1
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Li J, Her AS, Besch A, Ramirez-Cordero B, Crames M, Banigan JR, Mueller C, Marsiglia WM, Zhang Y, Traaseth NJ. Dynamics underlie the drug recognition mechanism by the efflux transporter EmrE. Nat Commun 2024; 15:4537. [PMID: 38806470 PMCID: PMC11133458 DOI: 10.1038/s41467-024-48803-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/14/2024] [Indexed: 05/30/2024] Open
Abstract
The multidrug efflux transporter EmrE from Escherichia coli requires anionic residues in the substrate binding pocket for coupling drug transport with the proton motive force. Here, we show how protonation of a single membrane embedded glutamate residue (Glu14) within the homodimer of EmrE modulates the structure and dynamics in an allosteric manner using NMR spectroscopy. The structure of EmrE in the Glu14 protonated state displays a partially occluded conformation that is inaccessible for drug binding by the presence of aromatic residues in the binding pocket. Deprotonation of a single Glu14 residue in one monomer induces an equilibrium shift toward the open state by altering its side chain position and that of a nearby tryptophan residue. This structural change promotes an open conformation that facilitates drug binding through a conformational selection mechanism and increases the binding affinity by approximately 2000-fold. The prevalence of proton-coupled exchange in efflux systems suggests a mechanism that may be shared in other antiporters where acid/base chemistry modulates access of drugs to the substrate binding pocket.
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Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, New York, NY, USA
| | - Ampon Sae Her
- Department of Chemistry, New York University, New York, NY, USA
| | - Alida Besch
- Department of Chemistry, New York University, New York, NY, USA
| | | | - Maureen Crames
- Department of Chemistry, New York University, New York, NY, USA
| | - James R Banigan
- Department of Chemistry, New York University, New York, NY, USA
| | - Casey Mueller
- Department of Chemistry, New York University, New York, NY, USA
| | | | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, USA
- Simons Center for Computational Physical Chemistry, New York University, New York, NY, USA
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2
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Shi J, Cho JH, Hwang W. Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding. J Chem Theory Comput 2023; 19:1875-1887. [PMID: 36820489 PMCID: PMC10848206 DOI: 10.1021/acs.jctc.2c00776] [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: 07/27/2022] [Indexed: 02/24/2023]
Abstract
Atomistic-level understanding of surface hydration mediating protein-protein interactions and ligand binding has been a challenge due to the dynamic nature of water molecules near the surface. We develop a computational method to evaluate the solvation free energy based on the density map of the first hydration shell constructed from all-atom molecular dynamics simulation and use it to examine the binding of two intrinsically disordered ligands to their target protein domain. One ligand is from the human protein, and the other is from the 1918 Spanish flu virus. We find that the viral ligand incurs a 6.9 kcal/mol lower desolvation penalty upon binding to the target, which is consistent with its stronger binding affinity. The difference arises from the spatially fragmented and nonuniform water density profiles of the first hydration shell. In particular, residues that are distal from the ligand-binding site contribute to a varying extent to the desolvation penalty, among which the "entropy hotspot" residues contribute significantly. Thus, ligand binding alters hydration on remote sites in addition to affecting the binding interface. The nonlocal effect disappears when the conformational motion of the protein is suppressed. The present results elucidate the interplay between protein conformational dynamics and surface hydration. Our approach of measuring the solvation free energy based on the water density of the first hydration shell is tolerant of the conformational fluctuation of protein, and we expect it to be applicable to investigating a broad range of biomolecular interfaces.
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Affiliation(s)
- Jie Shi
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 777843, United States
| | - Jae-Hyun Cho
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas 77843, United States
| | - Wonmuk Hwang
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College Station, Texas 77843, United States
- Department
of Physics and Astronomy, Texas A&M
University, College Station, Texas 77843, United States
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3
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Gavrilov Y, Prestel A, Lindorff-Larsen K, Teilum K. Slow conformational changes in the rigid and highly stable chymotrypsin inhibitor 2. Protein Sci 2023; 32:e4604. [PMID: 36807681 PMCID: PMC10031225 DOI: 10.1002/pro.4604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023]
Abstract
Slow conformational changes are often directly linked to protein function. It is however less clear how such processes may perturb the overall folding stability of a protein. We previously found that the stabilizing double mutant L49I/I57V in the small protein chymotrypsin inhibitor 2 from barley led to distributed increased nanosecond and faster dynamics. Here we asked what effects the L49I and I57V substitutions, either individually or together, have on the slow conformational dynamics of CI2. We used 15 N CPMG spin relaxation dispersion experiments to measure the kinetics, thermodynamics and structural changes associated with slow conformational change in CI2. These changes result in an excited state that is populated to 4.3% at 1 °C. As the temperature is increased the population of the excited state decreases. Structural changes in the excited state are associated with residues that interact with water molecules that have well defined positions and are found at these positions in all crystal structures of CI2. The substitutions in CI2 have only little effect on the structure of the excited state whereas the stability of the excited state to some extent follows the stability of the main state. The minor state is thus most populated for the most stable CI2 variant and least populated for the least stable variant. We hypothesize that the interactions between the substituted residues and the well-ordered water molecules links subtle structural changes around the substituted residues to the region in the protein that experience slow conformational changes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yulian Gavrilov
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
- Present address: Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, Lund, Sweden
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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4
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Dhurua S, Jana M. Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation. Chemphyschem 2023; 24:e202200440. [PMID: 36239153 DOI: 10.1002/cphc.202200440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/13/2022] [Indexed: 11/11/2022]
Abstract
Atomistic molecular dynamics simulations were performed under ambient conditions to explore the conformational features and binding affinities of hexameric glycosaminoglycans (GAGs) with chemokine Interleukin8 (IL8) in an aqueous medium. We tried to understand the role of hydrogen bonds (HBs) involving conserved water in mediating the interactions. The Luzar-Chandler model was adopted to study the kinetics of HB breaking and formation concerning different water-mediated HBs. The conformational flexibilities of bound GAGs are due to the flexible glycosidic linkages than the occasional/rare ring pucker conformation. The free energy landscape constructed with ϕ, and ψ, depicted that different conformational minima associated with the glycosidic linkage flexibility of the GAGs in bound states are separated by energy barriers. The binding affinities of IL8 towards GAGs are favored through the electrostatic and non-polar solvation interactions. 4-different types of conserved water were explored in the solvent-mediated binding of GAGs with IL8. The average lifetime of the IL8-GAG direct HB pairs was ∼ten times less than the IL8-GAG-shared water HBs. This is due to the rapid establishment of HB breaking and reformation kinetics involving water of a shared layer. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein.
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Affiliation(s)
- Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, 769008, Rourkela, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, 769008, Rourkela, India
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5
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Jaiswal VK, Kabaciński P, Nogueira de Faria BE, Gentile M, de Paula AM, Borrego-Varillas R, Nenov A, Conti I, Cerullo G, Garavelli M. Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan. J Am Chem Soc 2022; 144:12884-12892. [PMID: 35796759 PMCID: PMC9305959 DOI: 10.1021/jacs.2c04565] [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] [Indexed: 11/29/2022]
Abstract
![]()
By combining UV transient
absorption spectroscopy with sub-30-fs
temporal resolution and CASPT2/MM calculations, we present a complete
description of the primary photoinduced processes in solvated tryptophan.
Our results shed new light on the role of the solvent in the relaxation
dynamics of tryptophan. We unveil two consecutive coherent population
transfer events involving the lowest two singlet excited states: a
sub-50-fs nonadiabatic La → Lb transfer
through a conical intersection and a subsequent 220 fs reverse Lb → La transfer due to solvent-assisted adiabatic
stabilization of the La state. Vibrational fingerprints
in the transient absorption spectra provide compelling evidence of
a vibronic coherence established between the two excited states from
the earliest times after photoexcitation and lasting until the back-transfer
to La is complete. The demonstration of response to the
environment as a driver of coherent population dynamics among the
excited states of tryptophan closes the long debate on its solvent-assisted
relaxation mechanisms and extends its application as a local probe
of protein dynamics to the ultrafast time scales.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Piotr Kabaciński
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | | | - Marziogiuseppe Gentile
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
| | - Rocio Borrego-Varillas
- Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.,Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
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6
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Nishida K, Anada T, Tanaka M. Roles of interfacial water states on advanced biomedical material design. Adv Drug Deliv Rev 2022; 186:114310. [PMID: 35487283 DOI: 10.1016/j.addr.2022.114310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 12/15/2022]
Abstract
When biomedical materials come into contact with body fluids, the first reaction that occurs on the material surface is hydration; proteins are then adsorbed and denatured on the hydrated material surface. The amount and degree of denaturation of adsorbed proteins affect subsequent cell behavior, including cell adhesion, migration, proliferation, and differentiation. Biomolecules are important for understanding the interactions and biological reactions of biomedical materials to elucidate the role of hydration in biomedical materials and their interaction partners. Analysis of the water states of hydrated materials is complicated and remains controversial; however, knowledge about interfacial water is useful for the design and development of advanced biomaterials. Herein, we summarize recent findings on the hydration of synthetic polymers, supramolecular materials, inorganic materials, proteins, and lipid membranes. Furthermore, we present recent advances in our understanding of the classification of interfacial water and advanced polymer biomaterials, based on the intermediate water concept.
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Affiliation(s)
- Kei Nishida
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan; Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Japan(1)
| | - Takahisa Anada
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan.
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7
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Kistwal T, Mukhopadhyay A, Dasgupta S, Sharma KP, Datta A. Ultraslow Biological Water-Like Dynamics in Waterless Liquid Protein. J Phys Chem Lett 2022; 13:4389-4393. [PMID: 35548934 DOI: 10.1021/acs.jpclett.2c00702] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fluorescence correlation spectroscopy and time-dependent fluorescence Stokes shift have been employed to elucidate dynamics in different time scales, ranging from picoseconds to nanoseconds, for human serum albumin, in its native and cationized forms as well as in the self-assembled complex of the cationized protein with the polymer surfactant (PS) glycolic acid ethoxylate lauryl ether. The effect of crowding in this complex, especially in the waterless condition, is of prime importance in this context. Excellent correlation of the dynamics with the structures, obtained by circular dichroism and Fourier transform infrared spectroscopy, has been observed. Slow solvation, associated classically with biological water, has been observed in these systems, even in the waterless condition. This apparently intriguing observation has been rationalized by the relaxation of segments of the protein and the PS in the microenvironment of the fluorescent probe.
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Affiliation(s)
- Tanuja Kistwal
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anasua Mukhopadhyay
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Souradip Dasgupta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kamendra P Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anindya Datta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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8
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Busi B, Yarava JR, Bertarello A, Freymond F, Adamski W, Maurin D, Hiller M, Oschkinat H, Blackledge M, Emsley L. Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation. J Phys Chem B 2021; 125:2212-2221. [PMID: 33635078 DOI: 10.1021/acs.jpcb.0c10188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R1) measurements to determine the hierarchical activation energies of motions of four different proteins: two small globular proteins (GB1 and the SH3 domain of α-spectrin), an intrinsically disordered protein (the C-terminus of the nucleoprotein of the Sendai virus, Sendai Ntail), and an outer membrane protein (OmpG). The activation energies map the motions occurring in the side chains, in the backbone, and in the hydration shells of the proteins. We were able to identify similarities and differences in the average motions of the proteins. We find that the NMR relaxation properties of the four proteins do share similar features. The data characterizing average backbone motions are found to be very similar, the same for methyl group rotations, and similar activation energies are measured. The main observed difference occurs for the intrinsically disordered Sendai Ntail, where we observe much lower energy of activation for motions of protons associated with the protein-solvent interface as compared to the others. We also observe variability between the proteins regarding side chain 15N relaxation of lysine residues, with a higher activation energy observed in OmpG. This hints at strong interactions with negatively charged lipids in the bilayer and provides a possible mechanistic clue for the "positive-inside" rule for helical membrane proteins. Overall, these observations refine the understanding of the similarities and differences between hierarchical dynamics in proteins.
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Affiliation(s)
- Baptiste Busi
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Jayasubba Reddy Yarava
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Andrea Bertarello
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - François Freymond
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Wiktor Adamski
- Université Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Damien Maurin
- Université Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Matthias Hiller
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | | | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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9
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Li Y, Zhang R, Xu Y. Structure-based mechanisms: On the way to apply alcohol dehydrogenases/reductases to organic-aqueous systems. Int J Biol Macromol 2020; 168:412-427. [PMID: 33316337 DOI: 10.1016/j.ijbiomac.2020.12.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/20/2022]
Abstract
Alcohol dehydrogenases/reductases catalyze enantioselective syntheses of versatile chiral compounds relying on direct hydride transfer from cofactor to substrates, or to an intermediate and then to substrates. Since most of the substrates catalyzed by alcohol dehydrogenases/reductases are insoluble in aqueous solutions, increasing interest has been turning to organic-aqueous systems. However, alcohol dehydrogenases/reductases are normally instable in organic solvents, leading to the unsatisfied enantioselective synthesis efficiency. The behaviors of these enzymes in organic solvents at an atomic level are unclear, thus it is of great importance to understand its structure-based mechanisms in organic-aqueous systems to improve their relative stability. Here, we summarized the accessible structures of alcohol dehydrogenases/reductases in Protein Data Bank crystallized in organic-aqueous systems, and compared the structures of alcohol dehydrogenases/reductases which have different tolerance towards organic solvents. By understanding the catalytic behaviors and mechanisms of these enzymes in organic-aqueous systems, the efficient enantioselective syntheses mediated by alcohol dehydrogenases/reductases and further challenges are also discussed through solvent engineering and enzyme-immobilization in the last decade.
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Affiliation(s)
- Yaohui Li
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; Department of Biological Science, Columbia University, New York, NY 10025, United States
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
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10
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Joseph RE, Amatya N, Fulton DB, Engen JR, Wales TE, Andreotti A. Differential impact of BTK active site inhibitors on the conformational state of full-length BTK. eLife 2020; 9:60470. [PMID: 33226337 PMCID: PMC7834017 DOI: 10.7554/elife.60470] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) is targeted in the treatment of B-cell disorders including leukemias and lymphomas. Currently approved BTK inhibitors, including Ibrutinib, a first-in-class covalent inhibitor of BTK, bind directly to the kinase active site. While effective at blocking the catalytic activity of BTK, consequences of drug binding on the global conformation of full-length BTK are unknown. Here, we uncover a range of conformational effects in full-length BTK induced by a panel of active site inhibitors, including large-scale shifts in the conformational equilibria of the regulatory domains. Additionally, we find that a remote Ibrutinib resistance mutation, T316A in the BTK SH2 domain, drives spurious BTK activity by destabilizing the compact autoinhibitory conformation of full-length BTK, shifting the conformational ensemble away from the autoinhibited form. Future development of BTK inhibitors will need to consider long-range allosteric consequences of inhibitor binding, including the emerging application of these BTK inhibitors in treating COVID-19. Treatments for blood cancers, such as leukemia and lymphoma, rely heavily on chemotherapy, using drugs that target a vulnerable aspect of the cancer cells. B-cells, a type of white blood cell that produces antibodies, require a protein called Bruton’s tyrosine kinase, or BTK for short, to survive. The drug ibrutinib (Imbruvica) is used to treat B-cell cancers by blocking BTK. The BTK protein consists of several regions. One of them, known as the kinase domain, is responsible for its activity as an enzyme (which allows it to modify other proteins by adding a ‘tag’ known as a phosphate group). The other regions of BTK, known as regulatory modules, control this activity. In BTK’s inactive form, the regulatory modules attach to the kinase domain, blocking the regulatory modules from interacting with other proteins. When BTK is activated, it changes its conformation so the regulatory regions detach and become available for interactions with other proteins, at the same time exposing the active kinase domain. Ibrutinib and other BTK drugs in development bind to the kinase domain to block its activity. However, it is not known how this binding affects the regulatory modules. Previous efforts to study how drugs bind to BTK have used a version of the protein that only had the kinase domain, instead of the full-length protein. Now, Joseph et al. have studied full-length BTK and how it binds to five different drugs. The results reveal that ibrutinib and another drug called dasatinib both indirectly disrupt the normal position of the regulatory domains pushing BTK toward a conformation that resembles the activated state. By contrast, the three other compounds studied do not affect the inactive structure. Joseph et al. also examined a mutation in BTK that confers resistance against ibrutinib. This mutation increases the activity of BTK by disrupting the inactive structure, leading to B cells surviving better. Understanding how drug resistance mechanisms can work will lead to better drug treatment strategies for cancer. BTK is also a target in other diseases such as allergies or asthma and even COVID-19. If interactions between partner proteins and the regulatory domain are important in these diseases, then they may be better treated with drugs that maintain the regulatory modules in their inactive state. This research will help to design drugs that are better able to control BTK activity.
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Affiliation(s)
- Raji E Joseph
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - Neha Amatya
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - D Bruce Fulton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Amy Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
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11
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Bolmatov D, Kinnun JJ, Katsaras J, Lavrentovich MO. Phonon-mediated lipid raft formation in biological membranes. Chem Phys Lipids 2020; 232:104979. [PMID: 32980352 DOI: 10.1016/j.chemphyslip.2020.104979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Short-wavelength collective molecular motions, also known as phonons, have recently attracted much interest in revealing dynamic properties of biological membranes through the use of neutron and X-ray scattering, infrared and Raman spectroscopies, and molecular dynamics simulations. Experimentally detecting unique vibrational patterns such as, shear phonon excitations, viscoelastic crossovers, transverse acoustic phonon gaps, and continuous and truncated optical phonon modes in cellular membranes, to name a few, has proven non-trivial. Here, we review recent advances in liquid thermodynamics that have resulted in the development of the phonon theory of liquids. The theory has important predictions regarding the shear vibrational spectra of fluids, namely the emergence of viscoelastic crossovers and transverse acoustic phonon gaps. Furthermore, we show that these vibrational patterns are common in soft (non-crystalline) materials, including, but not limited to liquids, colloids, liquid crystals (mesogens), block copolymers, and biological membranes. The existence of viscoelastic crossovers and acoustic phonon gaps define the self-diffusion properties of cellular membranes and provide a molecular picture of the transient nature of lipid rafts (Bolmatov et al., 2020). Importantly, the timescales (picoseconds) for the formation and dissolution of transient lipid rafts match the lifetime of the formation and breakdown of interfacial water hydrogen bonds. Apart from acoustic propagating phonon modes, biological membranes can also support more energetic non-propagating optical phonon excitations, also known as standing waves or breathing modes. Importantly, optical phonons can be truncated due to the existence of finite size nanodomains made up of strongly correlated lipid-cholesterol molecular pairs. These strongly coupled molecular pairs can serve as nucleation centers for the formation of stable rafts at larger length scales, due to correlations of spontaneous fluctuations (Onsager's regression hypothesis). Finally and importantly, molecular level viscoelastic crossovers, acoustic phonon gaps, and continuous and truncated optical phonon modes may offer insights as to how lipid-lipid and lipid-protein interactions enable biological function.
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Affiliation(s)
- Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
| | - Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - John Katsaras
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States; Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - Maxim O Lavrentovich
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
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12
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Matsuda Y, Hirano Y, Mizutani S, Sakai D, Fujii A, Maeda S, Ohno K. Migrations and Catalytic Action of Water Molecules in the Ionized Formamide-(H 2O) 2 Cluster. J Phys Chem A 2020; 124:2802-2807. [PMID: 32187496 DOI: 10.1021/acs.jpca.0c00637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isomerization dynamics involving the migrations, proton transfer reaction, and catalytic actions of water molecules upon vertical ionization of the formamide (FA)-(H2O)2 cluster is investigated by the infrared spectroscopy and theoretical reaction path search calculation. The infrared spectroscopic result indicates the [FA-(H2O)2]+ cation has the hydrogen-bonded structure of the enol isomer cation of formamide and the water dimer. This structure is formed by proton transfer from the CH bond to the carbonyl group through the catalytic action of the water molecules. The isomerization paths involving this enolization in ionized FA-(H2O)2 are explored by using the anharmonic downward distortion following method. We found multiple enolization paths which accompany proton exchanges among the formamide moiety and water molecules through the catalytic actions of the water molecules.
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Affiliation(s)
- Yoshiyuki Matsuda
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Yutaro Hirano
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Shinichi Mizutani
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Daichi Sakai
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.,National Institute for Materials Science (NIMS) Research and Services Division of Materials Data and Integrated System (MaDIS) Tsukuba, 305-0044, Japan
| | - Koichi Ohno
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan.,Institute for Quantum Chemical Exploration, 13F Area Shinagawa, Konan 1-9-36, Minato-ku, Tokyo, 108-0075, Japan
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13
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Bera S, Xue B, Rehak P, Jacoby G, Ji W, Shimon LJW, Beck R, Král P, Cao Y, Gazit E. Self-Assembly of Aromatic Amino Acid Enantiomers into Supramolecular Materials of High Rigidity. ACS NANO 2020; 14:1694-1706. [PMID: 31944667 PMCID: PMC7123433 DOI: 10.1021/acsnano.9b07307] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/16/2020] [Indexed: 05/12/2023]
Abstract
Most natural biomolecules may exist in either of two enantiomeric forms. Although in nature, amino acid biopolymers are characterized by l-type homochirality, incorporation of d-amino acids in the design of self-assembling peptide motifs has been shown to significantly alter enzyme stability, conformation, self-assembly behavior, cytotoxicity, and even therapeutic activity. However, while functional metabolite assemblies are ubiquitous throughout nature and play numerous important roles including physiological, structural, or catalytic functions, the effect of chirality on the self-assembly nature and function of single amino acids is not yet explored. Herein, we investigated the self-assembly mechanism of amyloid-like structure formation by two aromatic amino acids, phenylalanine (Phe) and tryptophan (Trp), both previously found as extremely important for the nucleation and self-assembly of aggregation-prone peptide regions into functional structures. Employing d-enantiomers, we demonstrate the critical role that amino acid chirality plays in their self-assembly process. The kinetics and morphology of pure enantiomers is completely altered upon their coassembly, allowing to fabricate different nanostructures that are mechanically more robust. Using diverse experimental techniques, we reveal the different molecular arrangement and self-assembly mechanism of the dl-racemic mixtures that resulted in the formation of advanced supramolecular materials. This study provides a simple yet sophisticated engineering model for the fabrication of attractive materials with bionanotechnological applications.
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Affiliation(s)
- Santu Bera
- School
of Molecular Cell Biology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Bin Xue
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu 210093, People’s Republic of China
| | - Pavel Rehak
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
| | - Guy Jacoby
- The
Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Wei Ji
- School
of Molecular Cell Biology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Linda J. W. Shimon
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Roy Beck
- The
Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Petr Král
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
- Department
of Biopharmaceutical Sciences, University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Yi Cao
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu 210093, People’s Republic of China
| | - Ehud Gazit
- School
of Molecular Cell Biology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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14
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Zhuo XF, Wang J, Zhang J, Jiang LL, Hu HY, Lu JX. Solid-State NMR Reveals the Structural Transformation of the TDP-43 Amyloidogenic Region upon Fibrillation. J Am Chem Soc 2020; 142:3412-3421. [PMID: 32003979 DOI: 10.1021/jacs.9b10736] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
TDP-43 is a primary pathological hallmark protein of amyotrophic lateral sclerosis and frontotemporal lobar degeneration, which may exist in the form of amyloid inclusions in the cells of patients. In addition to serving as a biomarker for these diseases, TDP-43 can also directly trigger neurodegeneration. We previously determined the amyloidogenic core region of TDP-43 (residues 311-360) and showed by solution NMR that this region includes two α-helices [(321-330) and (335-343)] in solution. We suggested that the helix-to-sheet structural transformation initiates TDP-43 aggregation. In the present study, X-ray diffraction shows that TDP-43 (311-360) aggregates adopt a cross-β structure. Thioredoxin (Trx)-fused TDP-43 (311-360) can undergo liquid-liquid phase separation (LLPS) before fibrillation, suggesting that phase separation is an intermediate step before amyloid formation. Solid-state NMR (SSNMR), carried out to elucidate the structural changes of TDP-43 (311-360) at the atomic level, indicates five β-strands of the amyloids formed, with the major two β-strands contributed by the first helical region in the solution structure. The NMR evidence is also in support of the fibril having a parallel in-register conformation, implying a mechanism in which the helix-helix interactions in LLPS are converted into β-strand parallel lateral association upon fibrillation. Our studies have assigned many key interresidue interactions that contribute to the stability of the fibril, including F316 with I318 and Q327 and W334 with A325, A326, A329, and S332. SSNMR with 1H detection reveals a unique close interaction between the indole Nε1-Hε1 of W334 and the side-chain carbonyl of Q343. This interaction could be a very important factor in initiating TDP-43 (311-360) folding/misfolding in LLPS.
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Affiliation(s)
- Xiao-Feng Zhuo
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Jian Wang
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China
| | - Jing Zhang
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China
| | - Jun-Xia Lu
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China
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15
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Singh H, Vasa SK, Jangra H, Rovó P, Päslack C, Das CK, Zipse H, Schäfer LV, Linser R. Fast Microsecond Dynamics of the Protein–Water Network in the Active Site of Human Carbonic Anhydrase II Studied by Solid-State NMR Spectroscopy. J Am Chem Soc 2019; 141:19276-19288. [DOI: 10.1021/jacs.9b05311] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Himanshu Singh
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Suresh K. Vasa
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Harish Jangra
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Petra Rovó
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Christopher Päslack
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Hendrik Zipse
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
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16
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Thompson MC, Barad BA, Wolff AM, Sun Cho H, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nat Chem 2019; 11:1058-1066. [PMID: 31527847 PMCID: PMC6815256 DOI: 10.1038/s41557-019-0329-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 08/09/2019] [Indexed: 12/21/2022]
Abstract
Correlated motions of proteins are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved X-ray methods hold promise for addressing this challenge, but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature jumps, through thermal excitation of the solvent, have been utilized to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform temperature-jump small- and wide-angle X-ray scattering measurements on a dynamic enzyme, cyclophilin A, demonstrating that these experiments are able to capture functional intramolecular protein dynamics on the microsecond timescale. We show that cyclophilin A displays rich dynamics following a temperature jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes. Two relaxation processes are resolved: a fast process is related to surface loop motions, and a slower process is related to motions in the core of the protein that are critical for catalytic turnover.
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Affiliation(s)
- Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin A Barad
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander M Wolff
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Hyun Sun Cho
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Friedrich Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M C Schwarz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Philip Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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17
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Mehrabi P, Schulz EC, Dsouza R, Müller-Werkmeister HM, Tellkamp F, Miller RJD, Pai EF. Time-resolved crystallography reveals allosteric communication aligned with molecular breathing. Science 2019; 365:1167-1170. [DOI: 10.1126/science.aaw9904] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework’s dynamics and entropy constitute crucial components of the catalytic machinery.
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18
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Mishra KK, Singh SK, Kumar S, Singh G, Sarkar B, Madhusudhan MS, Das A. Water-Mediated Selenium Hydrogen-Bonding in Proteins: PDB Analysis and Gas-Phase Spectroscopy of Model Complexes. J Phys Chem A 2019; 123:5995-6002. [PMID: 31268326 DOI: 10.1021/acs.jpca.9b04159] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-resolution X-ray crystallography and two-dimensional NMR studies demonstrate that water-mediated conventional hydrogen-bonding interactions (N-H···N, O-H···N, etc.) bridging two or more amino acid residues contribute to the stability of proteins and protein-ligand complexes. In this work, we have investigated single water-mediated selenium hydrogen-bonding interactions (unconventional hydrogen-bonding) between amino acid residues in proteins through extensive protein data bank (PDB) analysis coupled with gas-phase spectroscopy and quantum chemical calculation of a model complex consisting of indole, dimethyl selenide, and water. Here, indole and dimethyl selenide represent the amino acid residues tryptophan and selenomethionine, respectively. The current investigation demonstrates that the most stable structure of the model complex observed in the IR spectroscopy mimics single water-mediated selenium hydrogen-bonded structural motifs present in the crystal structures of proteins. The present work establishes that water-mediated Se hydrogen-bonding interactions are ubiquitous in proteins and the number of these interactions observed in the PDB is more than that of direct Se hydrogen-bonds present there.
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Affiliation(s)
| | | | | | | | - Biplab Sarkar
- Department of Chemistry , North Eastern Hill University , Shillong , Meghalaya 793022 , India
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19
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Jiang X, Yu J, Zhou Z, Kongsted J, Song Y, Pannecouque C, De Clercq E, Kang D, Poongavanam V, Liu X, Zhan P. Molecular design opportunities presented by solvent‐exposed regions of target proteins. Med Res Rev 2019; 39:2194-2238. [DOI: 10.1002/med.21581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 03/09/2019] [Accepted: 03/16/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Ji Yu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Zhongxia Zhou
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Jacob Kongsted
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Odense Denmark
| | - Yuning Song
- Department of Clinical PharmacyQilu Hospital of Shandong University Jinan China
| | - Christophe Pannecouque
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Erik De Clercq
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Dongwei Kang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | | | - Xinyong Liu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Peng Zhan
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
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20
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Ultrafast energy relaxation dynamics of amide I vibrations coupled with protein-bound water molecules. Nat Commun 2019; 10:1010. [PMID: 30824834 PMCID: PMC6397197 DOI: 10.1038/s41467-019-08899-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 02/06/2019] [Indexed: 12/11/2022] Open
Abstract
The influence of hydration water on the vibrational energy relaxation in a protein holds the key to understand ultrafast protein dynamics, but its detection is a major challenge. Here, we report measurements on the ultrafast vibrational dynamics of amide I vibrations of proteins at the lipid membrane/H2O interface using femtosecond time-resolved sum frequency generation vibrational spectroscopy. We find that the relaxation time of the amide I mode shows a very strong dependence on the H2O exposure, but not on the D2O exposure. This observation indicates that the exposure of amide I bond to H2O opens up a resonant relaxation channel and facilitates direct resonant vibrational energy transfer from the amide I mode to the H2O bending mode. The protein backbone motions can thus be energetically coupled with protein-bound water molecules. Our findings highlight the influence of H2O on the ultrafast structure dynamics of proteins.
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21
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Functional Hydration Behavior: Interrelation between Hydration and Molecular Properties at Lipid Membrane Interfaces. J CHEM-NY 2019. [DOI: 10.1155/2019/4867327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Water is an abundant commodity and has various important functions. It stabilizes the structure of biological macromolecules, controls biochemical activities, and regulates interfacial/intermolecular interactions. Common aspects of interfacial water can be obtained by overviewing fundamental functions and properties at different temporal and spatial scales. It is important to understand the hydrogen bonding and structural properties of water and to evaluate the individual molecular species having different hydration properties. Water molecules form hydrogen bonds with biomolecules and contribute to the adjustment of their properties, such as surface charge, hydrophilicity, and structural flexibility. In this review, the fundamental properties of water molecules and the methods used for the analyses of water dynamics are summarized. In particular, the interrelation between the hydration properties, determined by molecules, and the properties of molecules, determined by their hydration properties, are discussed using the lipid membrane as an example. Accordingly, interesting water functions are introduced that provide beneficial information in the fields of biochemistry, medicine, and food chemistry.
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