1
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Reetz MT, Garcia-Borràs M. The Unexplored Importance of Fleeting Chiral Intermediates in Enzyme-Catalyzed Reactions. J Am Chem Soc 2021; 143:14939-14950. [PMID: 34491742 PMCID: PMC8461649 DOI: 10.1021/jacs.1c04551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Indexed: 02/07/2023]
Abstract
Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.
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Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Marc Garcia-Borràs
- Institute
of Computational Chemistry and Catalysis (IQCC) and Departament de
Química, Universitat de Girona, Carrer Maria Aurèlia Capmany
69, 17003 Girona, Spain
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2
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Lin CY, Boxer SG. Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems. J Phys Chem B 2020; 124:9513-9525. [DOI: 10.1021/acs.jpcb.0c07730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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3
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Studying hydrogen bonding and dynamics of the acetylate groups of the Special Pair of Rhodobacter sphaeroides WT. Sci Rep 2019; 9:10528. [PMID: 31324886 PMCID: PMC6642110 DOI: 10.1038/s41598-019-46903-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/08/2019] [Indexed: 11/17/2022] Open
Abstract
Although the cofactors in the bacterial reaction centre of Rhodobacter sphaeroides wild type (WT) are arranged almost symmetrically in two branches, the light-induced electron transfer occurs selectively in one branch. As origin of this functional symmetry break, a hydrogen bond between the acetyl group of PL in the primary donor and His-L168 has been discussed. In this study, we investigate the existence and rigidity of this hydrogen bond with solid-state photo-CIDNP MAS NMR methods offering information on the local electronic structure due to highly sensitive and selective NMR experiments. On the time scale of the experiment, the hydrogen bond between PL and His-L168 appears to be stable and not to be affected by illumination confirming a structural asymmetry within the Special Pair.
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4
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Belyanko TI, Gursky YG, Dobrynina NI, Orlova AV, Rutkevich NM, Savochkina LP, Skamrov AV, Skrypina NA, Bibilashvilli RS. A Study of the Structure of Trypsin-Like Serine Proteinases: 1. Study of Mini-Plasminogen Activation Using Tryptophan Fluorescence. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918050032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Khirich G, Loria JP. Complexity of protein energy landscapes studied by solution NMR relaxation dispersion experiments. J Phys Chem B 2015; 119:3743-54. [PMID: 25680027 DOI: 10.1021/acs.jpcb.5b00212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The millisecond time scale motions in ribonuclease A (RNase A) were studied by solution NMR CPMG and off-resonance R1ρ relaxation dispersion experiments over a wide pH and temperature range. These experiments identify three separate protein regions termed Cluster 1, Cluster 2, and R33, whose motions are governed by distinct thermodynamic parameters. Moreover, each of these regions has motions with different pH dependencies. Cluster 1 shows an increase in activation enthalpy and activation entropy as the pH is lowered, whereas Cluster 2 exhibits the opposite behavior. In contrast, the activation enthalpy and entropy of R33 show no pH dependence. Compounding the differences, Δω values for Cluster 2 are characteristic of two-site conformational exchange, yet similar analysis for Cluster 1 indicates that this region of the enzyme exhibits conformational fluctuations between a major conformer and a pH-dependent average of protonated and deprotonated minor conformers.
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Affiliation(s)
- Gennady Khirich
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06520, United States
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6
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Barman A, Hamelberg D. Cysteine-mediated dynamic hydrogen-bonding network in the active site of Pin1. Biochemistry 2014; 53:3839-50. [PMID: 24840168 DOI: 10.1021/bi5000977] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Enzymes catalyze a plethora of chemical reactions that are tightly regulated and intricately coupled in biology. Catalysis of phosphorylation-dependent cis-trans isomerization of peptidyl-prolyl bonds, which act as conformational switches in regulating many post-phosphorylation processes, is considered to be one of the most critical. Pin1 is a cis-trans isomerase of peptidyl-prolyl(ω-) bonds of phosphorylated-Ser/Thr-Pro motifs and has been implicated in many diseases. Structural and experimental studies are still unable to resolve the mechanistic role and protonation states of two adjacent histidines (His59 and His157) and a cysteine (Cys113) in the active site of Pin1. Here, we show that the protonation state of Cys113 mediates a dynamic hydrogen-bonding network in the active site of Pin1, involving the two adjacent histidines and several other residues that are highly conserved and necessary for catalysis. We have used detailed free energy calculations and molecular dynamics simulations, complementing previous experiments, to resolve the ambiguities in the orientations of the histidines and protonation states of these key active site residues, details that are critical for fully understanding the mechanism of Pin1 and necessary for developing potent inhibitors. Importantly, Cys113 is shown to alternate between the unprotonated and neutral states, unprotonated in free Pin1 and neutral in substrate-bound Pin1. Our results are consistent with experiments and provide an explanation for the chemical reactivity of free Pin1 that is suggested to be necessary for the regulation of the enzyme.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University , Atlanta, Georgia 30302-4098, United States
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7
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Hansen AL, Kay LE. Measurement of histidine pKa values and tautomer populations in invisible protein states. Proc Natl Acad Sci U S A 2014; 111:E1705-12. [PMID: 24733918 PMCID: PMC4035968 DOI: 10.1073/pnas.1400577111] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The histidine imidazole side chain plays a critical role in protein function and stability. Its importance for catalysis is underscored by the fact that histidines are localized to active sites in ∼ 50% of all enzymes. NMR spectroscopy has become an important tool for studies of histidine side chains through the measurement of site-specific pK(a)s and tautomer populations. To date, such studies have been confined to observable protein ground states; however, a complete understanding of the role of histidine electrostatics in protein function and stability requires that similar investigations be extended to rare, transiently formed conformers that populate the energy landscape, yet are often "invisible" in standard NMR spectra. Here we present NMR experiments and a simple strategy for studies of such conformationally excited states based on measurement of histidine (13)Cγ, (13)Cδ2 chemical shifts and (1)Hε-(13)Cε one-bond scalar couplings. The methodology is first validated and then used to obtain pKa values and tautomer distributions for histidine residues of an invisible on-pathway folding intermediate of the colicin E7 immunity protein. Our results imply that the side chains of H40 and H47 are exposed in the intermediate state and undergo significant conformational rearrangements during folding to the native structure. Further, the pKa values explain the pH-dependent stability differences between native and intermediate states over the pH range 5.5-6.5 and they suggest that imidazole deprotonation is not a barrier to the folding of this protein.
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Affiliation(s)
- Alexandar L. Hansen
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
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8
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Blankenship E, Vukoti K, Miyagi M, Lodowski DT. Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:833-40. [PMID: 24598752 PMCID: PMC3949523 DOI: 10.1107/s1399004713033658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/12/2013] [Indexed: 05/20/2024]
Abstract
With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.
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Affiliation(s)
- Elise Blankenship
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Krishna Vukoti
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Opthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T. Lodowski
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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9
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Yuwen T, Skrynnikov NR. CP-HISQC: a better version of HSQC experiment for intrinsically disordered proteins under physiological conditions. JOURNAL OF BIOMOLECULAR NMR 2014; 58:175-92. [PMID: 24496557 DOI: 10.1007/s10858-014-9815-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/24/2014] [Indexed: 05/25/2023]
Abstract
(1)H-(15)N HSQC spectroscopy is a workhorse of protein NMR. However, under physiological conditions the quality of HSQC spectra tends to deteriorate due to fast solvent exchange. For globular proteins only a limited number of surface residues are affected, but in the case of intrinsically disordered proteins (IDPs) HSQC spectra are thoroughly degraded, suffering from both peak broadening and loss of intensity. To alleviate this problem, we make use of the following two concepts. (1) Proton-decoupled HSQC. Regular HSQC and its many variants record the evolution of multi-spin modes, 2NxHz or 2NxHx, in indirect dimension. Under the effect of fast solvent exchange these modes undergo rapid decay, which results in severe line-broadening. In contrast, proton-decoupled HSQC relies on Nx coherence which is essentially insensitive to the effects of solvent exchange. Moreover, for measurements involving IDPs at or near physiological temperature, Nx mode offers excellent relaxation properties, leading to very sharp resonances. (2) Cross-polarization (1)H-to-(15)N transfer. If CP element is designed such as to lock both (1)H(N) and water magnetization, the following transfer is effected: [Formula: see text] Thus water magnetization is successfully exploited to boost the amount of signal. In addition, CP element suffers less loss from solvent exchange, conformational exchange, and dipolar relaxation compared to the more popular INEPT element. Combining these two concepts, we have implemented the experiment termed CP-HISQC (cross-polarization assisted heteronuclear in-phase single-quantum correlation). The pulse sequence has been designed such as to preserve water magnetization and therefore can be executed with reasonably short recycling delays. In the presence of fast solvent exchange, kex ~ 100 s(-1), CP-HISQC offers much better spectral resolution than conventional HSQC-type experiments. At the same time it offers up to twofold gain in sensitivity compared to plain proton-decoupled HSQC. The new sequence has been tested on the sample of drkN SH3 domain at pH 7.5, 30 °C. High-quality spectrum has been recorded in less than 1 h, containing resonances from both folded and unfolded species. High-quality spectra have also been obtained for arginine side-chain H(ε)N(ε) groups in the sample of short peptide Sos. For Arg side chains, we have additionally implemented (HE)NE(CD)HD experiment. Using (13)C-labeled sample of Sos, we have demonstrated that proton-to-nitrogen CP transfer remains highly efficient in the presence of solvent exchange as fast as kex = 620 s(-1). In contrast, INEPT transfer completely fails in this regime.
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Affiliation(s)
- Tairan Yuwen
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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10
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Leclaire J, Mazari M, Zhang Y, Bonduelle C, Thillaye du Boullay O, Martin-Vaca B, Bourissou D, De Riggi I, Fortrie R, Fotiadu F, Buono G. Bare Histidine-Serine Models: Implication and Impact of Hydrogen Bonding on Nucleophilicity. Chemistry 2013; 19:11301-9. [DOI: 10.1002/chem.201301275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Indexed: 11/11/2022]
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11
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Smoum R, Rubinstein A, Dembitsky VM, Srebnik M. Boron containing compounds as protease inhibitors. Chem Rev 2012; 112:4156-220. [PMID: 22519511 DOI: 10.1021/cr608202m] [Citation(s) in RCA: 298] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Reem Smoum
- The School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel.
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12
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Everill P, Sudmeier JL, Bachovchin WW. Direct NMR Observation and pKa Determination of the Asp102 Side Chain in a Serine Protease. J Am Chem Soc 2012; 134:2348-54. [PMID: 22229736 DOI: 10.1021/ja210091q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Everill
- Department of Biochemistry,
Sackler School of Graduate
Biomedical Sciences, Tufts University,
136 Harrison Avenue, Boston, Massachusetts 02111, United States
| | - James L. Sudmeier
- Department of Biochemistry,
Sackler School of Graduate
Biomedical Sciences, Tufts University,
136 Harrison Avenue, Boston, Massachusetts 02111, United States
| | - William W. Bachovchin
- Department of Biochemistry,
Sackler School of Graduate
Biomedical Sciences, Tufts University,
136 Harrison Avenue, Boston, Massachusetts 02111, United States
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13
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Li S, Hong M. Protonation, tautomerization, and rotameric structure of histidine: a comprehensive study by magic-angle-spinning solid-state NMR. J Am Chem Soc 2011; 133:1534-44. [PMID: 21207964 DOI: 10.1021/ja108943n] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Histidine structure and chemistry lie at the heart of many enzyme active sites, ion channels, and metalloproteins. While solid-state NMR spectroscopy has been used to study histidine chemical shifts, the full pH dependence of the complete panel of (15)N, (13)C, and (1)H chemical shifts and the sensitivity of these chemical shifts to tautomeric structure have not been reported. Here we use magic-angle-spinning solid-state NMR spectroscopy to determine the (15)N, (13)C, and (1)H chemical shifts of histidine from pH 4.5 to 11. Two-dimensional homonuclear and heteronuclear correlation spectra indicate that these chemical shifts depend sensitively on the protonation state and tautomeric structure. The chemical shifts of the rare π tautomer were observed for the first time, at the most basic pH used. Intra- and intermolecular hydrogen bonding between the imidazole nitrogens and the histidine backbone or water was detected, and N-H bond length measurements indicated the strength of the hydrogen bond. We also demonstrate the accurate measurement of the histidine side-chain torsion angles χ(1) and χ(2) through backbone-side chain (13)C-(15)N distances; the resulting torsion angles were within 4° of the crystal structure values. These results provide a comprehensive set of benchmark values for NMR parameters of histidine over a wide pH range and should facilitate the study of functionally important histidines in proteins.
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Affiliation(s)
- Shenhui Li
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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14
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Zhou Y, Zhang Y. Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate. Chem Commun (Camb) 2010; 47:1577-9. [PMID: 21116528 DOI: 10.1039/c0cc04112b] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The acylation mechanism of a prototypical serine protease trypsin and its complete free energy reaction profile have been determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling.
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Affiliation(s)
- Yanzi Zhou
- Department of Chemistry, New York University, New York, NY 10003, USA
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15
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Khan MN. Can a Typical Protein Assist the Rate of its Own Aqueous Cleavage? PROGRESS IN REACTION KINETICS AND MECHANISM 2010. [DOI: 10.3184/146867810x12700573609126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A recent finding of a large rate enhancement in the intramolecular secondary amide group-assisted cleavage of an adjacent tertiary amide bond predicts the possibility of the cleavage of the peptide bond of a protein through a similar reaction mechanism. Based upon enzymatic partial model reactions, the usual proton-switch mechanism has been suggested for the acylation step of the chymotrypsin–catalysed cleavage of the peptide bond which does not favour a His57-shift mechanism - an essential component of the classical charge relay mechanism. Also, the proton-switch mechanism does not necessarily require the two proton-transfer of the classical charge relay mechanism. The unique structural feature of the imidazole moiety of His57 is concluded to be essential in decreasing the rate of collapse of the proposed reactive tetrahedral intermediate back to the reactants. The proposed intramolecular intimate ion-pair formation between anionic Asp102 and cationic His57 is attributed to the energetically preferred location of the proton at Nδ1 of the imidazole moiety of His57. Thus, the analysis described in this review does not favour the necessary requirements of a two proton-transfer and His57-shift as proposed in the classical charge relay mechanism as well as the relatively recently proposed His57-flip mechanism.
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Affiliation(s)
- Mohammad Niyaz Khan
- Department of Chemistry, University of Malaya, Faculty of Science, 50603 Kuala Lumpur, Malaysia
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16
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Agarwal V, Linser R, Fink U, Faelber K, Reif B. Identification of Hydroxyl Protons, Determination of Their Exchange Dynamics, and Characterization of Hydrogen Bonding in a Microcrystallin Protein. J Am Chem Soc 2010; 132:3187-95. [DOI: 10.1021/ja910167q] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vipin Agarwal
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany, and Charité Universitätsmedizin, D-10115 Berlin, Germany
| | - Rasmus Linser
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany, and Charité Universitätsmedizin, D-10115 Berlin, Germany
| | - Uwe Fink
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany, and Charité Universitätsmedizin, D-10115 Berlin, Germany
| | - Katja Faelber
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany, and Charité Universitätsmedizin, D-10115 Berlin, Germany
| | - Bernd Reif
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany, and Charité Universitätsmedizin, D-10115 Berlin, Germany
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17
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Structure of West Nile Virus NS3 Protease: Ligand Stabilization of the Catalytic Conformation. J Mol Biol 2009; 385:1568-77. [DOI: 10.1016/j.jmb.2008.11.026] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Revised: 11/14/2008] [Accepted: 11/18/2008] [Indexed: 11/20/2022]
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18
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Hass MAS, Hansen DF, Christensen HEM, Led JJ, Kay LE. Characterization of Conformational Exchange of a Histidine Side Chain: Protonation, Rotamerization, and Tautomerization of His61 in Plastocyanin from Anabaena variabilis. J Am Chem Soc 2008; 130:8460-70. [DOI: 10.1021/ja801330h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mathias A. S. Hass
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - D. Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Hans E. M. Christensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Jens J. Led
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lewis E. Kay
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
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19
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Affiliation(s)
- David D Boehr
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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20
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Fuhrmann CN, Daugherty MD, Agard DA. Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis. J Am Chem Soc 2007; 128:9086-102. [PMID: 16834383 DOI: 10.1021/ja057721o] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To address questions regarding the mechanism of serine protease catalysis, we have solved two X-ray crystal structures of alpha-lytic protease (alphaLP) that mimic aspects of the transition states: alphaLP at pH 5 (0.82 A resolution) and alphaLP bound to the peptidyl boronic acid inhibitor, MeOSuc-Ala-Ala-Pro-boroVal (0.90 A resolution). Based on these structures, there is no evidence of, or requirement for, histidine-flipping during the acylation step of the reaction. Rather, our data suggests that upon protonation of His57, Ser195 undergoes a conformational change that destabilizes the His57-Ser195 hydrogen bond, preventing the back-reaction. In both structures the His57-Asp102 hydrogen bond in the catalytic triad is a normal ionic hydrogen bond, and not a low-barrier hydrogen bond (LBHB) as previously hypothesized. We propose that the enzyme has evolved a network of relatively short hydrogen bonds that collectively stabilize the transition states. In particular, a short ionic hydrogen bond (SIHB) between His57 Nepsilon2 and the substrate's leaving group may promote forward progression of the TI1-to-acylenzyme reaction. We provide experimental evidence that refutes use of either a short donor-acceptor distance or a downfield 1H chemical shift as sole indicators of a LBHB.
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Affiliation(s)
- Cynthia N Fuhrmann
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94143-2240, USA
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21
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Wu WJ, Tyukhtenko SI, Huang TH. Direct NMR resonance assignments of the active site histidine residue in Escherichia coli thioesterase I/protease I/lysophospholipase L1. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:1037-40. [PMID: 16972310 DOI: 10.1002/mrc.1901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Owing to the hydrogen-bond interaction and rapid exchange rate with the bulk water, the transverse relaxation time for the N(delta1)-H proton of the catalytic histidine in Escherichia coli thioesterase I/protease I/lysophospholipase L1 (TEP-I) is rather short. Because of its catalytic importance, it is desirable to detect and assign this proton resonance. In this paper, we report the first direct NMR correlation between the short-lived N(delta1)-H proton and its covalently attached N(delta1)-nitrogen of the catalytic His157 residue in E. coli thioesterase/protease I. We have used gradient-enhanced jump-return spin-echo HMQC (GE-JR SE HMQC) to obtain a direct correlation between the short-lived N(delta1)-H proton and its covalently attached N(delta1)-nitrogen. The sensitivity of detection for the short-lived N(delta1)-H proton was enhanced substantially by improved water suppression, in particular, the suppression of radiation damping via pulsed field gradients.
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Affiliation(s)
- Wen-Jin Wu
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan 11529, Republic of China.
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Garoutte MP, Bibbs JA, Schowen RL. Solvent Isotope Effects and the Question of Quantum Tunneling in Hydrolytic Enzyme Action. J NUCL SCI TECHNOL 2006. [DOI: 10.1080/18811248.2006.9711123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mason A, Agrawal N, Washington MT, Lesley SA, Kohen A. A lag-phase in the reduction of flavin dependent thymidylate synthase (FDTS) revealed a mechanistic missing link. Chem Commun (Camb) 2006:1781-3. [PMID: 16609803 DOI: 10.1039/b517881a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An unexpected substrate-dependent lag-phase, found in the single turnover reduction of FDTS bound flavin, sheds light on the molecular mechanism of this alternative thymidylate synthase.
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Affiliation(s)
- Aaron Mason
- Department of Chemistry, University of Iowa, Iowa City, IA, USA.
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