation(s)
- Mohammad Golam Sabbir
- Department of Psychology and Neuroscience, College of Psychology, Nova Southeastern University, Fort Lauderdale, FL, United States
- Alzo Biosciences Inc., San Diego, CA, United States
| | - Nawab John Dar
- Salk Institute for Biological Studies, La Jolla, IL, United States
| | | | - Hamad H. Alanazi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakakah, Saudi Arabia
| | - Jeff Perry
- Hope National Medical Center Duarte, Santa Clara, CA, United States
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3
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Shelke Y, Camerin F, Marín-Aguilar S, Verweij RW, Dijkstra M, Kraft DJ. Flexible Colloidal Molecules with Directional Bonds and Controlled Flexibility. ACS NANO 2023. [PMID: 37363931 DOI: 10.1021/acsnano.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Colloidal molecules are ideal model systems for mimicking real molecules and can serve as versatile building blocks for the bottom-up self-assembly of flexible and smart materials. While most colloidal molecules are rigid objects, the development of colloidal joints has made it possible to endow them with conformational flexibility. However, their unrestricted range of motion does not capture the limited movement and bond directionality that is instead typical of real molecules. In this work, we create flexible colloidal molecules with an in situ controllable motion range and bond directionality by assembling spherical particles onto cubes functionalized with complementary surface-mobile DNA. By varying the sphere-to-cube size ratio, we obtain colloidal molecules with different coordination numbers and find that they feature a constrained range of motion above a critical size ratio. Using theory and simulations, we show that the particle shape together with the multivalent bonds creates an effective free-energy landscape for the motion of the sphere on the surface of the cube. We quantify the confinement of the spheres on the surface of the cube and the probability to change facet. We find that temperature can be used as an extra control parameter to switch in situ between full and constrained flexibility. These flexible colloidal molecules with a temperature switching motion range can be used to investigate the effect of directional yet flexible bonds in determining their self-assembly and phase behavior, and may be employed as constructional units in microrobotics and smart materials.
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Affiliation(s)
- Yogesh Shelke
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, Leiden 2300 RA, The Netherlands
| | - Fabrizio Camerin
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, Utrecht 3584 CC, The Netherlands
| | - Susana Marín-Aguilar
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, Utrecht 3584 CC, The Netherlands
| | - Ruben W Verweij
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, Leiden 2300 RA, The Netherlands
| | - Marjolein Dijkstra
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, Utrecht 3584 CC, The Netherlands
| | - Daniela J Kraft
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, Leiden 2300 RA, The Netherlands
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4
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Mills R, Vogler RJ, Bernard M, Concolino J, Hersh LB, Wei Y, Hastings JT, Dziubla T, Baldridge KC, Bhattacharyya D. Aerosol capture and coronavirus spike protein deactivation by enzyme functionalized antiviral membranes. COMMUNICATIONS MATERIALS 2022; 3:34. [PMID: 36406238 PMCID: PMC9674191 DOI: 10.1038/s43246-022-00256-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/02/2022] [Indexed: 06/16/2023]
Abstract
The airborne nature of coronavirus transmission makes it critical to develop new barrier technologies that can simultaneously reduce aerosol and viral spread. Here, we report nanostructured membranes with tunable thickness and porosity for filtering coronavirus-sized aerosols, combined with antiviral enzyme functionalization that can denature spike glycoproteins of the SARS-CoV-2 virus in low-hydration environments. Thin, asymmetric membranes with subtilisin enzyme and methacrylic functionalization show more than 98.90% filtration efficiency for 100-nm unfunctionalized and protein-functionalized polystyrene latex aerosol particles. Unfunctionalized membranes provided a protection factor of 540 ± 380 for coronavirus-sized particle, above the Occupational Safety and Health Administration's standard of 10 for N95 masks. SARS-CoV-2 spike glycoprotein on the surface of coronavirus-sized particles was denatured in 30 s by subtilisin enzyme-functionalized membranes with 0.02-0.2% water content on the membrane surface.
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Affiliation(s)
- Rollie Mills
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Ronald J. Vogler
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
- These authors contributed equally: Ronald J. Vogler, Matthew Bernard
| | - Matthew Bernard
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
- These authors contributed equally: Ronald J. Vogler, Matthew Bernard
| | - Jacob Concolino
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Louis B. Hersh
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Jeffrey Todd Hastings
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Thomas Dziubla
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Kevin C. Baldridge
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Dibakar Bhattacharyya
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
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5
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A stepwise docking molecular dynamics approach for simulating antibody recognition with substantial conformational changes. Comput Struct Biotechnol J 2022; 20:710-720. [PMID: 35198128 PMCID: PMC8816672 DOI: 10.1016/j.csbj.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/24/2021] [Accepted: 01/13/2022] [Indexed: 11/23/2022] Open
Abstract
Conformational changes or rearrangements are common events during inter-biomolecular recognition. Tracking these changes are essential for exploring the allosteric mechanism and it is usually achieved by molecular dynamics simulation in silico. We previously identified a broad-neutralizing antibody against H5 influenza virus, 13D4, and solved the crystal structures of the free 13D4 Fab and its complex with hemagglutinin (HA). Structural comparison of the unbound and bound 13D4 Fabs showed that the heavy chain complementarity-determining region 3 (HCDR3) undergoes a substantial conformational rearrangement when it recognizes the receptor-binding site (RBS). Here, we used molecular dynamics (MD) to simulate the conformational changes that occur during antibody recognition. We showed that neither conventional MD nor steered MD could recapitulate the loop fitting of the RBS structure contour. Consequently, to simulate these challenging conformational changes, we engaged a stepwise docking MD method that allowed for the gradual docking of the ligand to receptor. This new method recapitulates the bound shape of the HCDR3 and provides the best approximation of the shape rendered by the co-crystal structure, with an RMSD of 0.926 Å. This strategy affords a flexible MD approach for simulating complicated conformational changes that occur during molecular recognition, and helps to provide an understanding of the involved allosteric mechanism.
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6
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Jílková A, Rubešová P, Fanfrlík J, Fajtová P, Řezáčová P, Brynda J, Lepšík M, Mertlíková-Kaiserová H, Emal CD, Renslo AR, Roush WR, Horn M, Caffrey CR, Mareš M. Druggable Hot Spots in the Schistosomiasis Cathepsin B1 Target Identified by Functional and Binding Mode Analysis of Potent Vinyl Sulfone Inhibitors. ACS Infect Dis 2021; 7:1077-1088. [PMID: 33175511 PMCID: PMC8154419 DOI: 10.1021/acsinfecdis.0c00501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Schistosomiasis, a parasitic disease
caused by blood flukes of
the genus Schistosoma, is a global health problem
with over 200 million people infected. Treatment relies on just one
drug, and new chemotherapies are needed. Schistosoma mansoni cathepsin B1 (SmCB1) is a critical peptidase for the digestion of
host blood proteins and a validated drug target. We screened a library
of peptidomimetic vinyl sulfones against SmCB1 and identified the
most potent SmCB1 inhibitors reported to date that are active in the
subnanomolar range with second order rate constants (k2nd) of ∼2 × 105 M–1 s–1. High resolution crystal structures of the
two best inhibitors in complex with SmCB1 were determined. Quantum
chemical calculations of their respective binding modes identified
critical hot spot interactions in the S1′ and S2 subsites.
The most potent inhibitor targets the S1′ subsite with an N-hydroxysulfonic amide moiety and displays favorable functional
properties, including bioactivity against the pathogen, selectivity
for SmCB1 over human cathepsin B, and reasonable metabolic stability.
Our results provide structural insights for the rational design of
next-generation SmCB1 inhibitors as potential drugs to treat schistosomiasis.
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Affiliation(s)
- Adéla Jílková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Petra Rubešová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Pavla Fajtová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Cory D. Emal
- Eastern Michigan University, 541 Mark Jefferson, Ypsilanti, Michigan 48197, United States
| | - Adam R. Renslo
- University of California San Francisco, 600 16th Street, San Francisco, California 94143, United States
| | - William R. Roush
- The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
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7
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Tandon H, de Brevern AG, Srinivasan N. Transient association between proteins elicits alteration of dynamics at sites far away from interfaces. Structure 2020; 29:371-384.e3. [PMID: 33306961 DOI: 10.1016/j.str.2020.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
Proteins are known to undergo structural changes upon binding to partner proteins. However, the prevalence, extent, location, and function of change in protein dynamics due to transient protein-protein interactions is not well documented. Here, we have analyzed a dataset of 58 protein-protein complexes of known three-dimensional structure and structures of their corresponding unbound forms to evaluate dynamics changes induced by binding. Fifty-five percent of cases showed significant dynamics change away from the interfaces. This change is not always accompanied by an observed structural change. Binding of protein partner is found to alter inter-residue communication within the tertiary structure in about 90% of cases. Also, residue motions accessible to proteins in unbound form were not always maintained in the bound form. Further analyses revealed functional roles for the distant site where dynamics change was observed. Overall, the results presented here strongly suggest that alteration of protein dynamics due to binding of a partner protein commonly occurs.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, 75739 Paris, France; Univ Paris, UMR_S 1134, 75739 Paris, France; Institut National de la Transfusion Sanguine (INTS), 75739 Paris, France; Laboratoire d'Excellence GR-Ex, 75739 Paris, France
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8
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Kulikov KG, Koshlan TV. Modeling the impact of point mutations on the stability of proteins. J Bioinform Comput Biol 2020; 18:2050019. [PMID: 32649259 DOI: 10.1142/s0219720020500195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A new method has been introduced which allows us to determine the stability of protein complexes with point changes of amino acid residues that also take into account the three-dimensional structure of the complex. This formulated and proven theorem is aimed at determining the criterion for the stability of protein molecules. The algorithm and software package were developed for analyzing protein interactions, taking into account their three-dimensional structure from the PDB database.
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Affiliation(s)
- K G Kulikov
- Department of Medical Physics, Peter the Great, St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - T V Koshlan
- Department of Molecular Biophysics, St. Petersburg State University, 199034 St. Petersburg, Russia
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9
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Pachl P, Kapešová J, Brynda J, Biedermannová L, Pelantová H, Bojarová P, Křen V, Řezáčová P, Kotik M. Rutinosidase from
Aspergillus niger
: crystal structure and insight into the enzymatic activity. FEBS J 2020; 287:3315-3327. [DOI: 10.1111/febs.15208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/13/2019] [Accepted: 01/09/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Petr Pachl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
| | - Jana Kapešová
- Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
- Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic
| | - Lada Biedermannová
- Institute of Biotechnology of the Czech Academy of Sciences BIOCEV Vestec Czech Republic
| | - Helena Pelantová
- Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
- Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic
| | - Michael Kotik
- Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic
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10
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Zima V, Albiñana CB, Rojíková K, Pokorná J, Pachl P, Řezáčová P, Hudlicky J, Navrátil V, Majer P, Konvalinka J, Kožíšek M, Machara A. Investigation of flexibility of neuraminidase 150-loop using tamiflu derivatives in influenza A viruses H1N1 and H5N1. Bioorg Med Chem 2019; 27:2935-2947. [DOI: 10.1016/j.bmc.2019.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022]
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11
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Tajielyato N, Li L, Peng Y, Alper J, Alexov E. E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein. Sci Rep 2018; 8:13266. [PMID: 30185874 PMCID: PMC6125590 DOI: 10.1038/s41598-018-31480-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/15/2018] [Indexed: 01/14/2023] Open
Abstract
Macromolecular binding is a complex process that involves sensing and approaching the binding partner, adopting the proper orientation, and performing the physical binding. We computationally investigated the role of E-hooks, which are intrinsically disordered regions (IDRs) at the C-terminus of tubulin, on dynein microtubule binding domain (MTBD) binding to the microtubule as a function of the distance between the MTBD and its binding site on the microtubule. Our results demonstrated that the contacts between E-hooks and the MTBD are dynamical; multiple negatively charted patches of amino acids on the E-hooks grab and release the same positively charged patches on the MTBD as it approaches the microtubule. Even when the distance between the MTBD and the microtubule was greater than the E-hook length, the E-hooks sensed and guided MTBD via long-range electrostatic interactions in our simulations. Moreover, we found that E-hooks exerted electrostatic forces on the MTBD that were distance dependent; the force pulls the MTBD toward the microtubule at long distances but opposes binding at short distances. This mechanism provides a "soft-landing" for the MTBD as it binds to the microtubule. Finally, our analysis of the conformational states of E-hooks in presence and absence of the MTBD indicates that the binding process is a mixture of the induced-fit and lock-and-key macromolecular binding hypotheses. Overall, this novel binding mechanism is termed "guided-soft-binding" and could have broad-reaching impacts on the understanding of how IDRs dock to structured proteins.
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Affiliation(s)
- Nayere Tajielyato
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Lin Li
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
- Department of Physics, University of Texas at El Paso, El Paso, TX, 79912, USA
| | - Yunhui Peng
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Joshua Alper
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
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12
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Hogues H, Gaudreault F, Corbeil CR, Deprez C, Sulea T, Purisima EO. ProPOSE: Direct Exhaustive Protein-Protein Docking with Side Chain Flexibility. J Chem Theory Comput 2018; 14:4938-4947. [PMID: 30107730 DOI: 10.1021/acs.jctc.8b00225] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite decades of development, protein-protein docking remains a largely unsolved problem. The main difficulties are the immense space spanned by the translational and rotational degrees of freedom and the prediction of the conformational changes of proteins upon binding. FFT is generally the preferred method to exhaustively explore the translation-rotation space at a fine grid resolution, albeit with the trade-off of approximating force fields with correlation functions. This work presents a direct search alternative that samples the states in Cartesian space at the same resolution and computational cost as standard FFT methods. Operating in real space allows the use of standard force field functional forms used in typical non-FFT methods as well as the implementation of strategies for focused exploration of conformational flexibility. Currently, a few misplaced side chains can cause docking programs to fail. This work specifically addresses the problem of side chain rearrangements upon complex formation. Based on the observation that most side chains retain their unbound conformation upon binding, each rigidly docked pose is initially scored ignoring up to a limited number of side chain overlaps which are resolved in subsequent repacking and minimization steps. On test systems where side chains are altered and backbones held in their bound state, this implementation provides significantly better native pose recovery and higher quality (lower RMSD) predictions when compared with five of the most popular docking programs. The method is implemented in the software program ProPOSE (Protein Pose Optimization by Systematic Enumeration).
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Affiliation(s)
- Hervé Hogues
- Human Health Therapeutics , National Research Council Canada , 6100 Royalmount Avenue , Montreal , Quebec H4P 2R2 , Canada
| | - Francis Gaudreault
- Human Health Therapeutics , National Research Council Canada , 6100 Royalmount Avenue , Montreal , Quebec H4P 2R2 , Canada
| | - Christopher R Corbeil
- Human Health Therapeutics , National Research Council Canada , 6100 Royalmount Avenue , Montreal , Quebec H4P 2R2 , Canada
| | - Christophe Deprez
- Human Health Therapeutics , National Research Council Canada , 6100 Royalmount Avenue , Montreal , Quebec H4P 2R2 , Canada
| | - Traian Sulea
- Human Health Therapeutics , National Research Council Canada , 6100 Royalmount Avenue , Montreal , Quebec H4P 2R2 , Canada
| | - Enrico O Purisima
- Human Health Therapeutics , National Research Council Canada , 6100 Royalmount Avenue , Montreal , Quebec H4P 2R2 , Canada
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13
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Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Viruses 2018; 10:v10070339. [PMID: 29933553 PMCID: PMC6071225 DOI: 10.3390/v10070339] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 12/25/2022] Open
Abstract
Neuraminidase is the main target for current influenza drugs. Reduced susceptibility to oseltamivir, the most widely prescribed neuraminidase inhibitor, has been repeatedly reported. The resistance substitutions I223V and S247N, alone or in combination with the major oseltamivir-resistance mutation H275Y, have been observed in 2009 pandemic H1N1 viruses. We overexpressed and purified the ectodomain of wild-type neuraminidase from the A/California/07/2009 (H1N1) influenza virus, as well as variants containing H275Y, I223V, and S247N single mutations and H275Y/I223V and H275Y/S247N double mutations. We performed enzymological and thermodynamic analyses and structurally examined the resistance mechanism. Our results reveal that the I223V or S247N substitution alone confers only a moderate reduction in oseltamivir affinity. In contrast, the major oseltamivir resistance mutation H275Y causes a significant decrease in the enzyme’s ability to bind this drug. Combination of H275Y with an I223V or S247N mutation results in extreme impairment of oseltamivir’s inhibition potency. Our structural analyses revealed that the H275Y substitution has a major effect on the oseltamivir binding pose within the active site while the influence of other studied mutations is much less prominent. Our crystal structures also helped explain the augmenting effect on resistance of combining H275Y with both substitutions.
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14
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Zhu G, Liu W, Bao C, Tong D, Ji H, Shen Z, Yang D, Lu L. Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1. Proteins 2018; 86:501-514. [PMID: 29383828 DOI: 10.1002/prot.25468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 12/26/2017] [Accepted: 01/23/2018] [Indexed: 12/25/2022]
Abstract
The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates.
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Affiliation(s)
- Guanhua Zhu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Wei Liu
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Chenglong Bao
- Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge Road, Singapore, 119076, Singapore.,Yau Mathematical Sciences Center, Tsinghua University, Haidian District, Beijing, 100084, China
| | - Dudu Tong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Hui Ji
- Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge Road, Singapore, 119076, Singapore
| | - Zuowei Shen
- Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge Road, Singapore, 119076, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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15
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Škerlová J, Bláha J, Pachl P, Hofbauerová K, Kukačka Z, Man P, Pompach P, Novák P, Otwinowski Z, Brynda J, Vaněk O, Řezáčová P. Crystal structure of native β‐
N
‐acetylhexosaminidase isolated from
Aspergillus oryzae
sheds light onto its substrate specificity, high stability, and regulation by propeptide. FEBS J 2017; 285:580-598. [DOI: 10.1111/febs.14360] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/03/2017] [Accepted: 12/08/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Jana Škerlová
- Institute of Organic Chemistry and Biochemistry The Czech Academy of Sciences Prague Czech Republic
- Institute of Molecular Genetics The Czech Academy of Sciences Prague Czech Republic
| | - Jan Bláha
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry The Czech Academy of Sciences Prague Czech Republic
| | - Kateřina Hofbauerová
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
- Institute of Physics Faculty of Mathematics and Physics Charles University Prague Czech Republic
| | - Zdeněk Kukačka
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
| | - Petr Man
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
| | - Petr Pompach
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
| | - Petr Novák
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
| | | | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry The Czech Academy of Sciences Prague Czech Republic
- Institute of Molecular Genetics The Czech Academy of Sciences Prague Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry The Czech Academy of Sciences Prague Czech Republic
- Institute of Molecular Genetics The Czech Academy of Sciences Prague Czech Republic
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16
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Zhang C, Zhao DX, Wang Q, Yu L, Li GH, Yang ZZ. A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM σπmolecular dynamics simulations. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1350660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chao Zhang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China
| | - Qian Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China
| | - Ling Yu
- Liaoning Panjin Fine Chemical Industrial Park Administrative Committee, Panjin, China
| | - Guo-Hui Li
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China
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17
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Saravanan KM, Selvaraj S. Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins. J Biol Phys 2017; 43:265-278. [PMID: 28577238 PMCID: PMC5471173 DOI: 10.1007/s10867-017-9451-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
In theory, a polypeptide chain can adopt a vast number of conformations, each corresponding to a set of backbone rotation angles. Many of these conformations are excluded due to steric overlaps. Ramachandran and coworkers were the first to look into this problem by plotting backbone dihedral angles in a two-dimensional plot. The conformational space in the Ramachandran map is further refined by considering the energetic contributions of various non-bonded interactions. Alternatively, the conformation adopted by a polypeptide chain may also be examined by investigating interactions between the residues. Since the Ramachandran map essentially focuses on local interactions (residues closer in sequence), out of interest, we have analyzed the dihedral angle preferences of residues that make non-local interactions (residues far away in sequence and closer in space) in the folded structures of proteins. The non-local interactions have been grouped into different types such as hydrogen bond, van der Waals interactions between hydrophobic groups, ion pairs (salt bridges), and ππ-stacking interactions. The results show the propensity of amino acid residues in proteins forming local and non-local interactions. Our results point to the vital role of different types of non-local interactions and their effect on dihedral angles in forming secondary and tertiary structural elements to adopt their native fold.
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Affiliation(s)
- Konda Mani Saravanan
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, 600 025, India
| | - Samuel Selvaraj
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, 600 025, India.
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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18
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Pabon NA, Camacho CJ. Probing protein flexibility reveals a mechanism for selective promiscuity. eLife 2017; 6. [PMID: 28432789 PMCID: PMC5446241 DOI: 10.7554/elife.22889] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners. However, we lack an understanding of how an interface can select some ligands, but not others. Here, we present a molecular dynamics approach to identify and quantitatively evaluate the interactions responsible for this selective promiscuity. We apply this approach to the anticancer target PD-1 and its ligands PD-L1 and PD-L2. We discover that while unbound PD-1 exhibits a hard-to-drug hydrophilic interface, conserved specific triggers encoded in the cognate ligands activate a promiscuous binding pathway that reveals a flexible hydrophobic binding cavity. Specificity is then established by additional contacts that stabilize the PD-1 cavity into distinct bound-like modes. Collectively, our studies provide insight into the structural basis and evolution of multiple binding partners, and also suggest a biophysical approach to exploit innate binding pathways to drug seemingly undruggable targets. DOI:http://dx.doi.org/10.7554/eLife.22889.001 Many proteins need to interact with other proteins to carry out their various tasks in cells. Such interactions are essential for almost all biological processes and are often disrupted in disease. Cells have thousands of different types of proteins and each has a unique shape that determines which other proteins it can bind to. It was previously thought that two proteins bind to each other in a manner similar to that of a lock and a key, in which the rigid shape of one protein meshes perfectly with the rigid shape of its partner. However, many proteins are flexible and adopt different shapes depending on whether they are attached to their partner, or not. Moreover, an individual protein may also bind to several different partners, each requiring that protein to adopt several different shapes. These observations have challenged the lock and key model and suggest that flexibility in the structure of a protein plays a key role in its binding to other proteins. However, it is not clear how structural flexibility enables a protein to bind to several different partners while being selective enough to prevent the protein from binding to the wrong ones. A protein called PD-1 is involved in immune responses in humans and is an emerging target for drugs to treat cancer. Pabon and Camacho used computer simulations to model PD-1’s structural flexibility and to find out how this enables the protein to form different shapes when it binds to different partners. The experiments show that the region of PD-1 that binds to other proteins adopts a different shape in the absence and presence of its partners. The binding partners make initial contact with PD-1 via specific features that they share in common. This causes PD-1 to change shape, uncovering a surface of PD-1 that is flexible and is able to accommodate a variety of partners. After this, the binding partners form additional contacts with PD-1 that are specific to each partner. These findings suggest that the ability of a protein to bind to several different partners is unlocked by certain structures that are present in the binding partners. These structures are found in proteins produced by many different organisms, suggesting that this mechanism is likely to be widespread in nature. This work may open up new avenues for designing drugs to target PD-1 and other proteins that contribute to disease but have so far been impossible to target with drugs. DOI:http://dx.doi.org/10.7554/eLife.22889.002
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Affiliation(s)
- Nicolas A Pabon
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
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19
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Sharir-Ivry A, Xia Y. The Impact of Native State Switching on Protein Sequence Evolution. Mol Biol Evol 2017; 34:1378-1390. [DOI: 10.1093/molbev/msx071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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20
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Hasani HJ, Barakat KH. Protein-Protein Docking. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Protein-protein docking algorithms are powerful computational tools, capable of analyzing the protein-protein interactions at the atomic-level. In this chapter, we will review the theoretical concepts behind different protein-protein docking algorithms, highlighting their strengths as well as their limitations and pointing to important case studies for each method. The methods we intend to cover in this chapter include various search strategies and scoring techniques. This includes exhaustive global search, fast Fourier transform search, spherical Fourier transform-based search, direct search in Cartesian space, local shape feature matching, geometric hashing, genetic algorithm, randomized search, and Monte Carlo search. We will also discuss the different ways that have been used to incorporate protein flexibility within the docking procedure and some other future directions in this field, suggesting possible ways to improve the different methods.
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21
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Tan YS, Reeks J, Brown CJ, Thean D, Ferrer
Gago FJ, Yuen TY, Goh EL, Lee XEC, Jennings CE, Joseph TL, Lakshminarayanan R, Lane DP, Noble MEM, Verma CS. Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design. J Phys Chem Lett 2016; 7:3452-7. [PMID: 27532490 PMCID: PMC5515508 DOI: 10.1021/acs.jpclett.6b01525] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design.
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Affiliation(s)
- Yaw Sing Tan
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Judith Reeks
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Christopher J. Brown
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | - Dawn Thean
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | | | - Tsz Ying Yuen
- Institute
of Chemical & Engineering Sciences, A*STAR, 8 Biomedical
Grove, #07-01 Neuros, Singapore 138665
| | - Eunice
Tze Leng Goh
- Singapore
Eye Research Institute, 11 Third Hospital Avenue, Singapore 168751
| | - Xue Er Cheryl Lee
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | - Claire E. Jennings
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Thomas L. Joseph
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | | | - David P. Lane
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
- E-mail:
| | - Martin E. M. Noble
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
- E-mail:
| | - Chandra S. Verma
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, 14 Science
Drive 4, Singapore 117543
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang
Drive, Singapore 637551
- E-mail:
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22
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Abstract
Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation:https://bitbucket.org/mjamroz/flexscore Contact:dkihara@purdue.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michal Jamroz
- Department of Chemistry, University of Warsaw, Warsaw, 02-093, Poland
| | - Andrzej Kolinski
- Department of Chemistry, University of Warsaw, Warsaw, 02-093, Poland
| | - Daisuke Kihara
- Department of Biological Sciences Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
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23
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Kinetic, thermodynamic and structural analysis of tamiphosphor binding to neuraminidase of H1N1 (2009) pandemic influenza. Eur J Med Chem 2016; 121:100-109. [PMID: 27236066 DOI: 10.1016/j.ejmech.2016.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/11/2016] [Accepted: 05/03/2016] [Indexed: 11/22/2022]
Abstract
Influenza virus causes severe respiratory infections that are responsible for up to half a million deaths worldwide each year. Two inhibitors targeting viral neuraminidase have been approved to date (oseltamivir, zanamivir). However, the rapid development of antiviral drug resistance and the efficient transmission of resistant viruses among humans represent serious threats to public health. The approved influenza neuraminidase inhibitors have (oxa)cyclohexene scaffolds designed to mimic the oxonium transition state during enzymatic cleavage of sialic acid. Their active forms contain a carboxylate that interacts with three arginine residues in the enzyme active site. Recently, the phosphonate group was successfully used as an isostere of the carboxylate in oseltamivir, and the resulting compound, tamiphosphor, was identified as a highly active neuraminidase inhibitor. However, the structure of the complex of this promising inhibitor with neuraminidase has not yet been reported. Here, we analyzed the interaction of a set of oseltamivir and tamiphosphor derivatives with neuraminidase from the A/California/07/2009 (H1N1) influenza virus. We thermodynamically characterized the binding of oseltamivir carboxylate or tamiphosphor to the neuraminidase catalytic domain by protein microcalorimetry, and we determined crystal structure of the catalytic domain in complex with tamiphosphor at 1.8 Å resolution. This structural information should aid rational design of the next generation of neuraminidase inhibitors.
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24
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016; 12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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Affiliation(s)
- Tatiana Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Ryan Moffatt
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
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25
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Woods KN, Pfeffer J. Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes. Mol Biol Evol 2016; 33:40-61. [PMID: 26337549 PMCID: PMC4693973 DOI: 10.1093/molbev/msv178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
It is now widely accepted that protein function is intimately tied with the navigation of energy landscapes. In this framework, a protein sequence is not described by a distinct structure but rather by an ensemble of conformations. And it is through this ensemble that evolution is able to modify a protein's function by altering its landscape. Hence, the evolution of protein functions involves selective pressures that adjust the sampling of the conformational states. In this work, we focus on elucidating the evolutionary pathway that shaped the function of individual proteins that make-up the mammalian c-type lysozyme subfamily. Using both experimental and computational methods, we map out specific intermolecular interactions that direct the sampling of conformational states and accordingly, also underlie shifts in the landscape that are directly connected with the formation of novel protein functions. By contrasting three representative proteins in the family we identify molecular mechanisms that are associated with the selectivity of enhanced antimicrobial properties and consequently, divergent protein function. Namely, we link the extent of localized fluctuations involving the loop separating helices A and B with shifts in the equilibrium of the ensemble of conformational states that mediate interdomain coupling and concurrently moderate substrate binding affinity. This work reveals unique insights into the molecular level mechanisms that promote the progression of interactions that connect the immune response to infection with the nutritional properties of lactation, while also providing a deeper understanding about how evolving energy landscapes may define present-day protein function.
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26
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Frezza E, Lavery R. Internal Normal Mode Analysis (iNMA) Applied to Protein Conformational Flexibility. J Chem Theory Comput 2015; 11:5503-12. [DOI: 10.1021/acs.jctc.5b00724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elisa Frezza
- BMSSI, UMR 5086 CNRS/Univ.
Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Richard Lavery
- BMSSI, UMR 5086 CNRS/Univ.
Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
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27
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Wodak SJ, Malevanets A, MacKinnon SS. The Landscape of Intertwined Associations in Homooligomeric Proteins. Biophys J 2015; 109:1087-100. [PMID: 26340815 DOI: 10.1016/j.bpj.2015.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/06/2015] [Accepted: 08/03/2015] [Indexed: 01/22/2023] Open
Abstract
We present an overview of the full repertoire of intertwined associations in homooligomeric proteins. This overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. Furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers, with a particular focus on the mechanistic aspects that underpin intertwined self-association processes in proteins. Insights gained from this integrated overview into the physical and biological roles of intertwining are highlighted.
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Affiliation(s)
- Shoshana J Wodak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; VIB Structural Biology Research Center, Brussels, Belgium.
| | | | - Stephen S MacKinnon
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Cyclica, Inc., Toronto, Ontario, Canada
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28
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Saranya N, Saravanan KM, Michael Gromiha M, Selvaraj S. Analysis of secondary structural and physicochemical changes in protein-protein complexes. J Biomol Struct Dyn 2015; 34:508-16. [PMID: 25990569 DOI: 10.1080/07391102.2015.1050695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Conformation switching in protein-protein complexes is considered important for the molecular recognition process. Overall analysis of 123 protein-protein complexes in a benchmark data-set showed that 6.8% of residues switched over their secondary structure conformation upon complex formation. Amino acid residue-wise preference for conformation change has been analyzed in binding and non-binding site residues separately. In this analysis, residues such as Ser, Leu, Glu, and Lys had higher frequency of secondary structural conformation change. The change of helix to coil and sheet to coil conformation and vice versa has been observed frequently, whereas the conformation change of helix to extended sheet occurred rarely in the studied complexes. Influence of conformation change toward the N and C terminal on either side of the binding site residues has been analyzed. Further, analysis on φ and ψ angle variation, conservation, stability, and solvent accessibility have been performed on binding site residues. Knowledge obtained from the present study could be effectively employed in the protein-protein modeling and docking studies.
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Affiliation(s)
- N Saranya
- a Department of Bioinformatics , School of Life Sciences, Bharathidasan University , Tiruchirappalli 620024 , India.,b Department of Plant Molecular Biology and Bioinformatics , Tamil Nadu Agricultural University , Coimbatore , Tamil Nadu 641003 , India
| | - K M Saravanan
- a Department of Bioinformatics , School of Life Sciences, Bharathidasan University , Tiruchirappalli 620024 , India.,c Center of Excellence in Bioinformatics, School of Biotechnology , Madurai Kamaraj University , Madurai , Tamil Nadu 625 021 , India
| | - M Michael Gromiha
- d Department of Biotechnology , Indian Institute of Technology Madras , Chennai , Tamil Nadu 600036 , India
| | - S Selvaraj
- a Department of Bioinformatics , School of Life Sciences, Bharathidasan University , Tiruchirappalli 620024 , India
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29
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MacKinnon SS, Wodak SJ. Landscape of intertwined associations in multi-domain homo-oligomeric proteins. J Mol Biol 2014; 427:350-70. [PMID: 25451036 DOI: 10.1016/j.jmb.2014.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022]
Abstract
This study charts the landscape of multi-domain protein structures that form intertwined homodimers by exchanging structural domains between subunits. A representative dataset of such homodimers was derived from the Protein Data Bank, and their structural and topological properties were compared to those of a representative set of non-intertwined homodimers. Most of the intertwined dimers form closed assemblies with head-to-tail arrangements, where the subunit interface involves contacts between dissimilar domains. In contrast, the non-intertwined dimers form preferentially head-to-head arrangements, where the subunit interface involves contacts between identical domains. Most of these contacts engage only one structural domain from each subunit, leaving the remaining domains free to form other associations. Remarkably, we find that multi-domain proteins closely related to the intertwined homodimers are significantly more likely than relatives of the non-intertwined versions to adopt alternative intramolecular domain arrangements. In ~40% of the intertwined dimers, the plasticity in domain arrangements among relatives affords maintenance of the head-to-head or head-to-tail topology and conservation of the corresponding subunit interface. This property seems to be exploited in several systems to regulate DNA binding. In ~58%, however, intramolecular domain re-arrangements are associated with changes in oligomeric states and poorly conserved interfaces among relatives. This time, the corresponding structural plasticity appears to be exploited by evolution to modulate function by switching between active and inactive states of the protein. Surprisingly, in total, only three systems were found to undergo the classical monomer to intertwined dimer conversion associated with three-dimensional domain swapping.
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Affiliation(s)
- Stephen S MacKinnon
- Molecular Structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8
| | - Shoshana J Wodak
- Molecular Structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8.
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Mader P, Pecina A, Cígler P, Lepšík M, Šícha V, Hobza P, Grüner B, Fanfrlík J, Brynda J, Řezáčová P. Carborane-based carbonic anhydrase inhibitors: insight into CAII/CAIX specificity from a high-resolution crystal structure, modeling, and quantum chemical calculations. BIOMED RESEARCH INTERNATIONAL 2014; 2014:389869. [PMID: 25309911 PMCID: PMC4189773 DOI: 10.1155/2014/389869] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/08/2014] [Indexed: 12/03/2022]
Abstract
Carborane-based compounds are promising lead structures for development of inhibitors of carbonic anhydrases (CAs). Here, we report structural and computational analysis applicable to structure-based design of carborane compounds with selectivity toward the cancer-specific CAIX isoenzyme. We determined the crystal structure of CAII in complex with 1-methylenesulfamide-1,2-dicarba-closo-dodecaborane at 1.0 Å resolution and used this structure to model the 1-methylenesulfamide-1,2-dicarba-closo-dodecaborane interactions with CAIX. A virtual glycine scan revealed the contributions of individual residues to the energy of binding of 1-methylenesulfamide-1,2-dicarba-closo-dodecaborane to CAII and CAIX, respectively.
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Affiliation(s)
- Pavel Mader
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 140 00 Prague 4, Czech Republic
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Petr Cígler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Václav Šícha
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Hlavní 1001, 250 68 Řež near Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 77146 Olomouc, Czech Republic
| | - Bohumír Grüner
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Hlavní 1001, 250 68 Řež near Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 140 00 Prague 4, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 140 00 Prague 4, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
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31
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Škerlová J, Fábry M, Hubálek M, Otwinowski Z, Rezáčová P. Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis. FEBS J 2014; 281:4280-92. [PMID: 24863636 DOI: 10.1111/febs.12856] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 11/26/2022]
Abstract
UNLABELLED Deoxyribonucleoside regulator (DeoR) from Bacillus subtilis negatively regulates expression of enzymes involved in the catabolism of deoxyribonucleosides and deoxyribose. The DeoR protein is homologous to the sorbitol operon regulator family of metabolic regulators and comprises an N-terminal DNA-binding domain and a C-terminal effector-binding domain. We have determined the crystal structure of the effector-binding domain of DeoR (C-DeoR) in free form and in covalent complex with its effector deoxyribose-5-phosphate (dR5P). This is the first case of a covalently attached effector molecule captured in the structure of a bacterial transcriptional regulator. The dR5P molecule is attached through a Schiff base linkage to residue Lys141. The crucial role of Lys141 in effector binding was confirmed by mutational analysis and mass spectrometry of Schiff base adducts formed in solution. Structural analyses of the free and effector-bound C-DeoR structures provided a structural explanation for the mechanism of DeoR function as a molecular switch. DATABASES Atomic coordinates and structure factors for crystal structures of free C-DeoR and the covalent Schiff base complex of C-DeoR with dR5P have been deposited in the Protein Data Bank with accession codes 4OQQ and 4OQP, respectively. STRUCTURED DIGITAL ABSTRACT C-DeoR and C-DeoR bind by x-ray crystallography (View interaction) DeoR and DeoR bind by molecular sieving (1, 2).
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Affiliation(s)
- Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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A functional feature analysis on diverse protein–protein interactions: application for the prediction of binding affinity. J Comput Aided Mol Des 2014; 28:619-29. [DOI: 10.1007/s10822-014-9746-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/26/2014] [Indexed: 11/25/2022]
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Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. eLife 2014; 3:e02030. [PMID: 24842992 PMCID: PMC4034769 DOI: 10.7554/elife.02030] [Citation(s) in RCA: 444] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood-based method to covary across protein–protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, provided that the number of aligned sequences is greater than the average length of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter. DOI:http://dx.doi.org/10.7554/eLife.02030.001 Proteins are considered the ‘workhorse molecules’ of life and they are involved in virtually everything that cells do. Proteins are strings of amino acids that have folded into a specific three-dimensional shape. Proteins must have the correct shape to function properly, as they often work by binding to other proteins or molecules—much like a key fitting into a lock. Working out the structure of a protein can, therefore, provide major insights into how the protein does its job. Two or more proteins can bind together and form a complex to perform various tasks; and solving the structures of these complexes can be challenging, even if the structures of the protein subunits are known. Now, Ovchinnikov, Kamisetty, and Baker have developed a method for predicting which parts of the proteins make contact with each other in a two-protein complex. Different species can have copies of the same proteins; but a copy from one species might have different amino acids at certain positions when compared to a related copy from another species. As such, when pairs of interacting proteins from different species are compared, there will be many positions in the two proteins that vary. However, if the amino acid at a position in one protein (let's call it ‘X’) varies, and the amino acid at, say, position ‘Y’ in the other protein also varies such that for any given amino acid at position Y there is often a specific amino acid at position X; positions X and Y are said to ‘co-vary’. Ovchinnikov et al. noticed that when a pair of amino acids (one from each protein in a two-protein complex) co-varied, these two amino acids tended to make contact with each other at the protein–protein interface. Ovchinnikov et al. used the new method to make predictions about the protein–protein interfaces in 28 protein complexes found in bacteria, and also to make a prediction about the interface between protein subunits in the bacterial ribosome. When these predictions were checked against the actual structures, which were all known beforehand, they were found to be accurate if the number of copies of each protein being compared is greater than the average length of the two proteins. Ovchinnikov et al. went on to predict the amino acids on the protein–protein interfaces for another 36 bacterial protein complexes with unknown structures, and to present models for four larger complexes. The next challenge is to extend the method to protein complexes that are found only in eukaryotes (i.e., not in bacteria). Since the number of related copies for eukaryotic proteins tends to be smaller, there are fewer proteins to compare and it is therefore harder to detect ‘covariation’ when it occurs. DOI:http://dx.doi.org/10.7554/eLife.02030.002
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Affiliation(s)
- Sergey Ovchinnikov
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United States Molecular and Cellular Biology Program, University of Washington, Seattle, United States
| | - Hetunandan Kamisetty
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United States Facebook Inc., Seattle, United States
| | - David Baker
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United States
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THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions. J Biol Phys 2014; 40:121-37. [PMID: 24682643 DOI: 10.1007/s10867-014-9341-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 01/16/2014] [Indexed: 12/11/2022] Open
Abstract
Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster large-scale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG)3. These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG)3. Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α- and β- domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.
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35
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Krüger DM, Ignacio Garzón J, Chacón P, Gohlke H. DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking. PLoS One 2014; 9:e89466. [PMID: 24586799 PMCID: PMC3931789 DOI: 10.1371/journal.pone.0089466] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/20/2014] [Indexed: 02/06/2023] Open
Abstract
The distance-dependent knowledge-based DrugScorePPI potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated as a scoring and objective function for the structure prediction of protein-protein complexes. When applied for ranking “unbound perturbation” (“unbound docking”) decoys generated by Baker and coworkers a 4-fold (1.5-fold) enrichment of acceptable docking solutions in the top ranks compared to a random selection is found. When applied as an objective function in FRODOCK for bound protein-protein docking on 97 complexes of the ZDOCK benchmark 3.0, DrugScorePPI/FRODOCK finds up to 10% (15%) more high accuracy solutions in the top 1 (top 10) predictions than the original FRODOCK implementation. When used as an objective function for global unbound protein-protein docking, fair docking success rates are obtained, which improve by ∼2-fold to 18% (58%) for an at least acceptable solution in the top 10 (top 100) predictions when performing knowledge-driven unbound docking. This suggests that DrugScorePPI balances well several different types of interactions important for protein-protein recognition. The results are discussed in view of the influence of crystal packing and the type of protein-protein complex docked. Finally, a simple criterion is provided with which to estimate a priori if unbound docking with DrugScorePPI/FRODOCK will be successful.
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Affiliation(s)
- Dennis M. Krüger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - José Ignacio Garzón
- Rocasolano Physical Chemistry Institute, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pablo Chacón
- Rocasolano Physical Chemistry Institute, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail:
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36
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Pachl P, Fábry M, Veverka V, Brynda J, Řezáčová P. Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase. J Enzyme Inhib Med Chem 2014; 30:63-8. [PMID: 24506201 DOI: 10.3109/14756366.2013.879577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human mitochondrial 5'(3')-deoxyribonucleotidase (mdN) catalyzes dephosphorylation of nucleoside monophosphates, and thus helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Mature mdN is a 23-kDa dimeric protein with highest expression levels in the heart, brain and skeletal muscle. We have identified an alternative splice variant of the mdN gene containing an 18-nucleotide insertion encoding 6 amino acids (GKWPAT) at the 3'-end of the penultimate exon 4. We recombinantly expressed this enzyme variant and characterized its biochemical and kinetic properties as well as its three-dimensional structure. Our high-resolution (1.27 Å) crystal structure revealed that the insertion forms a loop located in the vicinity of the active site pocket and affects enzyme kinetic parameters as well as protein thermal stability.
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Affiliation(s)
- Petr Pachl
- Institute of Organic Chemistry and Biochemistry and
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37
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Pachl P, Fábry M, Rosenberg I, Simák O, Rezáčová P, Brynda J. Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors. ACTA ACUST UNITED AC 2014; 70:461-70. [PMID: 24531480 DOI: 10.1107/s1399004713030502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/06/2013] [Indexed: 11/10/2022]
Abstract
The human 5'(3')-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.
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Affiliation(s)
- Petr Pachl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Ondřej Simák
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Pavlína Rezáčová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
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38
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Nayarisseri A, Yadav M, Wishard R. Computational evaluation of new homologous down regulators of translationally controlled tumor protein (TCTP) targeted for tumor reversion. Interdiscip Sci 2014; 5:274-9. [DOI: 10.1007/s12539-013-0183-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 06/18/2012] [Accepted: 06/25/2012] [Indexed: 01/13/2023]
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Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R. PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun 2014; 445:717-23. [PMID: 24406170 DOI: 10.1016/j.bbrc.2013.12.132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 12/26/2013] [Indexed: 12/11/2022]
Abstract
We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include: (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a multimeric protein assembly with cofactors and metal ions and (3) analysis of consensus interaction motifs within the ensembles and identification of conserved determinants of these interactions. Currently the database contains 585 proteins with 650 peptide-binding sites. http://peptisite.ucsd.edu/ link allows searching for the sites of interest and interactive visualization of the ensembles using the ActiveICM web-browser plugin. This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark.
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Affiliation(s)
- Chayan Acharya
- UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Irina Kufareva
- UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Andrey V Ilatovskiy
- UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188300, Russia; Research and Education Center "Biophysics", PNPI and St. Petersburg State Polytechnical University, St. Petersburg 195251, Russia
| | - Ruben Abagyan
- UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
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40
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Andrabi M, Mizuguchi K, Ahmad S. Conformational changes in DNA-binding proteins: relationships with precomplex features and contributions to specificity and stability. Proteins 2013; 82:841-57. [PMID: 24265157 DOI: 10.1002/prot.24462] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/02/2013] [Accepted: 10/21/2013] [Indexed: 12/22/2022]
Abstract
Both Proteins and DNA undergo conformational changes in order to form functional complexes and also to facilitate interactions with other molecules. These changes have direct implications for the stability and specificity of the complex, as well as the cooperativity of interactions between multiple entities. In this work, we have extensively analyzed conformational changes in DNA-binding proteins by superimposing DNA-bound and unbound pairs of protein structures in a curated database of 90 proteins. We manually examined each of these pairs, unified the authors' annotations, and summarized our observations by classifying conformational changes into six structural categories. We explored a relationship between conformational changes and functional classes, binding motifs, target specificity, biophysical features of unbound proteins, and stability of the complex. In addition, we have also investigated the degree to which the intrinsic flexibility can explain conformational changes in a subset of 52 proteins with high quality coordinate data. Our results indicate that conformational changes in DNA-binding proteins contribute significantly to both the stability of the complex and the specificity of targets recognized by them. We also conclude that most conformational changes occur in proteins interacting with specific DNA targets, even though unbound protein structures may have sufficient information to interact with DNA in a nonspecific manner.
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Affiliation(s)
| | - Kenji Mizuguchi
- Bioinformatics project, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
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Abstract
Formation of protein-ligand complexes causes various changes in both the receptor and the ligand. This review focuses on changes in pK and protonation states of ionizable groups that accompany protein-ligand binding. Physical origins of these effects are outlined, followed by a brief overview of the computational methods to predict them and the associated corrections to receptor-ligand binding affinities. Statistical prevalence, magnitude and spatial distribution of the pK and protonation state changes in protein-ligand binding are discussed in detail, based on both experimental and theoretical studies. While there is no doubt that these changes occur, they do not occur all the time; the estimated prevalence varies, both between individual complexes and by method. The changes occur not only in the immediate vicinity of the interface but also sometimes far away. When receptor-ligand binding is associated with protonation state change at particular pH, the binding becomes pH dependent: we review the interplay between sub-cellular characteristic pH and optimum pH of receptor-ligand binding. It is pointed out that there is a tendency for protonation state changes upon binding to be minimal at physiologically relevant pH for each complex (no net proton uptake/release), suggesting that native receptor-ligand interactions have evolved to reduce the energy cost associated with ionization changes. As a result, previously reported statistical prevalence of these changes - typically computed at the same pH for all complexes - may be higher than what may be expected at optimum pH specific to each complex. We also discuss whether proper account of protonation state changes appears to improve practical docking and scoring outcomes relevant to structure-based drug design. An overview of some of the existing challenges in the field is provided in conclusion.
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Affiliation(s)
- Alexey V Onufriev
- Department of Computer Science and Physics, 2050 Torgersen Hall, Virginia Tech, Blacksburg, VA 24061, USA.
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42
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Loop A is critical for the functional interaction of two Beta vulgaris PIP aquaporins. PLoS One 2013; 8:e57993. [PMID: 23483963 PMCID: PMC3587573 DOI: 10.1371/journal.pone.0057993] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 01/29/2013] [Indexed: 01/03/2023] Open
Abstract
Research done in the last years strongly support the hypothesis that PIP aquaporin can form heterooligomeric assemblies, specially combining PIP2 monomers with PIP1 monomers. Nevertheless, the structural elements involved in the ruling of homo versus heterooligomeric organization are not completely elucidated. In this work we unveil some features of monomer-monomer interaction in Beta vulgaris PIP aquaporins. Our results show that while BvPIP2;2 is able to interact with BvPIP1;1, BvPIP2;1 shows no functional interaction. The lack of functional interaction between BvPIP2;1 and BvPIP1;1 was further corroborated by dose-response curves of water permeability due to aquaporin activity exposed to different acidic conditions. We also found that BvPIP2;1 is unable to translocate BvPIP1;1-ECFP from an intracellular position to the plasma membrane when co-expressed, as BvPIP2;2 does. Moreover we postulate that the first extracellular loop (loop A) of BvPIP2;1, could be relevant for the functional interaction with BvPIP1;1. Thus, we investigate BvPIP2;1 loop A at an atomic level by Molecular Dynamics Simulation (MDS) and by direct mutagenesis. We found that, within the tetramer, each loop A presents a dissimilar behavior. Besides, BvPIP2;1 loop A mutants restore functional interaction with BvPIP1;1. This work is a contribution to unravel how PIP2 and PIP1 interact to form functional heterooligomeric assemblies. We postulate that BvPIP2;1 loop A is relevant for the lack of functional interaction with BvPIP1;1 and that the monomer composition of PIP assemblies determines their functional properties.
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Tan YS, Śledź P, Lang S, Stubbs CJ, Spring DR, Abell C, Best RB. Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of polo-like kinase 1. Angew Chem Int Ed Engl 2012; 51:10078-81. [PMID: 22961729 PMCID: PMC3547296 DOI: 10.1002/anie.201205676] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Yaw Sing Tan
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Paweł Śledź
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Steffen Lang
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Christopher J Stubbs
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - David R Spring
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Chris Abell
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Robert B Best
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
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Tan YS, Śledź P, Lang S, Stubbs CJ, Spring DR, Abell C, Best RB. Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Zhao K, Wang X, Wong HC, Wohlhueter R, Kirberger MP, Chen G, Yang JJ. Predicting Ca2+ -binding sites using refined carbon clusters. Proteins 2012; 80:2666-79. [PMID: 22821762 DOI: 10.1002/prot.24149] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 06/14/2012] [Accepted: 07/11/2012] [Indexed: 12/13/2022]
Abstract
Identifying Ca(2+) -binding sites in proteins is the first step toward understanding the molecular basis of diseases related to Ca(2+) -binding proteins. Currently, these sites are identified in structures either through X-ray crystallography or NMR analysis. However, Ca(2+) -binding sites are not always visible in X-ray structures due to flexibility in the binding region or low occupancy in a Ca(2+) -binding site. Similarly, both Ca(2+) and its ligand oxygens are not directly observed in NMR structures. To improve our ability to predict Ca(2+) -binding sites in both X-ray and NMR structures, we report a new graph theory algorithm (MUG(C) ) to predict Ca(2+) -binding sites. Using carbon atoms covalently bonded to the chelating oxygen atoms, and without explicit reference to side-chain oxygen ligand co-ordinates, MUG(C) is able to achieve 94% sensitivity with 76% selectivity on a dataset of X-ray structures composed of 43 Ca(2+) -binding proteins. Additionally, prediction of Ca(2+) -binding sites in NMR structures was obtained by MUG(C) using a different set of parameters, which were determined by the analysis of both Ca(2+) -constrained and unconstrained Ca(2+) -loaded structures derived from NMR data. MUG(C) identified 20 of 21 Ca(2+) -binding sites in NMR structures inferred without the use of Ca(2+) constraints. MUG(C) predictions are also highly selective for Ca(2+) -binding sites as analyses of binding sites for Mg(2+) , Zn(2+) , and Pb(2+) were not identified as Ca(2+) -binding sites. These results indicate that the geometric arrangement of the second-shell carbon cluster is sufficient not only for accurate identification of Ca(2+) -binding sites in NMR and X-ray structures but also for selective differentiation between Ca(2+) and other relevant divalent cations.
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Affiliation(s)
- Kun Zhao
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA 30303, USA
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Grimme D, González-ruiz D, Gohlke* H. Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules. PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735377-00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Kirys T, Ruvinsky AM, Tuzikov AV, Vakser IA. Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding. Proteins 2012; 80:2089-98. [PMID: 22544766 DOI: 10.1002/prot.24103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 04/12/2012] [Accepted: 04/17/2012] [Indexed: 01/26/2023]
Abstract
Conformational changes in the side chains are essential for protein-protein binding. Rotameric states and unbound- to-bound conformational changes in the surface residues were systematically studied on a representative set of protein complexes. The side-chain conformations were mapped onto dihedral angles space. The variable threshold algorithm was developed to cluster the dihedral angle distributions and to derive rotamers, defined as the most probable conformation in a cluster. Six rotamer libraries were generated: full surface, surface noninterface, and surface interface-each for bound and unbound states. The libraries were used to calculate the probabilities of the rotamer transitions upon binding. The stability of amino acids was quantified based on the transition maps. The noninterface residues' stability was higher than that of the interface. Long side chains with three or four dihedral angles were less stable than the shorter ones. The transitions between the rotamers at the interface occurred more frequently than on the noninterface surface. Most side chains changed conformation within the same rotamer or moved to an adjacent rotamer. The highest percentage of the transitions was observed primarily between the two most occupied rotamers. The probability of the transition between rotamers increased with the decrease of the rotamer stability. The analysis revealed characteristics of the surface side-chain conformational transitions that can be utilized in flexible docking protocols.
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Affiliation(s)
- Tatsiana Kirys
- Center for Bioinformatics, The University of Kansas, Lawrence, Kansas 66047, USA
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Mutations in HIV-1 gag and pol compensate for the loss of viral fitness caused by a highly mutated protease. Antimicrob Agents Chemother 2012; 56:4320-30. [PMID: 22644035 DOI: 10.1128/aac.00465-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the last few decades, the treatment of HIV-infected patients by highly active antiretroviral therapy, including protease inhibitors (PIs), has become standard. Here, we present results of analysis of a patient-derived, multiresistant HIV-1 CRF02_AG recombinant strain with a highly mutated protease (PR) coding sequence, where up to 19 coding mutations have accumulated in the PR. The results of biochemical analysis in vitro showed that the patient-derived PR is highly resistant to most of the currently used PIs and that it also exhibits very poor catalytic activity. Determination of the crystal structure revealed prominent changes in the flap elbow region and S1/S1' active site subsites. While viral loads in the patient were found to be high, the insertion of the patient-derived PR into a HIV-1 subtype B backbone resulted in reduction of infectivity by 3 orders of magnitude. Fitness compensation was not achieved by elevated polymerase (Pol) expression, but the introduction of patient-derived gag and pol sequences in a CRF02_AG backbone rescued viral infectivity to near wild-type (wt) levels. The mutations that accumulated in the vicinity of the processing sites spanning the p2/NC, NC/p1, and p6pol/PR proteins lead to much more efficient hydrolysis of corresponding peptides by patient-derived PR in comparison to the wt enzyme. This indicates a very efficient coevolution of enzyme and substrate maintaining high viral loads in vivo under constant drug pressure.
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Swapna LS, Mahajan S, de Brevern AG, Srinivasan N. Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. BMC STRUCTURAL BIOLOGY 2012; 12:6. [PMID: 22554255 PMCID: PMC3427047 DOI: 10.1186/1472-6807-12-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 04/05/2012] [Indexed: 12/31/2022]
Abstract
BACKGROUND Most signalling and regulatory proteins participate in transient protein-protein interactions during biological processes. They usually serve as key regulators of various cellular processes and are often stable in both protein-bound and unbound forms. Availability of high-resolution structures of their unbound and bound forms provides an opportunity to understand the molecular mechanisms involved. In this work, we have addressed the question "What is the nature, extent, location and functional significance of structural changes which are associated with formation of protein-protein complexes?" RESULTS A database of 76 non-redundant sets of high resolution 3-D structures of protein-protein complexes, representing diverse functions, and corresponding unbound forms, has been used in this analysis. Structural changes associated with protein-protein complexation have been investigated using structural measures and Protein Blocks description. Our study highlights that significant structural rearrangement occurs on binding at the interface as well as at regions away from the interface to form a highly specific, stable and functional complex. Notably, predominantly unaltered interfaces interact mainly with interfaces undergoing substantial structural alterations, revealing the presence of at least one structural regulatory component in every complex.Interestingly, about one-half of the number of complexes, comprising largely of signalling proteins, show substantial localized structural change at surfaces away from the interface. Normal mode analysis and available information on functions on some of these complexes suggests that many of these changes are allosteric. This change is largely manifest in the proteins whose interfaces are altered upon binding, implicating structural change as the possible trigger of allosteric effect. Although large-scale studies of allostery induced by small-molecule effectors are available in literature, this is, to our knowledge, the first study indicating the prevalence of allostery induced by protein effectors. CONCLUSIONS The enrichment of allosteric sites in signalling proteins, whose mutations commonly lead to diseases such as cancer, provides support for the usage of allosteric modulators in combating these diseases.
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Affiliation(s)
| | - Swapnil Mahajan
- Univ de la Réunion, UMR_S 665, F-97715, Saint-Denis, France
- INSERM, U 665, Saint-Denis, F-97715, France
| | - Alexandre G de Brevern
- INSERM, U 665 DSIMB, Paris, F-75739, France
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, F- 75739, France
- INTS, F-75739, Paris, France
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Procházková K, Čermáková K, Pachl P, Sieglová I, Fábry M, Otwinowski Z, Řezáčová P. Structure of the effector-binding domain of the arabinose repressor AraR from Bacillus subtilis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:176-85. [PMID: 22281747 PMCID: PMC3337009 DOI: 10.1107/s090744491105414x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 12/15/2011] [Indexed: 11/10/2022]
Abstract
In Bacillus subtilis, the arabinose repressor AraR negatively controls the expression of genes in the metabolic pathway of arabinose-containing polysaccharides. The protein is composed of two domains of different phylogenetic origin and function: an N-terminal DNA-binding domain belonging to the GntR family and a C-terminal effector-binding domain that shows similarity to members of the GalR/LacI family. The crystal structure of the C-terminal effector-binding domain of AraR in complex with the effector L-arabinose has been determined at 2.2 Å resolution. The L-arabinose binding affinity was characterized by isothermal titration calorimetry and differential scanning fluorimetry; the K(d) value was 8.4 ± 0.4 µM. The effect of L-arabinose on the protein oligomeric state was investigated in solution and detailed analysis of the crystal identified a dimer organization which is distinctive from that of other members of the GalR/LacI family.
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Affiliation(s)
- Kateřina Procházková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, Czech Republic
| | - Kateřina Čermáková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic
| | - Irena Sieglová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic
| | | | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic
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