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Conti Nibali V, Sacchetti F, Paciaroni A, Petrillo C, Tarek M, D'Angelo G. Intra-protein interacting collective modes in the terahertz frequency region. J Chem Phys 2023; 159:161101. [PMID: 37870134 DOI: 10.1063/5.0142381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
Understanding how proteins work requires a thorough understanding of their internal dynamics. Proteins support a wide range of motions, from the femtoseconds to seconds time scale, relevant to crucial biological functions. In this context, the term "protein collective dynamics" refers to the complex patterns of coordinated motions of numerous atoms throughout the protein in the sub-picosecond time scale (terahertz frequency region). It is hypothesized that these dynamics have a substantial impact on the regulation of functional dynamical mechanisms, including ligand binding and allosteric signalling, charge transport direction, and the regulation of thermodynamic and thermal transport properties. Using the theoretical framework of hydrodynamics, the collective dynamics of proteins had previously been described in a manner akin to that of simple liquids, i.e. in terms of a single acoustic-like excitation, related to intra-protein vibrational motions. Here, we employ an interacting-mode model to analyse the results from molecular dynamics simulations and we unveil that the vibrational landscape of proteins is populated by multiple acoustic-like and low-frequency optic-like modes, with mixed symmetry and interfering with each other. We propose an interpretation at the molecular level of the observed scenario that we relate to the side-chains and the hydrogen-bonded networks dynamics. The present insights provide a perspective for understanding the molecular mechanisms underlying the energy redistribution processes in the interior of proteins.
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Affiliation(s)
- Valeria Conti Nibali
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, Messina University, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Francesco Sacchetti
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Mounir Tarek
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Giovanna D'Angelo
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, Messina University, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
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Gerlits O, Fajer M, Cheng X, Blumenthal DK, Radić Z, Kovalevsky A. Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering. Structure 2022; 30:1538-1549.e3. [PMID: 36265484 PMCID: PMC9637784 DOI: 10.1016/j.str.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/07/2022] [Accepted: 09/25/2022] [Indexed: 11/06/2022]
Abstract
Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ∼20-50 cm-1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.
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Affiliation(s)
- Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, USA
| | - Mikolai Fajer
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Zoran Radić
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093-0657, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Kneller DW, Gerlits O, Daemen LL, Pavlova A, Gumbart JC, Cheng Y, Kovalevsky A. Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor. Phys Chem Chem Phys 2022; 24:3586-3597. [PMID: 35089990 PMCID: PMC8940534 DOI: 10.1039/d1cp05487b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ∼5-50 cm-1. This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effects of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal mol-1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, U.S.A
| | - Luke L. Daemen
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Yongqiang Cheng
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Kneller DW, Li H, Galanie S, Phillips G, Labbé A, Weiss KL, Zhang Q, Arnould MA, Clyde A, Ma H, Ramanathan A, Jonsson CB, Head MS, Coates L, Louis JM, Bonnesen PV, Kovalevsky A. Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. J Med Chem 2021; 64:17366-17383. [PMID: 34705466 PMCID: PMC8565456 DOI: 10.1021/acs.jmedchem.1c01475] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 02/08/2023]
Abstract
Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Hui Li
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Audrey Labbé
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Mark A. Arnould
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Austin Clyde
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Computer Science, University of Chicago, Chicago, IL 60615, USA
| | - Heng Ma
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60615
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Martha S. Head
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Peter V. Bonnesen
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
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Parkins A, Skeens E, McCallum CM, Lisi GP, Pantouris G. The N-terminus of MIF regulates the dynamic profile of residues involved in CD74 activation. Biophys J 2021; 120:3893-3900. [PMID: 34437846 DOI: 10.1016/j.bpj.2021.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/03/2021] [Accepted: 08/19/2021] [Indexed: 11/18/2022] Open
Abstract
Macrophage migration inhibitory factor (MIF) is an immunomodulatory protein with a pathogenic activity in various inflammatory disorders, autoimmune diseases, and cancer. The majority of MIF-triggered pathological conditions are associated with activation of the cell surface receptor CD74. In the absence of small molecule antagonists that directly target CD74, MIF variants and MIF-ligand complexes have served as modulators of CD74 activity. These molecules have been reported to have either antagonistic or agonistic effects against the receptor, although the mechanistic parameters that distinguish the two groups are largely unknown. Through molecular dynamics simulations and NMR experiments, we explored the relationship between MIF's catalytically active N-terminus and the surface residues important for the activation of CD74. We found that the two sites are connected via backbone dynamics that are propagated to the CD74 activation surface of MIF, from the β2 and β4 strands. Our results also provide mechanistic evidence that explain the functional characteristics of MIF variants, serving as CD74 agonists or antagonists. Such findings are of high importance for understanding the MIF-induced activation of CD74 as well as for the development of highly potent CD74 therapeutics.
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Affiliation(s)
- Andrew Parkins
- Department of Chemistry, University of the Pacific, Stockton, California
| | - Erin Skeens
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, Rhode Island
| | - C Michael McCallum
- Department of Chemistry, University of the Pacific, Stockton, California
| | - George P Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, Rhode Island.
| | - Georgios Pantouris
- Department of Chemistry, University of the Pacific, Stockton, California.
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Spizzichino S, Pampalone G, Dindo M, Bruno A, Romani L, Cutruzzolà F, Zelante T, Pieroni M, Cellini B, Giardina G. Crystal structure of Aspergillus fumigatus AroH, an aromatic amino acid aminotransferase. Proteins 2021; 90:435-442. [PMID: 34495558 PMCID: PMC9290597 DOI: 10.1002/prot.26234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022]
Abstract
Aspergillus fumigatus is a saprophytic ubiquitous fungus whose spores can trigger reactions such as allergic bronchopulmonary aspergillosis or the fatal invasive pulmonary aspergillosis. To survive in the lungs, the fungus must adapt to a hypoxic and nutritionally restrictive environment, exploiting the limited availability of aromatic amino acids (AAAs) in the best possible way, as mammals do not synthesize them. A key enzyme for AAAs catabolism in A. fumigatus is AroH, a pyridoxal 5′‐phosphate‐dependent aromatic aminotransferase. AroH was recently shown to display a broad substrate specificity, accepting L‐kynurenine and α‐aminoadipate as amino donors besides AAAs. Given its pivotal role in the adaptability of the fungus to nutrient conditions, AroH represents a potential target for the development of innovative therapies against A. fumigatus‐related diseases. We have solved the crystal structure of Af‐AroH at 2.4 Å resolution and gained new insight into the dynamics of the enzyme's active site, which appears to be crucial for the design of inhibitors. The conformational plasticity of the active site pocket is probably linked to the wide substrate specificity of AroH.
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Affiliation(s)
| | - Gioena Pampalone
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Mirco Dindo
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Agostino Bruno
- Food and Drug Department, University of Parma, Parma, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | | | - Teresa Zelante
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome
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