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Miyagi M, Nakazawa T. Significance of Histidine Hydrogen-Deuterium Exchange Mass Spectrometry in Protein Structural Biology. BIOLOGY 2024; 13:37. [PMID: 38248468 PMCID: PMC10813008 DOI: 10.3390/biology13010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
Histidine residues play crucial roles in shaping the function and structure of proteins due to their unique ability to act as both acids and bases. In other words, they can serve as proton donors and acceptors at physiological pH. This exceptional property is attributed to the side-chain imidazole ring of histidine residues. Consequently, determining the acid-base dissociation constant (Ka) of histidine imidazole rings in proteins often yields valuable insights into protein functions. Significant efforts have been dedicated to measuring the pKa values of histidine residues in various proteins, with nuclear magnetic resonance (NMR) spectroscopy being the most commonly used technique. However, NMR-based methods encounter challenges in assigning signals to individual imidazole rings and require a substantial amount of proteins. To address these issues associated with NMR-based approaches, a mass-spectrometry-based method known as histidine hydrogen-deuterium exchange mass spectrometry (His-HDX-MS) has been developed. This technique not only determines the pKa values of histidine imidazole groups but also quantifies their solvent accessibility. His-HDX-MS has proven effective across diverse proteins, showcasing its utility. This review aims to clarify the fundamental principles of His-HDX-MS, detail the experimental workflow, explain data analysis procedures and provide guidance for interpreting the obtained results.
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Affiliation(s)
- Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4988, USA
| | - Takashi Nakazawa
- Department of Chemistry, Nara Women’s University, Nara 630-8506, Japan
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2
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Zhou S, Liu Y, Wang S, Wang L. Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds. Sci Rep 2023; 13:13741. [PMID: 37612311 PMCID: PMC10447522 DOI: 10.1038/s41598-023-40614-7] [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: 05/04/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 Å closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.
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Affiliation(s)
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Sijian Wang
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
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3
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Chen KW, Sun TY, Wu YD. New Insights into the Cooperativity and Dynamics of Dimeric Enzymes. Chem Rev 2023; 123:9940-9981. [PMID: 37561162 DOI: 10.1021/acs.chemrev.3c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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4
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Díaz-Cervantes E, Robles J, Solà M, Swart M. The peptide bond rupture mechanism in the serine proteases: an in silico study based on sequential scale models. Phys Chem Chem Phys 2023; 25:8043-8049. [PMID: 36876585 DOI: 10.1039/d2cp04872h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Given the importance of serine proteases for biochemical processes, we have studied the peptide bond rupture mechanism using three sequential scale models as representations of the KLK5 enzyme (a protein overexpressed in ovarian cancer). The first model contains the basic functional groups of the residues that conform to the catalytic triad present in serine proteases; the second model contains some additional residues and, finally, the last representation includes all atoms of the KLK5 protein together with 10.000 explicit water molecules. This separation into three scale models allows us to separate the intrinsic reactivity of the catalytic triad from the process taking place in the enzyme. The methodologies employed in this work include full DFT calculations with a dielectric continuum in the first two models and a multi-level setup with a Quantum Mechanics/Molecular Mechanics (QM/MM) partition in the whole protein system. Our results show that the peptide-bond rupture mechanism is a stepwise process involving two proton transfer reactions. The rate-determining step is the second proton transfer from the imidazole group to the amidic nitrogen of the substrate. In addition, we find that the simplest model does not provide accurate results compared to the full protein system. This can be attributed to the electronic stabilization conferred by the residues around the reaction site. Interestingly, the energy profile obtained with the second scale model with additional residues shows the same trends as the full system and could therefore be considered an appropriate model system. It could be used for studying the peptide bond rupture mechanism in case full QM/MM calculations cannot be performed, or as a rapid tool for screening purposes.
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Affiliation(s)
- Erik Díaz-Cervantes
- Departamento de Alimentos, Centro Interdisciplinario del Noreste, Universidad de Guanajuato, 37975 Tierra Blanca, Guanajuato, Mexico.,Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, 17003 Girona, Spain.
| | - Juvencio Robles
- Departamento de Farmacia, Universidad de Guanajuato, Noria Alta S/N, Gto. 36050, Guanajuato, Mexico
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, 17003 Girona, Spain.
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, 17003 Girona, Spain. .,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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5
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Marchenko AV, Ozeryanskii VA, Demidov OP, Antonov AS, Tupikina EY, Pozharskii AF. Organometallic Synthesis of 2,3,6,7-Tetrasubstituted 1,8-Bis(dimethylamino)naphthalenes for Investigation of the Double Buttressing Effect in Proton Sponges. J Org Chem 2022; 87:16506-16516. [DOI: 10.1021/acs.joc.2c02212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrey V. Marchenko
- Department of Chemistry, Southern Federal University, Zorge strasse 7, 344090 Rostov-on-Don, Russian Federation
| | - Valery A. Ozeryanskii
- Department of Chemistry, Southern Federal University, Zorge strasse 7, 344090 Rostov-on-Don, Russian Federation
| | - Oleg P. Demidov
- Department of Chemistry and Pharmacy, North Caucasus Federal University, 1a Pushkin St., 355017 Stavropol, Russian Federation
| | - Alexander S. Antonov
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504 St. Petersburg, Russian Federation
| | - Elena Yu. Tupikina
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504 St. Petersburg, Russian Federation
| | - Alexander F. Pozharskii
- Department of Chemistry, Southern Federal University, Zorge strasse 7, 344090 Rostov-on-Don, Russian Federation
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6
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Zhou S, Liu Y, Wang S, Wang L. Effective prediction of short hydrogen bonds in proteins via machine learning method. Sci Rep 2022; 12:469. [PMID: 35013487 PMCID: PMC8748993 DOI: 10.1038/s41598-021-04306-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
Short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry and functional roles of SHBs requires a protein to be at atomic resolution. In this work, we analyze 1260 high-resolution peptide and protein structures from the Protein Data Bank and develop a boosting based machine learning model to predict the formation of SHBs between amino acids. This model, which we name as machine learning assisted prediction of short hydrogen bonds (MAPSHB), takes into account 21 structural, chemical and sequence features and their interaction effects and effectively categorizes each hydrogen bond in a protein to a short or normal hydrogen bond. The MAPSHB model reveals that the type of the donor amino acid plays a major role in determining the class of a hydrogen bond and that the side chain Tyr-Asp pair demonstrates a significant probability of forming a SHB. Combining electronic structure calculations and energy decomposition analysis, we elucidate how the interplay of competing intermolecular interactions stabilizes the Tyr-Asp SHBs more than other commonly observed combinations of amino acid side chains. The MAPSHB model, which is freely available on our web server, allows one to accurately and efficiently predict the presence of SHBs given a protein structure with moderate or low resolution and will facilitate the experimental and computational refinement of protein structures.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Sijian Wang
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
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7
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Chen Y, Wei W, Zhou Y, Xie D. The role of hydrogen bond in catalytic triad of serine proteases. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Yani Chen
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wanqing Wei
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yanzi Zhou
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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8
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Kemp MT, Nichols DA, Zhang X, Defrees K, Na I, Renslo AR, Chen Y. Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Class A β-lactamase. FEBS Lett 2021; 595:2981-2994. [PMID: 34704263 DOI: 10.1002/1873-3468.14215] [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: 09/14/2021] [Revised: 10/07/2021] [Accepted: 10/21/2021] [Indexed: 11/07/2022]
Abstract
The Asp233-Asp246 pair is highly conserved in Class A β-lactamases, which hydrolyze β-lactam antibiotics. Here, we characterize its function using CTX-M-14 β-lactamase. The D233N mutant displayed decreased activity that is substrate-dependent, with reductions in kcat /Km ranging from 20% for nitrocefin to 6-fold for cefotaxime. In comparison, the mutation reduced the binding of a known reversible inhibitor by 10-fold. The mutant structures showed movement of the 213-219 loop and the loss of the Thr216-Thr235 hydrogen bond, which was restored by inhibitor binding. Mutagenesis of Thr216 further highlighted its contribution to CTX-M activity. These results demonstrate the importance of the aspartate pair to CTX-M hydrolysis of substrates with bulky side chains, while suggesting increased protein flexibility as a means to evolve drug resistance.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Derek A Nichols
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Insung Na
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
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9
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Omori A, Fujisawa Y, Sasaki S, Shimono K, Kikukawa T, Miyauchi S. Protonation State of a Histidine Residue in Human Oligopeptide Transporter 1 (hPEPT1) Regulates hPEPT1-Mediated Efflux Activity. Biol Pharm Bull 2021; 44:678-685. [PMID: 33952823 DOI: 10.1248/bpb.b20-01013] [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: 11/22/2022]
Abstract
To clarify the role of an amino acid residue in the pH-dependent efflux process in Chinese hamster ovary (CHO) cells expressing the human oligopeptide transporter hPEPT1 (CHO/hPEPT1), we determined the effect of extracellular pH on the hPEPT1-mediated efflux process. The efflux of glycylsarcosine (Gly-Sar), a typical substrate for hPEPT1, was determined using an infinite dilution method after cells were preloaded with [3H]-Gly-Sar. The efflux of [3H]-Gly-Sar was stimulated by 5 mM unlabeled hPEPT1 substrates in the medium. This trans-stimulation phenomenon showed that hPEPT1 mediated the efflux of [3H]-Gly-Sar from CHO/hPEPT1 and that hPEPT1 is a bi-directional transporter. We then determined the effect of extracellular pH (varying from 8.0 to 3.5) on the efflux activity. The efflux activity by hPEPT1 decreased with the decrease in extracellular pH. The Henderson-Hasselbälch-type equation, which fitted well to the pH-profile of efflux activity, indicated that a single amino acid residue with a pKa value of approximately 5.7 regulates the efflux activity. The pH-profile of the efflux activity remained almost unchanged irrespective of the proton gradient across the plasma membrane. In addition, the chemical modification of the histidine residue with diethylpyrocarbonate completely abolished the efflux activity from cells, which could be prevented by the presence of 10 mM Gly-Sar. These data indicate that the efflux process of hPEPT1 is also regulated in a pH-dependent manner by the protonation state of a histidine residue located at or near the substrate recognition site facing the extracellular space.
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Affiliation(s)
- Akiko Omori
- Faculty of Pharmaceutical Sciences, Toho University
| | - Yuki Fujisawa
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University
| | | | | | - Takashi Kikukawa
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University
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10
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Kovach IM. Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System. Life (Basel) 2021; 11:396. [PMID: 33925363 PMCID: PMC8146069 DOI: 10.3390/life11050396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Inquiries into the participation of short hydrogen bonds in stabilizing transition states and intermediate states in the thrombin, factor Xa, plasmin and activated protein C-catalyzed reactions revealed that specific binding of effectors at Sn, n = 1-4 and S'n, n = 1-3 and at remote exosites elicit complex patterns of hydrogen bonding and involve water networks. The methods employed that yielded these discoveries include; (1) kinetics, especially partial or full kinetic deuterium solvent isotope effects with short cognate substrates and also with the natural substrates, (2) kinetic and structural probes, particularly low-field high-resolution nuclear magnetic resonance (1H NMR), of mechanism-based inhibitors and substrate-mimic peptide inhibitors. Short hydrogen bonds form at the transition states of the catalytic reactions at the active site of the enzymes as they do with mechanism-based covalent inhibitors of thrombin. The emergence of short hydrogen bonds at the binding interface of effectors and thrombin at remote exosites has recently gained recognition. Herein, I describe our contribution, a confirmation of this discovery, by low-field 1H NMR. The principal conclusion of this review is that proton sharing at distances below the sum of van der Waals radii of the hydrogen and both donor and acceptor atoms contribute to the remarkable catalytic prowess of serine proteases of the blood clotting system and other enzymes that employ acid-base catalysis. Proton bridges also play a role in tight binding in proteins and at exosites, i.e., allosteric sites, of enzymes.
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Affiliation(s)
- Ildiko M Kovach
- Department of Chemistry, The Catholic University of America, Washington, DC 20064, USA
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11
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Wyshusek M, Reiss GJ, Frank W. The Triple Salt 2(C
7
H
9
N
4
O
2
)[MoOCl
4
(H
2
O)] ⋅ 2(C
7
H
9
N
4
O
2
)Cl ⋅ (H
17
O
8
)Cl Containing a
C
2
‐symmetrical Unbranched H
+
(H
2
O)
8
Zundel
type Species in a Framework Composed of Theophyllinium, Aquatetrachloridooxidomolybdate and Chloride Ions. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202100007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maik Wyshusek
- Institut für Anorganische Chemie und Strukturchemie Heinrich-Heine-Universität Düsseldorf Universitätsstr 1 40225 Düsseldorf Germany
| | - Guido J. Reiss
- Institut für Anorganische Chemie und Strukturchemie Heinrich-Heine-Universität Düsseldorf Universitätsstr 1 40225 Düsseldorf Germany
| | - Walter Frank
- Institut für Anorganische Chemie und Strukturchemie Heinrich-Heine-Universität Düsseldorf Universitätsstr 1 40225 Düsseldorf Germany
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12
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Ozeryanskii VA, Marchenko AV, Pozharskii AF, Filarowski A, Spiridonova DV. Combination of "Buttressing" and "Clothespin" Effects for Reaching the Shortest NHN Hydrogen Bond in Proton Sponge Cations. J Org Chem 2021; 86:3637-3647. [PMID: 33530682 DOI: 10.1021/acs.joc.0c03008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of previously unknown 2,4,5-tri- and 2,4,5,7-tetrasubstituted 1,8-bis(dimethylamino)naphthalenes and their salts with HBF4 containing bulky spherically shaped substituents (Me, Br, and SiMe3) in the naphthalene ring has been synthesized. Using XRD analysis of 11 samples, the influence of the so-called "buttressing" and "clothespin" effects on their molecular structure and the NHN hydrogen bond geometry in the solid cations were investigated. The combined action of both effects has been shown to significantly increase the compression of the hydrogen bond. As a result, the previous record of the hydrogen bond shortness (N···N = 2.524 Å) has been surpassed in favor of 2.502 Å found for the tetrafluoroborate of 2,4,5,7-tetramethyl-1,8-bis(dimethylamino)naphthalene. The molecular structure of the latter differs by perfect symmetry and practically barrier-free proton transfer in the [NHN]+ bond. On the basis of the results of quantum-chemical calculations, it is suggested that the value of 2.502 Å likely represents or lies very close to the theoretical limit for the short hydrogen bonds between the amine-type nitrogen atoms.
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Affiliation(s)
- Valery A Ozeryanskii
- Department of Organic Chemistry, Southern Federal University, Zorge str. 7, 344090 Rostov-on-Don, Russian Federation
| | - Andrey V Marchenko
- Department of Organic Chemistry, Southern Federal University, Zorge str. 7, 344090 Rostov-on-Don, Russian Federation
| | - Alexander F Pozharskii
- Department of Organic Chemistry, Southern Federal University, Zorge str. 7, 344090 Rostov-on-Don, Russian Federation
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Darya V Spiridonova
- Research park of St. Petersburg State University, Universitetskaya Emb. 7/9, 199034 St. Petersburg, Russian Federation
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13
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Hu Q, Jayasinghe-Arachchige VM, Prabhakar R. Degradation of a Main Plastic Pollutant Polyethylene Terephthalate by Two Distinct Proteases (Neprilysin and Cutinase-like Enzyme). J Chem Inf Model 2021; 61:764-776. [PMID: 33534993 DOI: 10.1021/acs.jcim.0c00797] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In this DFT study, hydrolysis of polyethylene terephthalate (PET), a major cause of plastic pollution, by two distinct enzymes, neprilysin (NEP, a mononuclear metalloprotease) and cutinase-like enzyme (CLE, a serine protease), has been investigated. These enzymes utilize different mechanisms for the degradation of PET. NEP uses either the metal-bound hydroxide attack (MH) mechanism or reverse protonation (RP) mechanism, while CLE utilizes a general acid/base mechanism that includes acylation and deacylation processes. Additionally, the RP mechanism of NEP can proceed through three pathways, RP0, RP1, and RP2. The DFT calculations predict that, among all these mechanisms, the MH mechanism is the energetically most favorable one for the NEP enzyme. In comparison, CLE catalyzes this reaction with a significantly higher barrier. These results suggest that the Lewis acid and nucleophile activations provided by the Zn metal center of NEP are more effective than the hydrogen bonding interactions afforded by the catalytic Ser85-His180-Asp165 triad of CLE. They have provided intrinsic details regarding PET degradation and will pave the way for the design of efficient metal-based catalysts for this critical reaction.
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Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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14
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Gut bacteria are essential for normal cuticle development in herbivorous turtle ants. Nat Commun 2021; 12:676. [PMID: 33514729 PMCID: PMC7846594 DOI: 10.1038/s41467-021-21065-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/12/2021] [Indexed: 11/08/2022] Open
Abstract
Across the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to the formation of proteins, catecholamine cross-linkers, and chitin in the cuticle. This study identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution, and provides a framework for understanding the nitrogen flow from nutrients through bacteria into the insect cuticle.
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15
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He J, Zhang L, Liu L. The hydrogen-bond configuration modulates the energy transfer efficiency in helical protein nanotubes. NANOSCALE 2021; 13:991-999. [PMID: 33367447 DOI: 10.1039/d0nr06031c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Energy transport in proteins is critical to a variety of physical, chemical, and biological processes in living organisms. While strenuous efforts have been made to study vibrational energy transport in proteins, thermal transport processes across the most fundamental building blocks of proteins, i.e. helices, are not well understood. This work studies energy transport in a group of "isomer" helices. The π-helix is shown to have the highest thermal conductivity, 110% higher than that of the α-helix and 207% higher than that of the 310-helix. The H-bond connectivity is found to govern thermal transport mechanisms including the phonon spectral energy density, dispersion, mode-specific transport, group velocity, and relaxation time. The energy transport is strongly correlated with the H-bond strength which is also modulated by the H-bond connectivity. These fundamental insights provide a novel perspective for understanding energy transfer in proteins and guiding a rational molecule-level design of novel materials with configurable H-bonds.
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Affiliation(s)
- Jinlong He
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA. and Department of Mechanical and Aerospace Engineering, Utah State University, Logan, Utah 84322, USA
| | - Lin Zhang
- Department of Engineering Mechanics, School of Civil Engineering, Shandong University, Jinan, 250061, P.R. China and Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ling Liu
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA.
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16
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Kaiser SK, Chen Z, Faust Akl D, Mitchell S, Pérez-Ramírez J. Single-Atom Catalysts across the Periodic Table. Chem Rev 2020; 120:11703-11809. [PMID: 33085890 DOI: 10.1021/acs.chemrev.0c00576] [Citation(s) in RCA: 313] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isolated atoms featuring unique reactivity are at the heart of enzymatic and homogeneous catalysts. In contrast, although the concept has long existed, single-atom heterogeneous catalysts (SACs) have only recently gained prominence. Host materials have similar functions to ligands in homogeneous catalysts, determining the stability, local environment, and electronic properties of isolated atoms and thus providing a platform for tailoring heterogeneous catalysts for targeted applications. Within just a decade, we have witnessed many examples of SACs both disrupting diverse fields of heterogeneous catalysis with their distinctive reactivity and substantially enriching our understanding of molecular processes on surfaces. To date, the term SAC mostly refers to late transition metal-based systems, but numerous examples exist in which isolated atoms of other elements play key catalytic roles. This review provides a compositional encyclopedia of SACs, celebrating the 10th anniversary of the introduction of this term. By defining single-atom catalysis in the broadest sense, we explore the full elemental diversity, joining different areas across the whole periodic table, and discussing historical milestones and recent developments. In particular, we examine the coordination structures and associated properties accessed through distinct single-atom-host combinations and relate them to their main applications in thermo-, electro-, and photocatalysis, revealing trends in element-specific evolution, host design, and uses. Finally, we highlight frontiers in the field, including multimetallic SACs, atom proximity control, and possible applications for multistep and cascade reactions, identifying challenges, and propose directions for future development in this flourishing field.
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Affiliation(s)
- Selina K Kaiser
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Zupeng Chen
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Dario Faust Akl
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Sharon Mitchell
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Javier Pérez-Ramírez
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
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17
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Stoffers KM, Cronkright AA, Huggins GS, Baleja JD. Noninvasive Epidermal Metabolite Profiling. Anal Chem 2020; 92:12467-12472. [PMID: 32830947 DOI: 10.1021/acs.analchem.0c02274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A buffer placed in brief contact in the skin was assayed by 1H NMR spectroscopy. We found that this passive extraction of the skin surface yields abundant metabolites. Metabolites of the skin surface originate from a variety of sources, including the sweat gland, which produces lactate from the glucose received from its capillary bed. Little is known about how metabolites resident on and within the skin surface respond to a metabolic or hemodynamic perturbation. As a possible application of epidermal metabolite profiling, we asked whether metabolites extracted from the skin surface are indicative of heart failure. The levels of lactate and other molecules were significantly lower in patients in heart failure than in individuals who reported healthy heart function, possibly due to reduced blood flow to the sweat gland resulting in a lack of tissue perfusion. Most amino acids were unchanged in levels, except for glycine and serine that increased as a percentage of all amino acids. These results have the potential in the long term to help decide the extent to which a patient has heart failure for which objective measures are lacking. Moreover, the results suggest that epidermal metabolite profiling may be useful for other assessments of human health.
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Affiliation(s)
- Katarina M Stoffers
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts 02111, United States
| | - Ashley A Cronkright
- Molecular Cardiology Research Institute Center for Translational Genomics, Tufts Medical Center, 800 Washington Street, Boston, Massachusetts 02111, United States
| | - Gordon S Huggins
- Molecular Cardiology Research Institute Center for Translational Genomics, Tufts Medical Center, 800 Washington Street, Boston, Massachusetts 02111, United States
| | - James D Baleja
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts 02111, United States
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18
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Zhang Y, Liang Q, Zhang C, Zhang J, Du G, Kang Z. Improving production of Streptomyces griseus trypsin for enzymatic processing of insulin precursor. Microb Cell Fact 2020; 19:88. [PMID: 32284060 PMCID: PMC7155311 DOI: 10.1186/s12934-020-01338-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
Background Trypsin has many applications in food and pharmaceutical manufacturing. Although commercial trypsin is usually extracted from porcine pancreas, this source carries the risks of infectivity and immunogenicity. Microbial Streptomyces griseus trypsin (SGT) is a prime alternative because it possesses efficient hydrolysis activity without such risks. However, the remarkable hydrolysis efficiency of SGT causes autolysis, and five autolysis sites, R21, R32, K122, R153, and R201, were identified from its autolysate. Results The tbcf (K101A, R201V) mutant was screened by a directed selection approach for improved activity in flask culture (60.85 ± 3.42 U mL−1, increased 1.5-fold). From the molecular dynamics simulation, in the K101A/R201V mutant the distance between the catalytical residues D102 and H57 was shortened to 6.5 Å vs 7.0 Å in the wild type, which afforded the improved specific activity of 1527.96 ± 62.81 U mg−1. Furthermore, the production of trypsin was increased by 302.8% (689.47 ± 6.78 U mL−1) in a 3-L bioreactor, with co-overexpression of chaperones SSO2 and UBC1 in Pichia pastoris. Conclusions SGT protein could be a good source of trypsin for insulin production. As a result of the hydrolysates analysis and direct selection, the activity of the tbcf (K101A, R201V) mutant increased 1.5-fold. Furthermore, the production of trypsin was improved threefold by overexpressing chaperone protein in Pichia pastoris. Future studies should investigate the application of SGT to insulin and pharmaceutical manufacturing.
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Affiliation(s)
- Yunfeng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Center for Synthetic Biochemistry, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Qixing Liang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Chuanzhi Zhang
- Bio-Pharmaceutical Research Institute Lian Yun Gang Chia Tai Tianqing Pharmaceutical Group Co., Ltd, Lianyungang, Jiangsu, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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19
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Zhou S, Wang L. Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects. Phys Chem Chem Phys 2020; 22:4884-4895. [DOI: 10.1039/c9cp06840f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electronic and nuclear quantum effects determine the symmetry and highly downfield 1H NMR chemical shifts of short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
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20
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Wei W, Chen Y, Xie D, Zhou Y. Molecular insight into chymotrypsin inhibitor 2 resisting proteolytic degradation. Phys Chem Chem Phys 2019; 21:5049-5058. [PMID: 30762035 DOI: 10.1039/c8cp07784c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chymotrypsin inhibitor 2 (CI2) is a special serine protease inhibitor which can resist hydrolysis for several days with a rapid equilibrium between the Michaelis complex and acyl-enzyme intermediate. The energies and conformational changes for subtilisin-catalyzed proteolysis of CI2 were examined in this paper for the first time by employing pseudo bond ab initio QM/MM MD simulations. In the acylation reaction, a low-barrier hydrogen bond between His64 and Asp32 in the transition state together with the lack of covalent backbone constraints makes the peptide bonds of CI2 break more easily than in other serine protease inhibitors. After acyl-enzyme formation, molecular dynamics simulations showed that the access of hydrolytic water to the active site requires partial dissociation of the leaving group. However, retention of the leaving group mainly by the intra- and inter-molecular H-bonding networks hinders the access of water and retards the deacylation reaction. Instead of the dissociation constant of inhibitors, we suggest employing the free energy at the acyl-enzyme state to predict the relative hydrolysis rates of CI2 mutants, which are testified by the experimental relative hydrolysis rates.
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Affiliation(s)
- Wanqing Wei
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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21
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Gaffney KA, Hong H. The rhomboid protease GlpG has weak interaction energies in its active site hydrogen bond network. J Gen Physiol 2018; 151:282-291. [PMID: 30420443 PMCID: PMC6400518 DOI: 10.1085/jgp.201812047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/25/2018] [Indexed: 01/24/2023] Open
Abstract
Rhomboid proteases are membrane-integrated enzymes that hydrolyze peptide bonds in the transmembrane domains of protein substrates. Gaffney and Hong experimentally determine interaction energies between active site residues to reveal weak coupling, which may explain the slow proteolysis mediated by GlpG. Intramembrane rhomboid proteases are of particular interest because of their function to hydrolyze a peptide bond of a substrate buried in the membrane. Crystal structures of the bacterial rhomboid protease GlpG have revealed a catalytic dyad (Ser201-His254) and oxyanion hole (His150/Asn154/the backbone amide of Ser201) surrounded by the protein matrix and contacting a narrow water channel. Although multiple crystal structures have been solved, the catalytic mechanism of GlpG is not completely understood. Because it is a serine protease, hydrogen bonding interactions between the active site residues are thought to play a critical role in the catalytic cycle. Here, we dissect the interaction energies among the active site residues His254, Ser201, and Asn154 of Escherichia coli GlpG, which form a hydrogen bonding network. We combine double mutant cycle analysis with stability measurements using steric trapping. In mild detergent, the active site residues are weakly coupled with interaction energies (ΔΔGInter) of ‒1.4 kcal/mol between His254 and Ser201 and ‒0.2 kcal/mol between Ser201 and Asn154. Further, by analyzing the propagation of single mutations of the active site residues, we find that these residues are important not only for function but also for the folding cooperativity of GlpG. The weak interaction between Ser and His in the catalytic dyad may partly explain the unusually slow proteolysis by GlpG compared with other canonical serine proteases. Our result suggests that the weak hydrogen bonds in the active site are sufficient to carry out the proteolytic function of rhomboid proteases.
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Affiliation(s)
- Kristen A Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Heedeok Hong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI .,Department of Chemistry, Michigan State University, East Lansing, MI
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22
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Agback P, Agback T. Direct evidence of a low barrier hydrogen bond in the catalytic triad of a Serine protease. Sci Rep 2018; 8:10078. [PMID: 29973622 PMCID: PMC6031666 DOI: 10.1038/s41598-018-28441-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/21/2018] [Indexed: 11/28/2022] Open
Abstract
Serine proteases are one of the largest groups of enzymes, found in both eukaryotes and prokaryotes, and are responsible for many different functions. The detailed information about the hydrogen-bonds in the catalytic triad (Asp…His…Ser) of these enzymes is of importance in order to fully understand the mechanism of action. The aspartate of the triad is hydrogen bonded to the histidine but the exact nature of this bond has been under discussion for some time. It is either a common short ionic hydrogen bond (SIHB) or a delocalized low barrier hydrogen bond (LBHB) were the hydrogen bond is shorter. So far, the evidence for LBHB in proteins have not been conclusive. Here we show clear NMR evidence that LBHB does exist in NS3, a serine protease from Dengue. The one bond coupling constant between the hydrogen and nitrogen was shown to be only 52 Hz instead of the usual 90 Hz. This together with a 1H chemical shift of 19.93 ppm is evidence that the hydrogen bond distance between His and Asp is shorter than for SIHB. Our result clearly shows the existence of LBHB and will help in understanding the mechanism of the catalytic triad in the important group of serine proteases.
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden.
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23
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Abstract
Hydrogen bonds play integral roles in biological structure, function, and conformational dynamics and are fundamental to life as it has evolved on Earth. However, our understanding of these fundamental and ubiquitous interactions has seemed fractured and incomplete, and it has been difficult to extract generalities and principles about hydrogen bonds despite thousands of papers published on this topic, perhaps in part because of the expanse of this subject and the density of studies. Fortunately, recent hydrogen bond proposals, discussions, and debates have stimulated new tests and models and have led to a remarkably simple picture of the structure of hydrogen bonds. This knowledge also provides clarity concerning hydrogen bond energetics, limiting and simplifying the factors that need be considered. Herein we recount the advances that have led to this simpler view of hydrogen bond structure, dynamics, and energetics. A quantitative predictive model for hydrogen bond length can now be broadly and deeply applied to evaluate current proposals and to uncover structural features of proteins, their conformational restraints, and their correlated motions. In contrast, a quantitative energetic description of molecular recognition and catalysis by proteins remains an important ongoing challenge, although our improved understanding of hydrogen bonds may aid in testing predictions from current and future models. We close by codifying our current state of understanding into five "Rules for Hydrogen Bonding" that may provide a foundation for understanding and teaching about these vital interactions and for building toward a deeper understanding of hydrogen bond energetics.
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24
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Yan S, Yao L, Kang B, Lee JY. Solvent effect on hydrogen bonded Tyr⋯Asp⋯Arg triads: Enzymatic catalyzed model system. Comput Biol Chem 2016; 65:140-147. [PMID: 27825065 DOI: 10.1016/j.compbiolchem.2016.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/06/2016] [Accepted: 10/29/2016] [Indexed: 10/20/2022]
Abstract
The hydrogen bond plays a vital role in structural arrangement, intermediate state stabilization, materials function, and biological activity of certain enzymatic reactions. The solvent and electronic effects on hydrogen bonds are illustrated employing the polarizable contimuum model at B3LYP/6-311++G(d,p) level. Geometry optimizations reflect the significant solvent and electronic effect. The proton departs spontaneously upon oxidation from the hydroxyl group of tyrosyl in hydrogen bonded Tyr⋯Asp⋯Arg triads in both gas phase and solvents. The electron transfer isomers are observed for anionic triads, no matter what the solvent is. The difference of distance between two hydrogen bonds is enlarged in solvent as compared to that in gas phase. The electronic effect on IR spectra is distinctive. The tyrosyl fragment tends to be oxidized and the arginine moiety is easier to bind an excess electron. The variations of chemical shift and spin-spin coupling constant are more significant upon electron transfer than upon solvent dielectric constant. The augmentation of solvent dielectric constant stabilizes the system, enhances the difference of isomers, and increases the vertical ionization potential and vertical electron affinity values.
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Affiliation(s)
- Shihai Yan
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Lishan Yao
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.
| | - Baotao Kang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China.
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, 440746, Republic of Korea, Republic of Korea.
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25
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Green AP, Hayashi T, Mittl PRE, Hilvert D. A Chemically Programmed Proximal Ligand Enhances the Catalytic Properties of a Heme Enzyme. J Am Chem Soc 2016; 138:11344-52. [DOI: 10.1021/jacs.6b07029] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anthony P. Green
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Takahiro Hayashi
- Laboratory
of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - Peer R. E. Mittl
- Department
of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory
of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland
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26
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Yan S, Kang B, Lee JY, Sun L. Hydration effect on proton transfer in melamine-cyanuric acid complex. J Mol Model 2016; 22:169. [PMID: 27351422 DOI: 10.1007/s00894-016-3038-5] [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: 04/14/2016] [Accepted: 06/09/2016] [Indexed: 11/29/2022]
Abstract
Self-assembly of melamine-cyanuric acid (MC) leads to urinary tract calculi and renal failure. The hydration effects on molecular geometry, the IR spectra, the frontier molecular orbital, the energy barrier of proton transfer (PT), as well as the stability of MC were explored by density functional theory (DFT) calculations. The intramolecular PT breaks the big π-conjugated ring of melamine or converts the p-π conjugation (:N-C'=O) to π-π conjugation (O=C-N=C') of cyanuric acid. The intermolecular PT varies the coupling between melamine and cyanuric acid from pure hydrogen bonds (Na…HNd and NH…O) to the cooperation of cation…anion electrostatic interaction (NaH(+)…Nd (-)) and two NH…O hydrogen bonds. Distinct IR spectra shifts occur for Na…HNd stretching mode upon PT, i.e., blue-shift upon intramolecular PT and red-shift upon intermolecular PT. It is expected that the PT would inhibit the generation of rosette-like structure or one-dimensional tape conformer for the MC complexes. Hydration obviously effects the local geometric structure around the water binding site, as well as the IR spectra of NH…O and N…HN hydrogen bonds. Hydration decreases the intramolecular PT barrier from ~45 kcal mol(-1) in anhydrous complex to ~11.5 kcal mol(-1) in trihydrated clusters. While, the hydration effects on intermolecular PT barrier is slight. The relative stability of MC varies slightly by hydration due to the strong hydrogen bond interaction between melamine and cyanuric acid fragments. Graphical Abstract Hydration effect on proton transfer in melamine-cyanuric acid complex.
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Affiliation(s)
- Shihai Yan
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Baotao Kang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China.
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, 440746, South Korea.
| | - Lixiang Sun
- School of Chemistry and Materials Science, Ludong University, Yantai, 264025, China
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27
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Chu C, Lundeen RA, Sander M, McNeill K. Assessing the Indirect Photochemical Transformation of Dissolved Combined Amino Acids through the Use of Systematically Designed Histidine-Containing Oligopeptides. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12798-12807. [PMID: 26425803 DOI: 10.1021/acs.est.5b03498] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Photooxidation is an important abiotic transformation pathway for amino acids (AAs) in sunlit waters. Although dissolved free AAs are well studied, the photooxidation of dissolved combined AAs (DCAAs) remains poorly investigated. This study is a systematic investigation of the effect of neighboring photostable AA residues (i.e., aliphatic, cationic, anionic, or aromatic residues) on the environmental indirect photochemical transformation of histidine (His) in His-containing oligopeptides. The pKa values of His residues in the studied oligopeptides were found to be between 4.3 and 8.1. Accordingly, the phototransformation rate constants of the His-containing oligopeptides were highly pH-dependent in an environmentally relevant pH range with higher reactivity for neutral His than for the protonated species. The photostable AA residues significantly modulated the photoreactivity of oligopeptides either through altering the accessibility of His to photochemically produced oxidants or through shifting the pKa values of His residues. In addition, the influence of neighboring photostable AA residues on the sorption-enhanced phototransformation of oligopeptides in solutions containing chromophoric dissolved organic matter (CDOM) was assessed. The constituent photostable AA residues promoted sorption of His-containing oligopeptides to CDOM macromolecules through electrostatic attraction, hydrophobic effects, and/or low-barrier hydrogen bonds, and subsequently increased the apparent phototransformation rate constants by up to 2 orders of magnitude.
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Affiliation(s)
- Chiheng Chu
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Rachel A Lundeen
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
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28
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Nichols DA, Hargis JC, Sanishvili R, Jaishankar P, Defrees K, Smith E, Wang KK, Prati F, Renslo AR, Woodcock HL, Chen Y. Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography. J Am Chem Soc 2015; 137:8086-95. [PMID: 26057252 PMCID: PMC4530788 DOI: 10.1021/jacs.5b00749] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligand binding can change the pKa of protein residues and influence enzyme catalysis. Herein, we report three ultrahigh resolution X-ray crystal structures of CTX-M β-lactamase, directly visualizing protonation state changes along the enzymatic pathway: apo protein at 0.79 Å, precovalent complex with nonelectrophilic ligand at 0.89 Å, and acylation transition state (TS) analogue at 0.84 Å. Binding of the noncovalent ligand induces a proton transfer from the catalytic Ser70 to the negatively charged Glu166, and the formation of a low-barrier hydrogen bond (LBHB) between Ser70 and Lys73, with a length of 2.53 Å and the shared hydrogen equidistant from the heteroatoms. QM/MM reaction path calculations determined the proton transfer barrier to be 1.53 kcal/mol. The LBHB is absent in the other two structures although Glu166 remains neutral in the covalent complex. Our data represents the first X-ray crystallographic example of a hydrogen engaged in an enzymatic LBHB, and demonstrates that desolvation of the active site by ligand binding can provide a protein microenvironment conducive to LBHB formation. It also suggests that LBHBs may contribute to stabilization of the TS in general acid/base catalysis together with other preorganized features of enzyme active sites. These structures reconcile previous experimental results suggesting alternatively Glu166 or Lys73 as the general base for acylation, and underline the importance of considering residue protonation state change when modeling protein-ligand interactions. Additionally, the observation of another LBHB (2.47 Å) between two conserved residues, Asp233 and Asp246, suggests that LBHBs may potentially play a special structural role in proteins.
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Affiliation(s)
- Derek A. Nichols
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
| | | | - Ruslan Sanishvili
- GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - Emmanuel Smith
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
| | - Kenneth K. Wang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620
| | - Yu Chen
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
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29
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Jang DS, Choi G, Cha HJ, Shin S, Hong BH, Lee HJ, Lee HC, Choi KY. Contribution of a low-barrier hydrogen bond to catalysis is not significant in ketosteroid isomerase. Mol Cells 2015; 38:409-15. [PMID: 25947291 PMCID: PMC4443282 DOI: 10.14348/molcells.2015.2266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 02/14/2015] [Accepted: 02/16/2015] [Indexed: 11/27/2022] Open
Abstract
Low-barrier hydrogen bonds (LBHBs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. Δ(5)-3-ketosteroid isomerase (KSI) catalyzes the allylic isomerization of Δ(5)-3-ketosteroid to its conjugated Δ(4)-isomers at a rate that approaches the diffusion limit. Tyr14, a catalytic residue of KSI, has been hypothesized to form an LBHB with the oxyanion of a dienolate steroid intermediate generated during the catalysis. The unusual chemical shift of a proton at 16.8 ppm in the nuclear magnetic resonance spectrum has been attributed to an LBHB between Tyr14 Oη and C3-O of equilenin, an intermediate analogue, in the active site of D38N KSI. This shift in the spectrum was not observed in Y30F/Y55F/D38N and Y30F/Y55F/Y115F/D38N mutant KSIs when each mutant was complexed with equilenin, suggesting that Tyr14 could not form LBHB with the intermediate analogue in these mutant KSIs. The crystal structure of Y30F/Y55F/Y115F/D38N-equilenin complex revealed that the distance between Tyr14 Oη and C3-O of the bound steroid was within a direct hydrogen bond. The conversion of LBHB to an ordinary hydrogen bond in the mutant KSI reduced the binding affinity for the steroid inhibitors by a factor of 8.1-11. In addition, the absence of LBHB reduced the catalytic activity by only a factor of 1.7-2. These results suggest that the amount of stabilization energy of the reaction intermediate provided by LBHB is small compared with that provided by an ordinary hydrogen bond in KSI.
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Affiliation(s)
- Do Soo Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Research Institute, Genexine Co., Seongnam 463-400,
Korea
| | - Gildon Choi
- Korea Research Institute of Chemical Technology, Daejeon 305-343,
Korea
| | - Hyung Jin Cha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Sejeong Shin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115,
USA
| | - Bee Hak Hong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Research Institute, Genexine Co., Seongnam 463-400,
Korea
| | - Hyeong Ju Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Hee Cheon Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Kwan Yong Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
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Asztalos P, Müller A, Hölke W, Sobek H, Rudolph MG. Atomic resolution structure of a lysine-specific endoproteinase fromLysobacter enzymogenessuggests a hydroxyl group bound to the oxyanion hole. ACTA ACUST UNITED AC 2014; 70:1832-43. [DOI: 10.1107/s1399004714008463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/14/2014] [Indexed: 11/10/2022]
Abstract
Lysobacter enzymogeneslysyl endoproteinase (LysC) is a trypsin-type serine protease with a high pH optimum that hydrolyses all Lys-Xaa peptide bonds. The high specificity of LysC renders it useful for biotechnological purposes. The K30R variant of a related lysyl endoproteinase fromAchromobacter lyticushas favourable enzymatic properties that might be transferrable to LysC. To visualize structural differences in the substrate-binding sites, the crystal structures of wild-type and the K30R variant of LysC were determined. The mutation is located at a distance of 12 Å from the catalytic triad and subtly changes the surface properties of the substrate-binding site. The high pH optimum of LysC can be attributed to electrostatic effects of an aromatic Tyr/His stack on the catalytic aspartate and is a general feature of this enzyme subfamily. LysC crystals in complex with the covalent inhibitorNα-p-tosyl-lysyl chloromethylketone yielded data to 1.1 and 0.9 Å resolution, resulting in unprecedented precision of the active and substrate-binding sites for this enzyme subfamily. Error estimates on bond lengths and difference electron density indicate that instead of the expected oxyanion a hydroxyl group binds to the partially solvent-exposed oxyanion hole. Protonation of the alkoxide catalytic intermediate might be a recurring feature during serine protease catalysis.
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31
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Shokhen M, Hirsch M, Khazanov N, Ozeri R, Perlman N, Traube T, Vijayakumar S, Albeck A. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases. Isr J Chem 2014. [DOI: 10.1002/ijch.201300144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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32
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Agarwal V, Linser R, Dasari M, Fink U, del Amo JML, Reif B. Hydrogen bonding involving side chain exchangeable groups stabilizes amyloid quarternary structure. Phys Chem Chem Phys 2014; 15:12551-7. [PMID: 23719770 DOI: 10.1039/c3cp44653k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The amyloid β-peptide (Aβ) is the major structural component of amyloid fibrils in the plaques of brains of Alzheimer's disease patients. Numerous studies have addressed important aspects of secondary and tertiary structure of fibrils. In electron microscopic images, fibrils often bundle together. The mechanisms which drive the association of protofilaments into bundles of fibrils are not known. We show here that amino acid side chain exchangeable groups like e.g. histidines can provide useful restraints to determine the quarternary assembly of an amyloid fibril. Exchangeable protons are only observable if a side chain hydrogen bond is formed and the respective protons are protected from exchange. The method relies on deuteration of the Aβ peptide. Exchangeable deuterons are substituted with protons, before fibril formation is initiated.
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Affiliation(s)
- Vipin Agarwal
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin-Buch, Germany
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33
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Zhao Y, Chen N, Wu R, Cao Z. A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase. Phys Chem Chem Phys 2014; 16:18406-17. [DOI: 10.1039/c4cp01609b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM MD and MM MD simulations reveal pH-dependent proton-shuttle ring-opening mechanisms of GlcN6P and dynamical behavior of the lid motif inSmuNagB.
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Affiliation(s)
- Yuan Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005, P. R. China
| | - Nanhao Chen
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, P. R. China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005, P. R. China
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34
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Kovach IM, Kakalis L, Jordan F, Zhang D. Proton bridging in the interactions of thrombin with hirudin and its mimics. Biochemistry 2013; 52:2472-81. [PMID: 23517305 DOI: 10.1021/bi301625a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thrombin is the pivotal serine protease enzyme in the blood cascade system and thus a target of drug design for control of its activity. The most efficient nonphysiologic inhibitor of thrombin is hirudin, a naturally occurring small protein. Hirudin and its synthetic mimics employ a range of hydrogen bonding, salt bridging, and hydrophobic interactions with thrombin to achieve tight binding with K(i) values in the nano- to femtomolar range. The one-dimensional (1)H nuclear magnetic resonance spectrum recorded at 600 MHz reveals a resonance 15.33 ppm downfield from silanes in complexes between human α-thrombin and r-hirudin in pH 5.6-8.8 buffers and between 5 and 35 °C. There is also a resonance between 15.17 and 15.54 ppm seen in complexes of human α-thrombin with hirunorm IV, hirunorm V, an Nα(Me)Arg peptide, RGD-hirudin, and Nα-2-naphthylsulfonyl-glycyl-DL-4-amidinophenylalanyl-piperidide acetate salt (NAPAP), while there is no such low-field resonance observed in a complex of porcine trypsin and NAPAP. The chemical shifts suggest that these resonances represent H-bonded environments. H-Donor-acceptor distances in the corresponding H-bonds are estimated to be <2.7 Å. Addition of Phe-Pro-Arg-chloromethylketone (PPACK) to a complex of human α-thrombin with r-hirudin results in an additional signal at 18.03 ppm, which is 0.10 ppm upfield from the observed signal [Kovach, I. M., et al. (2009) Biochemistry 48, 7296-7304] for thrombin covalently modified with PPACK. In contrast, the peak at 15.33 ppm remains unchanged. The fractionation factors for the thrombin-hirudin complexes are near 1.0 within 20% error. The most likely site of the short H-bond in complexes of thrombin with the hirudin family of inhibitors is in the hydrophobic patch of the C-terminus of hirudin where Glu(57') and Glu(58') are embedded and interact with Arg(75) and Arg(77) and their solvate water (on thrombin). Glu(57') and Glu(58') present in the hirudin family of inhibitors make up a key binding epitope of fibrinogen, thrombin's prime substrate, which lends substantial interest to the short hydrogen bond as a binding element at the fibrinogen recognition site.
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Affiliation(s)
- Ildiko M Kovach
- Department of Chemistry, The Catholic University of America, Washington, DC 20064, USA
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35
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Perumalla SR, Sun CC. Synthon preference in O-protonated amide crystals – dominance of short strong hydrogen bonds. CrystEngComm 2013. [DOI: 10.1039/c3ce41271g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Hossain MA, Kang SO, Kut JA, Day VW, Bowman-James K. Influence of Charge on Anion Receptivity in Amide-Based Macrocycles. Inorg Chem 2012; 51:4833-40. [DOI: 10.1021/ic300260g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Md. Alamgir Hossain
- Department of Chemistry and
Biochemistry, Jackson State University,
1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
| | - Sung Ok Kang
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United
States
| | - Jerry Alan Kut
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United
States
| | - Victor W. Day
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United
States
| | - Kristin Bowman-James
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United
States
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37
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Basu A, Das G. Amidothiourea as a potential receptor for organic bases by resonance assisted low barrier hydrogen bond formation: Structure and Hirshfeld surface analysis. CrystEngComm 2012. [DOI: 10.1039/c2ce06541j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Biliškov N, Kojić-Prodić B, Mali G, Molčanov K, Stare J. A Partial Proton Transfer in Hydrogen Bond O−H···O in Crystals of Anhydrous Potassium and Rubidium Complex Chloranilates. J Phys Chem A 2011; 115:3154-66. [DOI: 10.1021/jp112380f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nikola Biliškov
- Rudjer Bošković Institute, POB 180, HR-10002 Zagreb, Croatia
| | | | - Gregor Mali
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Dunajska c. 156, SI-1000 Ljubljana
| | | | - Jernej Stare
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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39
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Wang W, Gong S, Chen Y, Meng L. The Effects of Intramolecular Hydrogen Bonding on the Reaction of Phenols with Epoxide in the Presence of Nano Calcium Carbonate. Supramol Chem 2011. [DOI: 10.1080/10610270600564793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Wei Wang
- a Wuhan University, Department of Chemistry , Wuhan, P. R, China
| | - Shuling Gong
- a Wuhan University, Department of Chemistry , Wuhan, P. R, China
| | - Yuanyin Chen
- a Wuhan University, Department of Chemistry , Wuhan, P. R, China
| | - Lingzhi Meng
- a Wuhan University, Department of Chemistry , Wuhan, P. R, China
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40
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Liu L, He C, Wang H, Li Z, Chang S, Sun J, Zhang X, Zhang S. Synthesis and characterization of ethylenediaminium nitrophenolate. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.12.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Jezierska-Mazzarello A, Panek JJ, Vuilleumier R, Koll A, Ciccotti G. Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases—A comparative molecular dynamics study. J Chem Phys 2011; 134:034308. [DOI: 10.1063/1.3528721] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Wahlgren WY, Pál G, Kardos J, Porrogi P, Szenthe B, Patthy A, Gráf L, Katona G. The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action. J Biol Chem 2010; 286:3587-96. [PMID: 21097875 PMCID: PMC3030363 DOI: 10.1074/jbc.m110.161604] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The mechanism of serine proteases prominently illustrates how charged amino acid residues and proton transfer events facilitate enzyme catalysis. Here we present an ultrahigh resolution (0.93 Å) x-ray structure of a complex formed between trypsin and a canonical inhibitor acting through a substrate-like mechanism. The electron density indicates the protonation state of all catalytic residues where the catalytic histidine is, as expected, in its neutral state prior to the acylation step by the catalytic serine. The carboxyl group of the catalytic aspartate displays an asymmetric electron density so that the Oδ2–Cγ bond appears to be a double bond, with Oδ2 involved in a hydrogen bond to His-57 and Ser-214. Only when Asp-102 is protonated on Oδ1 atom could a density functional theory simulation reproduce the observed electron density. The presence of a putative hydrogen atom is also confirmed by a residual mFobs − DFcalc density above 2.5 σ next to Oδ1. As a possible functional role for the neutral aspartate in the active site, we propose that in the substrate-bound form, the neutral aspartate residue helps to keep the pKa of the histidine sufficiently low, in the active neutral form. When the histidine receives a proton during the catalytic cycle, the aspartate becomes simultaneously negatively charged, providing additional stabilization for the protonated histidine and indirectly to the tetrahedral intermediate. This novel proposal unifies the seemingly conflicting experimental observations, which were previously seen as either supporting the charge relay mechanism or the neutral pKa histidine theory.
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Affiliation(s)
- Weixiao Yuan Wahlgren
- Department of Chemistry, University of Gothenburg, Medicinaregatan 9C, 40530 Gothenburg, Sweden
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43
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Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, Mayer C. Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism. J Biol Chem 2010; 285:35675-84. [PMID: 20826810 PMCID: PMC2975192 DOI: 10.1074/jbc.m110.131037] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 09/03/2010] [Indexed: 11/06/2022] Open
Abstract
Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain β-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-Å resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His(234) of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp(232) for proper function. Replacement of both His(234) and Asp(232) with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4'-methylumbelliferyl N-acetyl-β-D-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and β-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within β-N-acetylglucosaminidases but otherwise absent in β-glycosidases of family 3, which instead carry a "classical" glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His(234) of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 β-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of β-lactamase.
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Affiliation(s)
| | - Stefanie Fischer
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
| | - Patrick Polzer
- the Max-Planck-Institute of Quantum Optics, 85748 Garching, Germany
| | - Kay Diederichs
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
| | - Wolfram Welte
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
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44
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Characterization of Bafinivirus main protease autoprocessing activities. J Virol 2010; 85:1348-59. [PMID: 21068254 DOI: 10.1128/jvi.01716-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The production of functional nidovirus replication-transcription complexes involves extensive proteolytic processing by virus-encoded proteases. In this study, we characterized the viral main protease (M(pro)) of the type species, White bream virus (WBV), of the newly established genus Bafinivirus (order Nidovirales, family Coronaviridae, subfamily Torovirinae). Comparative sequence analysis and mutagenesis data confirmed that the WBV M(pro) is a picornavirus 3C-like serine protease that uses a Ser-His-Asp catalytic triad embedded in a predicted two-β-barrel fold, which is extended by a third domain at its C terminus. Bacterially expressed WBV M(pro) autocatalytically released itself from flanking sequences and was able to mediate proteolytic processing in trans. Using N-terminal sequencing of autoproteolytic processing products we tentatively identified Gln↓(Ala, Thr) as a substrate consensus sequence. Mutagenesis data provided evidence to suggest that two conserved His and Thr residues are part of the S1 subsite of the enzyme's substrate-binding pocket. Interestingly, we observed two N-proximal and two C-proximal autoprocessing sites in the bacterial expression system. The detection of two major forms of M(pro), resulting from processing at two different N-proximal and one C-proximal site, in WBV-infected epithelioma papulosum cyprini cells confirmed the biological relevance of the biochemical data obtained in heterologous expression systems. To our knowledge, the use of alternative M(pro) autoprocessing sites has not been described previously for other nidovirus M(pro) domains. The data presented in this study lend further support to our previous conclusion that bafiniviruses represent a distinct group of viruses that significantly diverged from other phylogenetic clusters of the order Nidovirales.
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45
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Zhou Y, Wang S, Zhang Y. Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. J Phys Chem B 2010; 114:8817-25. [PMID: 20550161 DOI: 10.1021/jp104258d] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with a B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multistep free-energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack on the carbonyl carbon, with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of the His447 ring needs to be adjusted very slightly, and then, the proton transfers from His447 to the product, and the break of the scissile bond happens spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1-2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms.
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Affiliation(s)
- Yanzi Zhou
- Department of Chemistry, New York University, New York, New York 10003, USA
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46
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Lankau T, Yu CH. A model study of the efficiency of the Asp-His-Ser triad. J Comput Chem 2010; 31:1853-9. [DOI: 10.1002/jcc.21470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Tamada T, Kinoshita T, Kurihara K, Adachi M, Ohhara T, Imai K, Kuroki R, Tada T. Combined high-resolution neutron and X-ray analysis of inhibited elastase confirms the active-site oxyanion hole but rules against a low-barrier hydrogen bond. J Am Chem Soc 2009; 131:11033-40. [PMID: 19603802 DOI: 10.1021/ja9028846] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To help resolve long-standing questions regarding the catalytic activity of the serine proteases, the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron and X-ray crystallography. To mimic the tetrahedral transition intermediate, a peptidic inhibitor was used. A single large crystal was used to collect room-temperature neutron data to 1.65 A resolution and X-ray data to 1.20 A resolution. Another crystal provided a low-temperature X-ray data set to 0.94 A resolution. The neutron data are to higher resolution than previously reported for a serine protease and the X-ray data are comparable with other studies. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 (chymotrypsin numbering) is 2.60 A in length and that the hydrogen-bonding hydrogen is 0.80-0.96 A from the histidine nitrogen. This is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The observed interaction between His57 and Asp102 is essentially a short but conventional hydrogen bond, sometimes described as a short ionic hydrogen bond. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the "oxyanion hole" in stabilizing the tetrahedral intermediate in catalysis.
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Affiliation(s)
- Taro Tamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
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Kovach IM, Kelley P, Eddy C, Jordan F, Baykal A. Proton bridging in the interactions of thrombin with small inhibitors. Biochemistry 2009; 48:7296-304. [PMID: 19530705 PMCID: PMC2800789 DOI: 10.1021/bi900098s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombin is the pivotal serine protease enzyme in the blood cascade system. Phe-Pro-Arg-chloromethylketone (PPACK), phosphate, and phosphonate ester inhibitors form a covalent bond with the active-site Ser of thrombin. PPACK, a mechanism-based inhibitor, and the phosphate/phosphonate esters form adducts that mimic intermediates formed in reactions catalyzed by thrombin. Therefore, the dependence of the inhibition of human alpha-thrombin on the concentration of these inhibitors, pH, and temperature was investigated. The second-order rate constant (ki/Ki) and the inhibition constant (Ki) for inhibition of human alpha-thrombin by PPACK are (1.1 +/- 0.2) x 10(7) M(-1) s(-1) and (2.4 +/- 1.3) x 10(-8) M, respectively, at pH 7.00 in 0.05 M phosphate buffer and 0.15 M NaCl at 25.0 +/- 0.1 degrees C, in good agreement with previous reports. The activation parameters at pH 7.00 in 0.05 M phosphate buffer and 0.15 M NaCl are as follows: DeltaH = 10.6 +/- 0.7 kcal/mol, and DeltaS = 9 +/- 2 cal mol(-1) degrees C(-1). The pH dependence of the second-order rate constants of inhibition is bell-shaped. Values of pKa1 and pKa2 are 7.3 +/- 0.2 and 8.8 +/- 0.3, respectively, at 25.0 +/- 0.1 degrees C. A phosphate and a phosphonate ester inhibitor gave higher values, 7.8 and 8.0 for pKa1 and 9.3 and 8.6 for pKa2, respectively. They inhibit thrombin more than 6 orders of magnitude less efficiently than PPACK does. The deuterium solvent isotope effect for the second-order rate constant at pH 7.0 and 8.3 at 25.0 +/- 0.1 degrees C is unity within experimental error in all three cases, indicating the absence of proton transfer in the rate-determining step for the association of thrombin with the inhibitors, but in a 600 MHz 1H NMR spectrum of the inhibition adduct at pH 6.7 and 30 degrees C, a peak at 18.10 ppm with respect to TSP appears with PPACK, which is absent in the 1H NMR spectrum of a solution of the enzyme between pH 5.3 and 8.5. The peak at low field is an indication of the presence of a short-strong hydrogen bond (SSHB) at the active site in the adduct. The deuterium isotope effect on this hydrogen bridge is 2.2 +/- 0.2 (phi = 0.45). The presence of an SSHB is also established with a signal at 17.34 ppm for a dealkylated phosphate adduct of thrombin.
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Affiliation(s)
- Ildiko M Kovach
- Department of Chemistry, The Catholic University of America, Washington, D.C. 20064, USA.
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Sakae Y, Matsubara T, Aida M, Kondo H, Masaki K, Iefuji H. ONIOM Study of the Mechanism of the Enzymatic Hydrolysis of Biodegradable Plastics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.338] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Abstract
Low-barrier hydrogen bonds (LBHBs) have been proposed to play roles in protein functions, including enzymatic catalysis and proton transfer. Transient formation of LBHBs is expected to stabilize specific reaction intermediates. However, based on experimental results and theoretical considerations, arguments against the importance of LBHB in proteins have been raised. The discrepancy is caused by the absence of direct identification of the hydrogen atom position. Here, we show by high-resolution neutron crystallography of photoactive yellow protein (PYP) that a LBHB exists in a protein, even in the ground state. We identified approximately 87% (819/942) of the hydrogen positions in PYP and demonstrated that the hydrogen bond between the chromophore and E46 is a LBHB. This LBHB stabilizes an isolated electric charge buried in the hydrophobic environment of the protein interior. We propose that in the excited state the fast relaxation of the LBHB into a normal hydrogen bond is the trigger for photo-signal propagation to the protein moiety. These results give insights into the novel roles of LBHBs and the mechanism of the formation of LBHBs.
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