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Guclu TF, Tayhan B, Cetin E, Atilgan AR, Atilgan C. High throughput mutational scanning of a protein via alchemistry on a high-performance computing resource. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.20.608765. [PMID: 39229108 PMCID: PMC11370492 DOI: 10.1101/2024.08.20.608765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Antibiotic resistance presents a significant challenge to public health, as bacteria can develop resistance to antibiotics through random mutations during their life cycles, making the drugs ineffective. Understanding how these mutations contribute to drug resistance at the molecular level is crucial for designing new treatment approaches. Recent advancements in molecular biology tools have made it possible to conduct comprehensive analyses of protein mutations. Computational methods for assessing molecular fitness, such as binding energies, are not as precise as experimental techniques like deep mutational scanning. Although full atomistic alchemical free energy calculations offer the necessary precision, they are seldom used to assess high throughput data as they require significantly more computational resources. We generated a computational library using deep mutational scanning for dihydrofolate reductase (DHFR), a protein commonly studied in antibiotic resistance research. Due to resource limitations, we analyzed 33 out of 159 positions, identifying 16 single amino acid replacements. Calculations were conducted for DHFR in its drug-free state and in the presence of two different inhibitors. We demonstrate the feasibility of such calculations, made possible due to the enhancements in computational resources and their optimized use.
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Affiliation(s)
- Tandac F Guclu
- Faculty of Natural Sciences and Engineering, Sabanci University, Tuzla, 34956, Istanbul, Turkey
| | - Busra Tayhan
- Faculty of Natural Sciences and Engineering, Sabanci University, Tuzla, 34956, Istanbul, Turkey
| | - Ebru Cetin
- Faculty of Natural Sciences and Engineering, Sabanci University, Tuzla, 34956, Istanbul, Turkey
| | - Ali Rana Atilgan
- Faculty of Natural Sciences and Engineering, Sabanci University, Tuzla, 34956, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Natural Sciences and Engineering, Sabanci University, Tuzla, 34956, Istanbul, Turkey
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2
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Babu CS, Chen JY, Lim C. Solution Ionic Strength Can Modulate Functional Loop Conformations in E. coli Dihydrofolate Reductase. J Phys Chem B 2024; 128:4111-4122. [PMID: 38651832 PMCID: PMC11075089 DOI: 10.1021/acs.jpcb.4c00677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
The observation of multiple conformations of a functional loop (termed M20) in the Escherichia coli dihydrofolate reductase (ecDHFR) enzyme triggered the proposition that large-scale motions of protein structural elements contribute to enzyme catalysis. The transition of the M20 loop from a closed conformation to an occluded conformation was thought to aid the rate-limiting release of the products. However, the influence of charged species in the solution environment on the observed M20 loop conformations, independent of charged ligands bound to the enzyme, had not been considered. Molecular dynamics simulations of ecDHFR in model CaCl2 solutions of varying molar ionic strengths IM reveal a substantial free energy barrier between occluded and closed M20 loop states at IM exceeding the E. coli threshold (∼0.24 M). This barrier may facilitate crystallization of ecDHFR in the occluded state, consistent with ecDHFR structures obtained at IM exceeding 0.3 M. At lower IM (≤0.15 M), the M20 loop can explore the occluded state, but prefers an open/partially closed conformation, again consistent with ecDHFR structures. Our findings caution against using ecDHFR structures obtained at nonphysiological ionic strengths in interpreting catalytic events or in structure-based drug design.
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Affiliation(s)
- C. Satheesan Babu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Jih-Ying Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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3
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Valiauga B, Bagdžiūnas G, Sharrock AV, Ackerley DF, Čėnas N. The Catalysis Mechanism of E. coli Nitroreductase A, a Candidate for Gene-Directed Prodrug Therapy: Potentiometric and Substrate Specificity Studies. Int J Mol Sci 2024; 25:4413. [PMID: 38673999 PMCID: PMC11049802 DOI: 10.3390/ijms25084413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
E. coli nitroreductase A (NfsA) is a candidate for gene-directed prodrug cancer therapy using bioreductively activated nitroaromatic compounds (ArNO2). In this work, we determined the standard redox potential of FMN of NfsA to be -215 ± 5 mV at pH 7.0. FMN semiquinone was not formed during 5-deazaflavin-sensitized NfsA photoreduction. This determines the two-electron character of the reduction of ArNO2 and quinones (Q). In parallel, we characterized the oxidant specificity of NfsA with an emphasis on its structure. Except for negative outliers nitracrine and SN-36506, the reactivity of ArNO2 increases with their electron affinity (single-electron reduction potential, E17) and is unaffected by their lipophilicity and Van der Waals volume up to 386 Å. The reactivity of quinoidal oxidants is not clearly dependent on E17, but 2-hydroxy-1,4-naphthoquinones were identified as positive outliers and a number of compounds with diverse structures as negative outliers. 2-Hydroxy-1,4-naphthoquinones are characterized by the most positive reaction activation entropy and the negative outlier tetramethyl-1,4-benzoquinone by the most negative. Computer modelling data showed that the formation of H bonds with Arg15, Arg133, and Ser40, plays a major role in the binding of oxidants to reduced NfsA, while the role of the π-π interaction of their aromatic structures is less significant. Typically, the calculated hydride-transfer distances during ArNO2 reduction are smallwer than for Q. This explains the lower reactivity of quinones. Another factor that slows down the reduction is the presence of positively charged aliphatic substituents.
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Affiliation(s)
- Benjaminas Valiauga
- Institute of Biochemistry of Life Sciences Center of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (B.V.); (G.B.)
| | - Gintautas Bagdžiūnas
- Institute of Biochemistry of Life Sciences Center of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (B.V.); (G.B.)
| | - Abigail V. Sharrock
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington 6140, New Zealand; (A.V.S.); (D.F.A.)
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington 6140, New Zealand; (A.V.S.); (D.F.A.)
| | - Narimantas Čėnas
- Institute of Biochemistry of Life Sciences Center of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (B.V.); (G.B.)
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4
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Chang X, Zhang T, Zang J, Lv C, Zhao G. Characterization and Structural Analyses of Enolase from Shrimp ( Litopenaeus vannamei). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19783-19790. [PMID: 38033172 DOI: 10.1021/acs.jafc.3c07135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Transcriptome analysis had recognized enolase from shrimp Litopenaeus vannamei (L. vannamei), which is termed LvEnolase, as one of the allergens, but its amino acid sequence and protein structure have been lacking. In this study, natural LvEnolase was isolated from L. vannamei and characterized for the first time. The full-length cDNA sequence of LvEnolase was effectively cloned, which encoded 434 amino acid residues. The crystal structure of LvEnolase was successfully determined at a resolution of 2.5 Å by X-ray crystallography (PDB: 8UEL). Notably, it was observed that near the active center, a loop exists in either an open or closed state, and the open loop was associated with the product release phase. Furthermore, enzyme activity assays were conducted to validate the catalytic capabilities of purified LvEnolase. These findings significantly enhance our comprehension of the enolase family and provide valuable support for delving into the functions and characteristics of LvEnolase.
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Affiliation(s)
- Xiaoxi Chang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
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5
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Bai M, Pratap R, Salarvand S, Lu Y. Correlation of temperature dependence of hydride kinetic isotope effects with donor-acceptor distances in two solvents of different polarities. Org Biomol Chem 2023; 21:5090-5097. [PMID: 37278324 PMCID: PMC10339711 DOI: 10.1039/d3ob00718a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recently observed nearly temperature (T)-independent kinetic isotope effects (KIEs) in wild-type enzymes and T-dependent KIEs in variants were used to suggest that H-tunneling in enzymes is assisted by the fast protein vibrations that help sample short donor-acceptor distances (DADs). This supports the recently proposed role of protein vibrations in DAD sampling catalysis. However, use of T-dependence of KIEs to suggest DAD sampling associated with protein vibrations is debated. We have formulated a hypothesis regarding the correlation and designed experiments in solution to investigate it. The hypothesis is, a more rigid system with shorter DADTRS's at the tunneling ready states (TRSs) gives rise to a weaker T-dependence of KIEs, i.e., a smaller ΔEa (= EaD - EaH). In a former work, the solvent effects of acetonitrile versus chloroform on the ΔEa of NADH/NAD+ model reactions were determined, and the DADPRC's of the productive reactant complexes (PRCs) were computed to substitute the DADTRS for the DADTRS-ΔEa correlation study. A smaller ΔEa was found in the more polar acetonitrile where the positively charged PRC is better solvated and has a shorter DADPRC, indirectly supporting the hypothesis. In this work, the TRS structures of different DADTRS's for the hydride tunneling reaction from 1,3-dimethyl-2-phenylimidazoline to 10-methylacridinium were computed. The N-CH3/CD3 secondary KIEs on both reactants were calculated and fitted to the observed values to find the DADTRS order in both solutions. It was found that the equilibrium DADTRS is shorter in acetonitrile than in chloroform. Results directly support the DADTRS-ΔEa correlation hypothesis as well as the explanation that links T-dependence of KIEs to DAD sampling catalysis in enzymes.
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Affiliation(s)
- Mingxuan Bai
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Rijal Pratap
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Sanaz Salarvand
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Yun Lu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
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6
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Deng J, Cui Q. Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA. J Am Chem Soc 2023; 145:11333-11347. [PMID: 37172218 PMCID: PMC10810092 DOI: 10.1021/jacs.3c02423] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Residues beyond the first coordination shell are often observed to make considerable cumulative contributions in enzymes. Due to typically indirect perturbations of multiple physicochemical properties of the active site, however, their individual and specific roles in enzyme catalysis and disease-causing mutations remain difficult to predict and understand at the molecular level. Here we analyze the contributions of several second-shell residues in phosphate-irrepressible alkaline phosphatase of flavobacterium (PafA), a representative system as one of the most efficient enzymes. By adopting a multifaceted approach that integrates quantum-mechanical/molecular-mechanical free energy computations, molecular-mechanical molecular dynamics simulations, and density functional theory cluster model calculations, we probe the rate-limiting phosphoryl transfer step and structural properties of all relevant enzyme states. In combination with available experimental data, our computational results show that mutations of the studied second-shell residues impact catalytic efficiency mainly by perturbation of the apo state and therefore substrate binding, while they do not affect the ground state or alter the nature of phosphoryl transfer transition state significantly. Several second-shell mutations also modulate the active site hydration level, which in turn influences the energetics of phosphoryl transfer. These mechanistic insights also help inform strategies that may improve the efficiency of enzyme design and engineering by going beyond the current focus on the first coordination shell.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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7
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Giese TJ, York DM. Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations. J Chem Phys 2023; 158:174105. [PMID: 37125722 PMCID: PMC10154067 DOI: 10.1063/5.0147218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/17/2023] [Indexed: 05/02/2023] Open
Abstract
We use the modified Bigeleisen-Mayer equation to compute kinetic isotope effect values for non-enzymatic phosphoryl transfer reactions from classical and path integral molecular dynamics umbrella sampling. The modified form of the Bigeleisen-Mayer equation consists of a ratio of imaginary mode vibrational frequencies and a contribution arising from the isotopic substitution's effect on the activation free energy, which can be computed from path integral simulation. In the present study, we describe a practical method for estimating the frequency ratio correction directly from umbrella sampling in a manner that does not require normal mode analysis of many geometry optimized structures. Instead, the method relates the frequency ratio to the change in the mass weighted coordinate representation of the minimum free energy path at the transition state induced by isotopic substitution. The method is applied to the calculation of 16/18O and 32/34S primary kinetic isotope effect values for six non-enzymatic phosphoryl transfer reactions. We demonstrate that the results are consistent with the analysis of geometry optimized transition state ensembles using the traditional Bigeleisen-Mayer equation. The method thus presents a new practical tool to enable facile calculation of kinetic isotope effect values for complex chemical reactions in the condensed phase.
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Affiliation(s)
- Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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8
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Adhikari P, Song M, Bai M, Rijal P, DeGroot N, Lu Y. Solvent Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects: Correlation to the Donor-Acceptor Distances. J Phys Chem A 2022; 126:7675-7686. [PMID: 36228057 DOI: 10.1021/acs.jpca.2c06065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein structural effects on the temperature (T) dependence of kinetic isotope effects (KIEs) in H-tunneling reactions have recently been used to discuss about the role of enzyme thermal motions in catalysis. Frequently observed nearly T-independent KIEs in the wild-type enzymes and T-dependent KIEs in variants suggest that H-tunneling in the former is assisted by the naturally evolved protein constructive vibrations that help sample short donor-acceptor distances (DADs) needed. This explanation that correlates the T-dependence of KIEs with DAD sampling has been highly debated as simulations following other H-tunneling models sometimes gave alternative explanations. In this paper, solvent effects on the T-dependence of KIEs of two hydride tunneling reactions of NADH/NAD+ analogues (represented by ΔEa = EaD - EaH) were determined in attempts to replicate the observations in enzymes and test the protein vibration-assisted DAD sampling concept. Effects of selected aprotic solvents on the DADPRC's of the productive reactant complexes (PRCs) and the DADTRS's of the activated tunneling ready states (TRSs) were obtained through computations and analyses of the kinetic data, including 2° KIEs, respectively. A weaker T-dependence of KIEs (i.e., smaller ΔEa) was found in a more polar aprotic solvent in which the system has a shorter average DADPRC and DADTRS. Further results show that a charge-transfer (CT) complexation made of a stronger donor/acceptor gives rise to a smaller ΔEa. Overall, the shorter and less broadly distributed DADs resulting from the stronger CT complexation vibrations give rise to a smaller ΔEa. Our results appear to support the explanation that links the T-dependence of KIEs to the donor-acceptor rigidity in enzymes.
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Affiliation(s)
- Pratichhya Adhikari
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Meimei Song
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Mingxuan Bai
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratap Rijal
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nicholas DeGroot
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
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9
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Mazmanian K, Chen T, Sargsyan K, Lim C. From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1607. [PMID: 35600063 PMCID: PMC9111396 DOI: 10.1002/wcms.1607] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 12/20/2022]
Abstract
The COVID-19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS-CoV-2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/continuum calculations led to a novel multi-targeting strategy against SARS-CoV-2, in contrast to developing potent drugs/vaccines against a single viral target such as the spike protein. Specifically, they led to the discovery of reactive cysteines in evolutionary conserved Zn2+-sites in several SARS-CoV-2 proteins that are crucial for viral polypeptide proteolysis as well as viral RNA synthesis, proofreading, and modification. These conserved, reactive cysteines, both free and Zn2+-bound, can be targeted using the same Zn-ejector drug (disulfiram/ebselen), which enables the use of broad-spectrum anti-virals that would otherwise be removed by the virus's proofreading mechanism. Our strategy of targeting multiple, conserved viral proteins that operate at different stages of the virus life cycle using a Zn-ejector drug combined with other broad-spectrum anti-viral drug(s) could enhance the barrier to drug resistance and antiviral effects, as compared to each drug alone. Since these functionally important nonstructural proteins containing reactive cysteines are highly conserved among coronaviruses, our proposed strategy has the potential to tackle future coronaviruses. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and CatalysisStructure and Mechanism > Computational Biochemistry and BiophysicsElectronic Structure Theory > Density Functional Theory.
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Affiliation(s)
| | - Ting Chen
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
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10
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Deuterium Isotope Effects on Acid-Base Equilibrium of Organic Compounds. Molecules 2021; 26:molecules26247687. [PMID: 34946769 PMCID: PMC8705040 DOI: 10.3390/molecules26247687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
Deuterium isotope effects on acid-base equilibrium have been investigated using a combined path integral and free-energy perturbation simulation method. To understand the origin of the linear free-energy relationship of ΔpKa=pKaD2O-pKaH2O versus pKaH2O, we examined two theoretical models for computing the deuterium isotope effects. In Model 1, only the intrinsic isotope exchange effect of the acid itself in water was included by replacing the titratable protons with deuterons. Here, the dominant contribution is due to the difference in zero-point energy between the two isotopologues. In Model 2, the medium isotope effects are considered, in which the free energy change as a result of replacing H2O by D2O in solute-solvent hydrogen-bonding complexes is determined. Although the average ΔpKa change from Model 1 was found to be in reasonable agreement with the experimental average result, the pKaH2O dependence of the solvent isotope effects is absent. A linear free-energy relationship is obtained by including the medium effect in Model 2, and the main factor is due to solvent isotope effects in the anion-water complexes. The present study highlights the significant roles of both the intrinsic isotope exchange effect and the medium solvent isotope effect.
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11
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Bai M, Koirala S, Lu Y. Direct Correlation between Donor-Acceptor Distance and Temperature Dependence of Kinetic Isotope Effects in Hydride-Tunneling Reactions of NADH/NAD + Analogues. J Org Chem 2021; 86:7500-7507. [PMID: 34037396 DOI: 10.1021/acs.joc.1c00497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent study of structural effects on primary kinetic isotope effects (1° KIEs) of H-transfer reactions in enzymes and solution revealed that a more rigid reaction system gave rise to a weaker temperature dependence of 1° KIEs, i.e., a smaller isotopic activation energy difference (ΔEa = EaD - EaH). This has been explained within the contemporary vibrationally assisted activated H-tunneling (VA-AHT) model in which rigidity is defined according to the density of donor-acceptor distance (DADTRS) populations at the tunneling ready state (TRS) sampled by heavy atom motions. To test the relationship between DADTRS and ΔEa in the model, we developed a computational method to obtain the TRS structures for H-transfer reactions. The method was applied to three hydride transfer reactions of NADH/NAD+ analogues for which the ΔEa's as well as secondary (2°) KIEs have been reported. The 2° KIEs computed from each TRS structure were fitted to the observed values to obtain the optimal TRSs/DADTRS's. It was found that a shorter DADTRS does correspond with a smaller ΔEa. This appears to support the VA-AHT model. Moreover, an analysis of hybridizations at the bent TRS structures shows that rehybridizations at the donor-acceptor centers are much more advanced than predicted from the classical mechanism. This implies that more orbital preparations are required for the nonclassical H-tunneling to take place.
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Affiliation(s)
- Mingxuan Bai
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Shailendra Koirala
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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12
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Singh P, Vandemeulebroucke A, Li J, Schulenburg C, Fortunato G, Kohen A, Hilvert D, Cheatum CM. Evolution of the Chemical Step in Enzyme Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | | | - Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Cindy Schulenburg
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Gabriel Fortunato
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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13
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Babu CS, Lim C. Influence of solution ionic strength on the stabilities of M20 loop conformations in apo E. coli dihydrofolate reductase. J Chem Phys 2021; 154:195103. [PMID: 34240890 DOI: 10.1063/5.0048968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interactions among ions and their specific interactions with macromolecular solutes are known to play a central role in biomolecular stability. However, similar effects in the conformational stability of protein loops that play functional roles, such as binding ligands, proteins, and DNA/RNA molecules, remain relatively unexplored. A well-characterized enzyme that has such a functional loop is Escherichia coli dihydrofolate reductase (ecDHFR), whose so-called M20 loop has been observed in three ordered conformations in crystal structures. To explore how solution ionic strengths may affect the M20 loop conformation, we proposed a reaction coordinate that could quantitatively describe the loop conformation and used it to classify the loop conformations in representative ecDHFR x-ray structures crystallized in varying ionic strengths. The Protein Data Bank survey indicates that at ionic strengths (I) below the intracellular ion concentration-derived ionic strength in E. coli (I ≤ 0.237M), the ecDHFR M20 loop tends to adopt open/closed conformations, and rarely an occluded loop state, but when I is >0.237M, the loop tends to adopt closed/occluded conformations. Distance-dependent electrostatic potentials around the most mobile M20 loop region from molecular dynamics simulations of ecDHFR in equilibrated CaCl2 solutions of varying ionic strengths show that high ionic strengths (I = 0.75/1.5M) can preferentially stabilize the loop in closed/occluded conformations. These results nicely correlate with conformations derived from ecDHFR structures crystallized in varying ionic strengths. Altogether, our results suggest caution in linking M20 loop conformations derived from crystal structures solved at ionic strengths beyond that tolerated by E. coli to the ecDHFR function.
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Affiliation(s)
- C Satheesan Babu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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14
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Lu S, Chen Y, Wei J, Zhao M, Ni D, He X, Zhang J. Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators. Acta Pharm Sin B 2021; 11:1355-1361. [PMID: 34094839 PMCID: PMC8148055 DOI: 10.1016/j.apsb.2020.09.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022] Open
Abstract
The recent discovery of activator compounds binding to an allosteric site on the NAD+-dependent protein lysine deacetylase, sirtuin 6 (SIRT6) has attracted interest and presents a pharmaceutical target for aging-related and cancer diseases. However, the mechanism underlying allosteric activation of SIRT6 by the activator MDL-801 remains largely elusive because no major conformational changes are observed upon activator binding. By combining molecular dynamics simulations with biochemical and kinetic analyses of wild-type SIRT6 and its variant M136A, we show that conformational rotation of 2-methyl-4-fluoro-5-bromo substituent on the right phenyl ring (R-ring) of MDL-801, which uncovers previously unseen hydrophobic interactions, contributes to increased activating deacetylation activity of SIRT6. This hypothesis is further supported by the two newly synthesized MDL-801 derivatives through the removal of the 5-Br atom on the R-ring (MDL-801-D1) or the restraint of the rotation of the R-ring (MDL-801-D2). We further propose that the 5-Br atom serves as an allosteric driver that controls the ligand allosteric efficacy. Our study highlights the effect of allosteric enzyme catalytic activity by activator binding and provides a rational approach for enhancing deacetylation activity.
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Key Words
- ADPR, ADP-ribose
- Allosteric driver
- Allosteric mechanisms
- Allosteric sites
- Drug design
- EC50, Effective concentration
- Enzyme catalysis
- FDL, Fluor de Lys
- H3K56, histone 3 lysine 56
- H3K9, histone 3 lysine 9
- HPLC, high-performance liquid chromatography
- MD, molecular dynamics
- MST, microscale thermophoresis
- Myr-H3K9, myristoyl H3K9
- NAM, nicotinamide
- PCA, principal component analysis
- Protein dynamics
- RMSD, root-mean-square deviation
- SIRT6, sirtuin 6
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15
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Goldstein M, Goodey NM. Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2253:185-219. [PMID: 33315225 DOI: 10.1007/978-1-0716-1154-8_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein motions play a fundamental role in enzyme catalysis and ligand binding. The relationship between protein motion and function has been extensively investigated in the model enzyme dihydrofolate reductase (DHFR). DHFR is an essential enzyme that catalyzes the reduction of dihydrofolate to tetrahydrofolate. Numerous experimental and computational methods have been used to probe the motions of DHFR through the catalytic cycle and to investigate the effect of distal mutations on DHFR motions and ligand binding. These experimental investigations have pushed forward the study of protein motions and their role in protein-ligand interactions. The introduction of mutations distal to the active site has been shown to have profound effects on ligand binding, hydride transfer rates and catalytic efficacy and these changes are captured by enzyme kinetics measurements. Distal mutations have been shown to exert their effects through a network of correlated amino acids and these effects have been investigated by NMR, protein dynamics, and analysis of coupled amino acids. The experimental methods and the findings that are reviewed here have broad implications for our understanding of enzyme mechanisms, ligand binding and for the future design and discovery of enzyme inhibitors.
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Affiliation(s)
- Melanie Goldstein
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA
| | - Nina M Goodey
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA.
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16
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Maness P, Koirala S, Adhikari P, Salimraftar N, Lu Y. Substituent Effects on Temperature Dependence of Kinetic Isotope Effects in Hydride-Transfer Reactions of NADH/NAD + Analogues in Solution: Reaction Center Rigidity Is the Key. Org Lett 2020; 22:5963-5967. [PMID: 32662653 DOI: 10.1021/acs.orglett.0c02049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Substituent effects on the temperature dependence of primary kinetic isotope effects, characterized by ΔEa = EaD - EaH, for two series of the title reactions in acetonitrile were studied. The change from ΔEa ≈ 0 for a highly rigid system to ΔEa > 0 for systems with reduced rigidities was observed. The rigidities were controlled by the electronic and steric effects. This work replicates the observations in enzymes and opens a new research direction that studies structure-ΔEa relationship.
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Affiliation(s)
- Peter Maness
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Shailendra Koirala
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratichhya Adhikari
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nasim Salimraftar
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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17
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Babu CS, Lim C. Sensitivity of Functional Loop Conformations on Long-Range Electrostatics: Implications for M20 Loop Dynamics in E. coli Dihydrofolate Reductase. J Chem Theory Comput 2020; 16:2028-2033. [PMID: 32192329 DOI: 10.1021/acs.jctc.9b01285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In E. coli dihydrofolate reductase, unusual conformational motions of a functional M20 loop that interacts with substrate and coenzyme have been construed as evidence for dynamical effects in enzyme catalysis. By computing this loop's conformational free energies in the apoenzyme, we show that it is sensitive to the treatment of long-range electrostatic interactions and the solvation box size in modeling/simulations. These results provide important guidelines for computing reaction/binding free energy profiles of proteins with functional loops.
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Affiliation(s)
- C Satheesan Babu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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18
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Ortega M, Vilhena JG, Zotti LA, Díez-Pérez I, Cuevas JC, Pérez R. Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations. Biomolecules 2019; 9:biom9100611. [PMID: 31618974 PMCID: PMC6843909 DOI: 10.3390/biom9100611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022] Open
Abstract
In the growing field of biomolecular electronics, blue-copper Azurin stands out as one of the most widely studied protein in single-molecule contacts. Interestingly, despite the paramount importance of the structure/dynamics of molecular contacts in their transport properties, these factors remain largely unexplored from the theoretical point of view in the context of single Azurin junctions. Here we address this issue using all-atom Molecular Dynamics (MD) of Pseudomonas Aeruginosa Azurin adsorbed to a Au(111) substrate. In particular, we focus on the structure and dynamics of the free/adsorbed protein and how these properties are altered upon single-point mutations. The results revealed that wild-type Azurin adsorbs on Au(111) along two well defined configurations: one tethered via cysteine groups and the other via the hydrophobic pocket surrounding the Cu 2 + . Surprisingly, our simulations revealed that single amino-acid mutations gave rise to a quenching of protein vibrations ultimately resulting in its overall stiffening. Given the role of amino-acid vibrations and reorientation in the dehydration process at the protein-water-substrate interface, we suggest that this might have an effect on the adsorption process of the mutant, giving rise to new adsorption configurations.
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Affiliation(s)
- Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
| | - Linda A Zotti
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Ismael Díez-Pérez
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
| | - Juan Carlos Cuevas
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
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19
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Li P, Hammes-Schiffer S. Substrate-to-Product Conversion Facilitates Active Site Loop Opening in Yeast Enolase: A Molecular Dynamics Study. ACS Catal 2019; 9:8985-8990. [PMID: 31853382 DOI: 10.1021/acscatal.9b03249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Yeast enolase serves as a prototype for metalloenzymes with labile, catalytic active site metal ions and is important for glycolysis and fermentation processes. Herein, microsecond molecular dynamics simulations of the protein-substrate and protein-product complexes are conducted to elucidate the mechanism of the opening of catalytically important active site loops. These simulations indicate that conversion of substrate to product is accompanied by diminished metal coordination and hydrogen-bonding interactions, as well as enhanced loop flexibility. Moreover, free energy simulations show that the loop opening is endergonic when substrate is bound but exergonic when product is bound. Thus, the conversion to product weakens the association of the loop with the ligand and binding site, thereby facilitating the loop opening after catalysis and enabling product release. These insights about active site loop motions in enzyme catalysis may be useful in guiding enzyme design efforts.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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20
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Nforneh B, Warncke K. Control of Solvent Dynamics around the B 12-Dependent Ethanolamine Ammonia-Lyase Enzyme in Frozen Aqueous Solution by Using Dimethyl Sulfoxide Modulation of Mesodomain Volume. J Phys Chem B 2019; 123:5395-5404. [PMID: 31244099 DOI: 10.1021/acs.jpcb.9b02239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The temperature-dependent structure and dynamics of two concentric solvent phases, the protein-associated domain (PAD) and the mesodomain, that surround the ethanolamine ammonia-lyase (EAL) protein from Salmonella typhimurium in frozen polycrystalline aqueous solution are addressed by using electron paramagnetic resonance spectroscopy of the paramagnetic nitroxide spin probe, TEMPOL, over the temperature ( T) range 190-265 K. Dimethyl sulfoxide (DMSO), added at 0.5, 2.0, and 4.0% v/v and present at the maximum freeze concentration at T ≤ 245 K, varies the volume of the interstitial aqueous DMSO mesodomain ( Vmeso) relative to a fixed PAD volume ( VPAD). The increase in Vmeso/ VPAD from 0.8 to 6.0 is quantified by the partitioning of TEMPOL between the two phases. As Vmeso/ VPAD is increased, the Arrhenius parameters for activated TEMPOL rotational motion in the mesodomain remain uniform, whereas the parameters for TEMPOL in the PAD show a progressive transformation toward the mesodomain values (higher mobility). An order-disorder transition (ODT) in the PAD is detected by the exclusion of TEMPOL from the PAD into the mesodomain. The ODT T value is systematically lowered by increased Vmeso/ VPAD (from 215 to 200 K), and PAD ordering kinks the mesodomain Arrhenius dependence. Thus there is reciprocity in PAD-mesodomain solvent coupling. The results are interpreted as a dominant influence of ice-boundary confinement on the PAD solvent structure and dynamics, which is transmitted through the mesodomain and which decreases with mesodomain volume at increased added DMSO. The systematic tuning of PAD and mesodomain solvent dynamics by the variation of added DMSO is an incisive approach for the resolution of contributions of protein-solvent dynamical coupling to EAL catalysis.
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Affiliation(s)
- Benjamen Nforneh
- Department of Physics , Emory University , Atlanta , Georgia 30322 , United States
| | - Kurt Warncke
- Department of Physics , Emory University , Atlanta , Georgia 30322 , United States
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21
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Matyushov DV, Newton MD. Thermodynamics of Reactions Affected by Medium Reorganization. J Phys Chem B 2018; 122:12302-12311. [PMID: 30514079 DOI: 10.1021/acs.jpcb.8b08865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a thermodynamic analysis of the activation barrier for reactions which can be monitored through the difference in the energies of reactants and products defined as the reaction coordinate (electron and atom transfer, enzyme catalysis, etc.). The free-energy surfaces along the reaction coordinate are separated into the enthalpy and entropy surfaces. For the Gaussian statistics of the reaction coordinate, the free-energy surfaces are parabolas, and the entropy surface is an inverted parabola. Its maximum coincides with the transition state for reactions with zero value of the reaction free energy. Maximum entropic depression of the activation barrier, anticipated by the concept of transition-state ensembles, can be achieved for such reactions. From Onsager's reversibility, the entropy of equilibrium fluctuations encodes the entropic component of the activation barrier. The reorganization entropy thus becomes the critical parameter of the theory reducing the problem of activation entropy to the problem of reorganization entropy. Standard solvation theories do not allow reorganization entropy sufficient for the barrier depression. Complex media, characterized by many relaxation processes, need to be involved. Proteins provide several routes for achieving large entropic effects through incomplete (nonergodic) sampling of the complex energy landscape and by facilitating an active role of water in the reaction mechanism.
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Affiliation(s)
- Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences , Arizona State University , PO Box 871504, Tempe , Arizona 85287 , United States
| | - Marshall D Newton
- Brookhaven National Laboratory , Chemistry Department , Box 5000, Upton , New York 11973-5000 , United States
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22
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Mhashal AR, Pshetitsky Y, Cheatum CM, Kohen A, Major DT. Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase. J Am Chem Soc 2018; 140:16650-16660. [DOI: 10.1021/jacs.8b09089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yaron Pshetitsky
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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23
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Dashnyam P, Mudududdla R, Hsieh TJ, Lin TC, Lin HY, Chen PY, Hsu CY, Lin CH. β-Glucuronidases of opportunistic bacteria are the major contributors to xenobiotic-induced toxicity in the gut. Sci Rep 2018; 8:16372. [PMID: 30401818 PMCID: PMC6219552 DOI: 10.1038/s41598-018-34678-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/23/2018] [Indexed: 02/07/2023] Open
Abstract
Gut bacterial β-D-glucuronidases (GUSs) catalyze the removal of glucuronic acid from liver-produced β-D-glucuronides. These reactions can have deleterious consequences when they reverse xenobiotic metabolism. The human gut contains hundreds of GUSs of variable sequences and structures. To understand how any particular bacterial GUS(s) contributes to global GUS activity and affects human health, the individual substrate preference(s) must be known. Herein, we report that representative GUSs vary in their ability to produce various xenobiotics from their respective glucuronides. To attempt to explain the distinct substrate preference, we solved the structure of a bacterial GUS complexed with coumarin-3-β-D-glucuronide. Comparisons of this structure with other GUS structures identified differences in loop 3 (or the α2-helix loop) and loop 5 at the aglycone-binding site, where differences in their conformations, hydrophobicities and flexibilities appear to underlie the distinct substrate preference(s) of the GUSs. Additional sequence, structural and functional analysis indicated that several groups of functionally related gut bacterial GUSs exist. Our results pinpoint opportunistic gut bacterial GUSs as those that cause xenobiotic-induced toxicity. We propose a structure-activity relationship that should allow both the prediction of the functional roles of GUSs and the design of selective inhibitors.
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Affiliation(s)
- Punsaldulam Dashnyam
- 0000 0000 9360 4962grid.469086.5Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, 11529 Taiwan ,0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan ,0000 0004 0532 3749grid.260542.7Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 40227 Taiwan
| | - Ramesh Mudududdla
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Tung-Ju Hsieh
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Ting-Chien Lin
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Hsien-Ya Lin
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Peng-Yuan Chen
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Chia-Yi Hsu
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Chun-Hung Lin
- 0000 0000 9360 4962grid.469086.5Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, 11529 Taiwan ,0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan ,0000 0004 0532 3749grid.260542.7Biotechnology Center, National Chung-Hsing University, Taichung, 40227 Taiwan ,0000 0004 0546 0241grid.19188.39Department of Chemistry and Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617 Taiwan
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24
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Liu M, Youmans KN, Gao J. Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution. Molecules 2018; 23:E2644. [PMID: 30326599 PMCID: PMC6222756 DOI: 10.3390/molecules23102644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 11/17/2022] Open
Abstract
A dual QM and MM approach for computing equilibrium isotope effects has been described. In the first partition, the potential energy surface is represented by a combined quantum mechanical and molecular mechanical (QM/MM) method, in which a solute molecule is treated quantum mechanically, and the remaining solvent molecules are approximated classically by molecular mechanics. In the second QM/MM partition, differential nuclear quantum effects responsible for the isotope effect are determined by a statistical mechanical double-averaging formalism, in which the nuclear centroid distribution is sampled classically by Newtonian molecular dynamics and the quantum mechanical spread of quantized particles about the centroid positions is treated using the path integral (PI) method. These partitions allow the potential energy surface to be properly represented such that the solute part is free of nuclear quantum effects for nuclear quantum mechanical simulations, and the double-averaging approach has the advantage of sampling efficiency for solvent configuration and for path integral convergence. Importantly, computational precision is achieved through free energy perturbation (FEP) theory to alchemically mutate one isotope into another. The PI-FEP approach is applied to model systems for the 18O enrichment found in cellulose of trees to determine the isotope enrichment factor of carbonyl compounds in water. The present method may be useful as a general tool for studying isotope fractionation in biological and geochemical systems.
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Affiliation(s)
- Meiyi Liu
- Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun 130023, China.
| | - Katelyn N Youmans
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jiali Gao
- Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun 130023, China.
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
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25
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Nagae T, Yamada H, Watanabe N. High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP . Acta Crystallogr D Struct Biol 2018; 74:895-905. [PMID: 30198899 PMCID: PMC6130465 DOI: 10.1107/s2059798318009397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022] Open
Abstract
A high-pressure crystallographic study was conducted on Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ in crystal forms containing both the open and closed conformations of the M20 loop under high-pressure conditions of up to 800 MPa. At pressures between 270 and 500 MPa the crystal form containing the open conformation exhibited a phase transition from P21 to C2. Several structural changes in ecDHFR were observed at high pressure that were also accompanied by structural changes in the NADP+ cofactor and the hydration structure. In the crystal form with the closed conformation the M20 loop moved as the pressure changed, with accompanying conformational changes around the active site, including NADP+ and folate. These movements were consistent with the suggested hypothesis that movement of the M20 loop was necessary for ecDHFR to catalyze the reaction. In the crystal form with the open conformation the nicotinamide ring of the NADP+ cofactor undergoes a large flip as an intermediate step in the reaction, despite being in a crystalline state. Furthermore, observation of the water molecules between Arg57 and folate elucidated an early step in the substrate-binding pathway. These results demonstrate the possibility of using high-pressure protein crystallography as a method to capture high-energy substates or transient structures related to the protein reaction cycle.
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Affiliation(s)
- Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Hiroyuki Yamada
- Venture Business Laboratory, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Nobuhisa Watanabe
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
- Venture Business Laboratory, Nagoya University, Chikusa, Nagoya 464-8603, Japan
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
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26
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Mhashal AR, Pshetitsky Y, Eitan R, Cheatum CM, Kohen A, Major DT. Effect of Asp122 Mutation on the Hydride Transfer in E. coli DHFR Demonstrates the Goldilocks of Enzyme Flexibility. J Phys Chem B 2018; 122:8006-8017. [PMID: 30040418 DOI: 10.1021/acs.jpcb.8b05556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF) in the presence of NADPH. The key hydride transfer step in the reaction is facilitated by a combination of enzyme active site preorganization and correlated protein motions in the Michaelis-Menten (E:NADPH:DHF) complex. The present theoretical study employs mutagenesis to examine the relation between structural and functional properties of the enzyme. We mutate Asp122 in Escherichia coli DHFR, which is a conserved amino acid in the DHFR family. The consequent effect of the mutation on enzyme catalysis is examined from an energetic, structural and short-time dynamic perspective. Our investigations suggest that the structural and short-time dynamic perturbations caused by Asp122X mutations (X = Asn, Ser, Ala) are along the reaction coordinate and lower the rate of hydride transfer. Importantly, analysis of the correlated and principle component motions in the enzyme suggest that the mutation alters the coupled motions that are present in the wild-type enzyme. In the case of D122N and D122S, the mutations inhibit coupled motion, whereas in the case of D122A, the mutation enhances coupled motion, although all mutations result in similar rate reduction. These results emphasize a Goldilocks principle of enzyme flexibility, that is, enzymes should neither be too rigid nor too flexible.
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Affiliation(s)
- Anil R Mhashal
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Yaron Pshetitsky
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Reuven Eitan
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Christopher M Cheatum
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Amnon Kohen
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
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27
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Shanmuganatham KK, Wallace RS, Ting-I Lee A, Plapp BV. Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Protein Sci 2018; 27:750-768. [PMID: 29271062 DOI: 10.1002/pro.3370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 01/06/2023]
Abstract
The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD+ and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.
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Affiliation(s)
- Karthik K Shanmuganatham
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Diagnostic Virology Laboratory, USDA, Ames, IA, 50010
| | - Rachel S Wallace
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Ann Ting-I Lee
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,No 92, Jing Mao 1st Rd., Taichung, Taiwan, 406, Republic of China
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109
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28
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Ranasinghe C, Guo Q, Sapienza PJ, Lee AL, Quinn DM, Cheatum CM, Kohen A. Protein Mass Effects on Formate Dehydrogenase. J Am Chem Soc 2017; 139:17405-17413. [PMID: 29083897 PMCID: PMC5800309 DOI: 10.1021/jacs.7b08359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isotopically labeled enzymes (denoted as "heavy" or "Born-Oppenheimer" enzymes) have been used to test the role of protein dynamics in catalysis. The original idea was that the protein's higher mass would reduce the frequency of its normal-modes without altering its electrostatics. Heavy enzymes have been used to test if the vibrations in the native enzyme are coupled to the chemistry it catalyzes, and different studies have resulted in ambiguous findings. Here the temperature-dependence of intrinsic kinetic isotope effects of the enzyme formate dehydrogenase is used to examine the distribution of H-donor to H-acceptor distance as a function of the protein's mass. The protein dynamics are altered in the heavy enzyme to diminish motions that determine the transition state sampling in the native enzyme, in accordance with a Born-Oppenheimer-like effect on bond activation. Findings of this work suggest components related to fast frequencies that can be explained by Born-Oppenheimer enzyme hypothesis (vibrational) and also slower time scale events that are non-Born-Oppenheimer in nature (electrostatic), based on evaluations of protein mass dependence of donor-acceptor distance and forward commitment to catalysis along with steady state and single turnover measurements. Together, the findings suggest that the mass modulation affected both local, fast, protein vibrations associated with the catalyzed chemistry and the protein's macromolecular electrostatics at slower time scales; that is, both Born-Oppenheimer and non-Born-Oppenheimer effects are observed. Comparison to previous studies leads to the conclusion that isotopic labeling of the protein may have different effects on different systems, however, making heavy enzyme studies a very exciting technique for exploring the dynamics link to catalysis in proteins.
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Affiliation(s)
- Chethya Ranasinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Qi Guo
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel M. Quinn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
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29
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Ojeda-May P, Nam K. Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations. J Chem Theory Comput 2017. [PMID: 28628742 DOI: 10.1021/acs.jctc.7b00322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in CHARMM are described. The serial version of the code was first profiled to identify routines that required parallelization. Afterward, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM message passage interface (MPI) machinery. In the second approach, two different self-consistent field (SCF) energy convergence accelerators were implemented using density and Fock matrices as targets for their extrapolations in the SCF procedure. In the third approach, the entire QM/MM and MM energy routines were accelerated by implementing the hybrid MPI/open multiprocessing (OpenMP) model in which both the task- and loop-level parallelization strategies were adopted to balance loads between different OpenMP threads. The present implementation was tested on two solvated enzyme systems (including <100 QM atoms) and an SN2 symmetric reaction in water. The MPI version exceeded existing SE QM methods in CHARMM, which include the SCC-DFTB and SQUANTUM methods, by at least 4-fold. The use of SCF convergence accelerators further accelerated the code by ∼12-35% depending on the size of the QM region and the number of CPU cores used. Although the MPI version displayed good scalability, the performance was diminished for large numbers of MPI processes due to the overhead associated with MPI communications between nodes. This issue was partially overcome by the hybrid MPI/OpenMP approach which displayed a better scalability for a larger number of CPU cores (up to 64 CPUs in the tested systems).
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Affiliation(s)
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington , Arlington, Texas 76019-0065, United States
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30
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Kohne M, Zhu C, Warncke K. Two Dynamical Regimes of the Substrate Radical Rearrangement Reaction in B 12-Dependent Ethanolamine Ammonia-Lyase Resolve Contributions of Native Protein Configurations and Collective Configurational Fluctuations to Catalysis. Biochemistry 2017; 56:3257-3264. [PMID: 28548844 DOI: 10.1021/acs.biochem.7b00294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The kinetics of the substrate radical rearrangement reaction step in B12-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium are measured over a 92 K temperature range. The observed first-order rate constants display a piecewise-continuous Arrhenius dependence, with linear regions over 295 → 220 K (monoexponential) and 214 → 203 K (biexponential) that are delineated by a kinetic bifurcation and kinks at 219 and 217 K, respectively. The results are interpreted by using a free energy landscape model and derived microscopic kinetic mechanism. The bifurcation and kink transitions correspond to the effective quenching of two distinct sets of native collective protein configurational fluctuations that (1) reconfigure the protein within the substrate radical free energy minimum, in a reaction-enabling step, and (2) create the protein configurations associated with the chemical step. Below 217 K, the substrate radical decay reaction persists. Increases in activation enthalpy and entropy of both the microscopic enabling and reaction steps indicate that this non-native reaction coordinate is conducted by local, incremental fluctuations. Continuity in the Arrhenius relations indicates that the same sets of protein groups and interactions mediate the rearrangement over the 295 to 203 K range, but with a repertoire of configurations below 217 K that is restricted, relative to the native configurations accessible above 219 K. The experimental features of a culled reaction step, first-order kinetic measurements, and wide room-to-cryogenic temperature range, allow the direct demonstration and kinetic characterization of protein dynamical contributions to the core adiabatic, bond-making/bond-breaking reaction in EAL.
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Affiliation(s)
- Meghan Kohne
- Department of Physics, Emory University , Atlanta, Georgia 30322, United States
| | - Chen Zhu
- Department of Physics, Emory University , Atlanta, Georgia 30322, United States
| | - Kurt Warncke
- Department of Physics, Emory University , Atlanta, Georgia 30322, United States
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31
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Mhashal AR, Vardi-Kilshtain A, Kohen A, Major DT. The role of the Met 20 loop in the hydride transfer in Escherichia coli dihydrofolate reductase. J Biol Chem 2017; 292:14229-14239. [PMID: 28620051 DOI: 10.1074/jbc.m117.777136] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/24/2017] [Indexed: 11/06/2022] Open
Abstract
A key question concerning the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) is whether the Met20 loop is dynamically coupled to the chemical step during catalysis. A more basic, yet unanswered question is whether the Met20 loop adopts a closed conformation during the chemical hydride transfer step. To examine the most likely conformation of the Met20 loop during the chemical step, we studied the hydride transfer in wild type (WT) ecDHFR using hybrid quantum mechanics-molecular mechanics free energy simulations with the Met20 loop in a closed and disordered conformation. Additionally, we investigated three mutant forms (I14X; X = Val, Ala, Gly) of the enzyme that have increased active site flexibility and donor-acceptor distance dynamics in closed and disordered Met20 loop states. We found that the conformation of the Met20 loop has a dramatic effect on the ordering of active site hydration, although the Met20 loop conformation only has a moderate effect on the hydride transfer rate and donor-acceptor distance dynamics. Finally, we evaluated the pKa of the substrate N5 position in closed and disordered Met20 loop states and found a strong correlation between N5 basicity and the conformation of the Met20 loop.
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Affiliation(s)
- Anil R Mhashal
- From the Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Alexandra Vardi-Kilshtain
- From the Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
| | - Dan Thomas Major
- From the Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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32
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Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. J Chem Phys 2017; 144:180901. [PMID: 27179464 DOI: 10.1063/1.4947037] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme's conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.
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Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| | - Ram Prasad Bora
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
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33
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Luk LYP, Loveridge EJ, Allemann RK. Protein motions and dynamic effects in enzyme catalysis. Phys Chem Chem Phys 2016; 17:30817-27. [PMID: 25854702 DOI: 10.1039/c5cp00794a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The role of protein motions in promoting the chemical step of enzyme catalysed reactions remains a subject of considerable debate. Here, a unified view of the role of protein dynamics in dihydrofolate reductase catalysis is described. Recently the role of such motions has been investigated by characterising the biophysical properties of isotopically substituted enzymes through a combination of experimental and computational analyses. Together with previous work, these results suggest that dynamic coupling to the chemical coordinate is detrimental to catalysis and may have been selected against during DHFR evolution. The full catalytic power of Nature's catalysts appears to depend on finely tuning protein motions in each step of the catalytic cycle.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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34
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Abstract
Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects.
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Affiliation(s)
- J Gao
- Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province, PR China; University of Minnesota, Minneapolis, MN, United States.
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35
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Abstract
Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions.
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Affiliation(s)
- P Singh
- University of Iowa, Iowa City, IA, United States
| | - Z Islam
- University of Iowa, Iowa City, IA, United States
| | - A Kohen
- University of Iowa, Iowa City, IA, United States.
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36
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González-Lafont À, Lluch JM. Kinetic isotope effects in chemical and biochemical reactions: physical basis and theoretical methods of calculation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Àngels González-Lafont
- Institut de Biotecnologia i de Biomedicina and Departament de Química; Universitat Autònoma de Barcelona; Bellaterra, Barcelona Spain
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina and Departament de Química; Universitat Autònoma de Barcelona; Bellaterra, Barcelona Spain
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37
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Reddish MJ, Vaughn MB, Fu R, Dyer RB. Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase. Biochemistry 2016; 55:1485-93. [PMID: 26901612 DOI: 10.1021/acs.biochem.5b01364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are known to change among several conformational states during turnover. The role of such dynamic structural changes in catalysis is not fully understood. The influence of dynamics in catalysis can be inferred, but not proven, by comparison of equilibrium structures of protein variants and protein-ligand complexes. A more direct way to establish connections between protein dynamics and the catalytic cycle is to probe the kinetics of specific protein motions in comparison to progress along the reaction coordinate. We have examined the enzyme model system dihydrofolate reductase (DHFR) from Escherichia coli with tryptophan fluorescence-probed temperature-jump spectroscopy. We aimed to observe the kinetics of the ligand binding and ligand-induced conformational changes of three DHFR complexes to establish the relationship among these catalytic steps. Surprisingly, in all three complexes, the observed kinetics do not match a simple sequential two-step process. Through analysis of the relationship between ligand concentration and observed rate, we conclude that the observed kinetics correspond to the ligand binding step of the reaction and a noncoupled enzyme conformational change. The kinetics of the conformational change vary with the ligand's identity and presence but do not appear to be directly related to progress along the reaction coordinate. These results emphasize the need for kinetic studies of DHFR with highly specific spectroscopic probes to determine which dynamic events are coupled to the catalytic cycle and which are not.
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Affiliation(s)
- Michael J Reddish
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - Morgan B Vaughn
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - Rong Fu
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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38
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Francis K, Sapienza PJ, Lee AL, Kohen A. The Effect of Protein Mass Modulation on Human Dihydrofolate Reductase. Biochemistry 2016; 55:1100-6. [PMID: 26813442 DOI: 10.1021/acs.biochem.5b00945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) from Escherichia coli has long served as a model enzyme with which to elucidate possible links between protein dynamics and the catalyzed reaction. Such physical properties of its human counterpart have not been rigorously studied so far, but recent computer-based simulations suggest that these two DHFRs differ significantly in how closely coupled the protein dynamics and the catalyzed C-H → C hydride transfer step are. To test this prediction, two contemporary probes for studying the effect of protein dynamics on catalysis were combined here: temperature dependence of intrinsic kinetic isotope effects (KIEs), which are sensitive to the physical nature of the chemical step, and protein mass modulation, which slows down fast dynamics (femto- to picosecond time scale) throughout the protein. The intrinsic H/T KIEs of human DHFR, like those of E. coli DHFR, are shown to be temperature-independent in the range from 5 to 45 °C, indicating fast sampling of donor and acceptor distances (DADs) at the reaction's transition state (or tunneling ready state, TRS). Mass modulation of these enzymes through isotopic labeling with (13)C, (15)N, and (2)H at nonexchangeable hydrogens yields an 11% heavier enzyme. The additional mass has no effect on the intrinsic KIEs of the human enzyme. This finding indicates that the mass modulation of the human DHFR affects neither DAD distribution nor the DAD's conformational sampling dynamics. Furthermore, reduction in the enzymatic turnover number and the dissociation rate constant for the product indicate that the isotopic substitution affects kinetic steps that are not the catalyzed C-H → C hydride transfer. The findings are discussed in terms of fast dynamics and their role in catalysis, the comparison of calculations and experiments, and the interpretation of isotopically modulated heavy enzymes in general.
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Affiliation(s)
- Kevin Francis
- The Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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39
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Khantwal CM, Abraham SJ, Han W, Jiang T, Chavan TS, Cheng RC, Elvington SM, Liu CW, Mathews II, Stein RA, Mchaourab HS, Tajkhorshid E, Maduke M. Revealing an outward-facing open conformational state in a CLC Cl(-)/H(+) exchange transporter. eLife 2016; 5. [PMID: 26799336 PMCID: PMC4769167 DOI: 10.7554/elife.11189] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/14/2016] [Indexed: 11/22/2022] Open
Abstract
CLC secondary active transporters exchange Cl- for H+. Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Gluex) upon its protonation. Using 19F NMR, we show that as [H+] is increased to protonate Gluex and enrich the outward-facing state, a residue ~20 Å away from Gluex, near the subunit interface, moves from buried to solvent-exposed. Consistent with functional relevance of this motion, constriction via inter-subunit cross-linking reduces transport. Molecular dynamics simulations indicate that the cross-link dampens extracellular gate-opening motions. In support of this model, mutations that decrease steric contact between Helix N (part of the extracellular gate) and Helix P (at the subunit interface) remove the inhibitory effect of the cross-link. Together, these results demonstrate the formation of a previously uncharacterized 'outward-facing open' state, and highlight the relevance of global structural changes in CLC function. DOI:http://dx.doi.org/10.7554/eLife.11189.001 Cells have transporter proteins on their surface to carry molecules in and out of the cell. For example, the CLC family of transporters move two chloride ions in one direction at the same time as moving one hydrogen ion in the opposite direction. To be able to move these ions in opposite directions, transporters have to cycle through a series of shapes in which the ions can only access alternate sides of the membrane. First, the transporter adopts an 'outward-facing' shape when the ions first bind to the transporter, then it switches into the 'occluded' shape to move the ions through the membrane. Finally, the transporter takes on the 'inward-facing' shape to release the ions on the other side of the membrane. However, structural studies of CLCs suggest that the structures of these proteins do not change much while they are moving ions, which suggests that they might work in a different way. Khantwal, Abraham et al. have now used techniques called “nuclear magnetic resonance” and "double electron-electron resonance" to investigate how a CLC from a bacterium moves ions. The experiments suggest that when the transporter adopts the outward-facing shape, points on the protein known as Y419 and D417 shift their positions. Chemically linking two regions of the CLC prevented this movement and inhibited the transport of chloride ions across the membrane. Khantwal, Abraham et al. then used a computer simulation to model how the protein changes shape in more detail. This model predicts that two regions of the transporter undergo major rearrangements resulting in a gate-opening motion that widens a passage to allow the chloride ions to bind to the protein. Khantwal, Abraham et al.’s findings will prompt future studies to reveal the other shapes and how CLCs transition between them. DOI:http://dx.doi.org/10.7554/eLife.11189.002
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Affiliation(s)
- Chandra M Khantwal
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Sherwin J Abraham
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Wei Han
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Tao Jiang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Tanmay S Chavan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Ricky C Cheng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Shelley M Elvington
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Corey W Liu
- Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,College of Medicine, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
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40
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Wang Z, Antoniou D, Schwartz SD, Schramm VL. Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects, and Heavy Enzyme Studies. Biochemistry 2015; 55:157-66. [PMID: 26652185 DOI: 10.1021/acs.biochem.5b01241] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Escherichia coli dihydrofolate reductase (ecDHFR) is used to study fundamental principles of enzyme catalysis. It remains controversial whether fast protein motions are coupled to the hydride transfer catalyzed by ecDHFR. Previous studies with heavy ecDHFR proteins labeled with (13)C, (15)N, and nonexchangeable (2)H reported enzyme mass-dependent hydride transfer kinetics for ecDHFR. Here, we report refined experimental and computational studies to establish that hydride transfer is independent of protein mass. Instead, we found the rate constant for substrate dissociation to be faster for heavy DHFR. Previously reported kinetic differences between light and heavy DHFRs likely arise from kinetic steps other than the chemical step. This study confirms that fast (femtosecond to picosecond) protein motions in ecDHFR are not coupled to hydride transfer and provides an integrative computational and experimental approach to resolve fast dynamics coupled to chemical steps in enzyme catalysis.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Dimitri Antoniou
- Department of Chemistry and Biochemistry, University of Arizona , P.O. Box 210041, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona , P.O. Box 210041, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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41
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Wang M, Zhu C, Kohne M, Warncke K. Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems. Methods Enzymol 2015; 563:59-94. [PMID: 26478482 PMCID: PMC6186429 DOI: 10.1016/bs.mie.2015.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Approaches to the resolution and characterization of individual chemical steps in enzyme catalytic sequences, by using temperatures in the cryogenic range of 190-250 K, and kinetics measured by time-resolved, full-spectrum electron paramagnetic resonance spectroscopy in fluid cryosolvent and frozen solution systems, are described. The preparation and performance of the adenosylcobalamin-dependent ethanolamine ammonia-lyase enzyme from Salmonella typhimurium in the two systems exemplifies the biochemical and spectroscopic methods. General advantages of low-temperature studies are (1) slowing of reaction steps, so that measurements can be made by using straightforward T-step kinetic methods and commercial instrumentation, (2) resolution of individual reaction steps, so that first-order kinetic analysis can be applied, and (3) accumulation of intermediates that are not detectable at room temperatures. The broad temperature range from room temperature to 190 K encompasses three regimes: (1) temperature-independent mean free energy surface (corresponding to native behavior); (2) the narrow temperature region of a glass-like transition in the protein, over which the free energy surface changes, revealing dependence of the native reaction on collective protein/solvent motions; and (3) the temperature range below the glass transition region, for which persistent reaction corresponds to nonnative, alternative reaction pathways, in the vicinity of the native configurational envelope. Representative outcomes of low-temperature kinetics studies are portrayed on Eyring and free energy surface (landscape) plots, and guidelines for interpretations are presented.
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Affiliation(s)
- Miao Wang
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Chen Zhu
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Meghan Kohne
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Kurt Warncke
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA.
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42
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Vardi-Kilshtain A, Nitoker N, Major DT. Nuclear quantum effects and kinetic isotope effects in enzyme reactions. Arch Biochem Biophys 2015; 582:18-27. [DOI: 10.1016/j.abb.2015.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
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Luk LYP, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angew Chem Int Ed Engl 2015; 54:9016-20. [PMID: 26079622 PMCID: PMC4985705 DOI: 10.1002/anie.201503968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/21/2022]
Abstract
Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes ((2) H, (13) C, (15) N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea that dynamic effects on catalysis mostly originate from the C-terminal segment. The use of isotope hybrids provides insights into the microscopic mechanism of dynamic coupling, which is difficult to obtain with other studies, and helps define the dynamic networks of intramolecular interactions central to enzyme catalysis.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK)
| | - J Javier Ruiz-Pernía
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló (Spain)
| | | | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK)
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot (Spain).
| | - Vincent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló (Spain).
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK).
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44
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Luk LYP, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Singh P, Francis K, Kohen A. Network of remote and local protein dynamics in dihydrofolate reductase catalysis. ACS Catal 2015; 5:3067-3073. [PMID: 27182453 DOI: 10.1021/acscatal.5b00331] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics calculations and bionformatic studies of dihydrofolate reductase (DHFR) have suggested a network of coupled motions across the whole protein that is correlated to the reaction coordinate. Experimental studies demonstrated that distal residues G121, M42 and F125 in E. coli DHFR participate in that network. The missing link in our understanding of DHFR catalysis is the lack of a mechanism by which such remote residues can affect the catalyzed chemistry at the active site. Here, we present a study of the temperature dependence of intrinsic kinetic isotope effects (KIEs) that indicates synergism between a remote residue in that dynamic network, G121, and the active site's residue I14. The intrinsic KIEs for the I14A-G121V double mutant showed steeper temperature dependence (ΔEa(T-H)) than expected from comparison of the wild type and two single mutants. That effect was non-additive, i.e., ΔEa(T-H)G121V +ΔEa(T-H) I14A < ΔEa(T-H) double mutant, which indicates a synergism between the two residues. This finding links the remote residues in the network under investigation to the enzyme's active site, providing a mechanism by which these residues can be coupled to the catalyzed chemistry. This experimental evidence validates calculations proposing that both remote and active site residues constitute a network of coupled promoting motions correlated to the bond activation step (C-H→C hydride transfer in this case). Additionally, the effect of I14A and G121V mutations on single turnover rates was additive rather than synergistic. Although single turnover rate measurements are more readily available and thus more popular than assessing intrinsic kinetic isotope effects, the current finding demonstrates that for these rates, which in DHFR reflect several microscopic rate constants, can fall short of revealing the nature of the C-H bond activation per se.
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Affiliation(s)
- Priyanka Singh
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Kevin Francis
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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46
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De Conto V, Braz ASK, Perahia D, Scott LPB. Recovery of the wild type atomic flexibility in the HIV-1 protease double mutants. J Mol Graph Model 2015; 59:107-16. [PMID: 25948548 DOI: 10.1016/j.jmgm.2015.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 02/04/2023]
Abstract
The emergence of drug resistant mutations due to the selective pressure exerted by antiretrovirals, including protease inhibitors (PIs), remains a major problem in the treatment of AIDS. During PIs therapy, the occurrence of primary mutations in the wild type HIV-1 protease reduces both the affinity for the inhibitors and the viral replicative capacity compared to the wild type (WT) protein, but additional mutations compensate for this reduced viral fitness. To investigate this phenomenon from the structural point of view, we combined Molecular Dynamics and Normal Mode Analysis to analyze and compare the variations of the flexibility of C-alpha atoms and the differences in hydrogen bond (h-bond) network between the WT and double mutants. In most cases, the flexibility profile of the double mutants was more often similar to that of the WT than to that of the related single base mutants. All single mutants showed a significant alteration in h-bond formation compared to WT. Most of the significant changes occur in the border between the flap and cantilever regions. We found that all the considered double mutants have their h-bond pattern significantly altered in comparison to the respective single base mutants affecting their flexibility profile that becomes more similar to that of WT. This WT flexibility restoration in the double mutants appears as an important factor for the HIV-1 fitness recovery observed in patients.
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Affiliation(s)
- Valderes De Conto
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Antônio S K Braz
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), Ecole Normale Supérieure de Cachan, Cachan, France
| | - Luis P B Scott
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil; Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), Ecole Normale Supérieure de Cachan, Cachan, France.
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47
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Dysfunctional conformational dynamics of protein kinase A induced by a lethal mutant of phospholamban hinder phosphorylation. Proc Natl Acad Sci U S A 2015; 112:3716-21. [PMID: 25775607 DOI: 10.1073/pnas.1502299112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamic interplay between kinases and substrates is crucial for the formation of catalytically committed complexes that enable phosphoryl transfer. However, a clear understanding on how substrates modulate kinase structural dynamics to control catalytic efficiency is still missing. Here, we used solution NMR spectroscopy to study the conformational dynamics of two complexes of the catalytic subunit of the cAMP-dependent protein kinase A with WT and R14 deletion phospholamban, a lethal human mutant linked to familial dilated cardiomyopathy. Phospholamban is a central regulator of heart muscle contractility, and its phosphorylation by protein kinase A constitutes a primary response to β-adrenergic stimulation. We found that the single deletion of arginine in phospholamban's recognition sequence for the kinase reduces its binding affinity and dramatically reduces phosphorylation kinetics. Structurally, the mutant prevents the enzyme from adopting conformations and motions committed for catalysis, with concomitant reduction in catalytic efficiency. Overall, these results underscore the importance of a well-tuned structural and dynamic interplay between the kinase and its substrates to achieve physiological phosphorylation levels for proper Ca(2+) signaling and normal cardiac function.
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48
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Abstract
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The role of the enzyme’s dynamic motions
in catalysis is at the center of heated contemporary debates among
both theoreticians and experimentalists. Resolving these apparent
disputes is of both intellectual and practical importance: incorporation
of enzyme dynamics could be critical for any calculation of enzymatic
function and may have profound implications for structure-based drug
design and the design of biomimetic catalysts. Analysis of the
literature suggests that while part of the dispute may reflect substantial
differences between theoretical approaches, much of the debate is
semantic. For example, the term “protein dynamics” is
often used by some researchers when addressing motions that are in
thermal equilibrium with their environment, while other researchers
only use this term for nonequilibrium events. The last cases are those
in which thermal energy is “stored” in a specific protein
mode and “used” for catalysis before it can dissipate
to its environment (i.e., “nonstatistical dynamics”).
This terminology issue aside, a debate has arisen among theoreticians
around the roles of nonstatistical vs statistical dynamics in catalysis.
However, the author knows of no experimental findings available today
that examined this question in enzyme catalyzed reactions. Another
source of perhaps nonsubstantial argument might stem from the varying
time scales of enzymatic motions, which range from seconds to femtoseconds.
Motions at different time scales play different roles in the many
events along the catalytic cascade (reactant binding, reprotonation
of reactants, structural rearrangement toward the transition state,
product release, etc.). In several cases, when various experimental
tools have been used to probe catalytic events at differing time scales,
illusory contradictions seem to have emerged. In this Account, recent
attempts to sort the merits of those questions are discussed along
with possible future directions. A possible summary of current
studies could be that enzyme, substrate, and solvent dynamics contribute
to enzyme catalyzed reactions in several ways: first via mutual “induced-fit”
shifting of their conformational ensemble upon binding; then via thermal
search of the conformational space toward the reaction’s transition-state
(TS) and the rare event of the barrier crossing toward products, which
is likely to be on faster time scales then the first and following
events; and finally via the dynamics associated with products release,
which are rate-limiting for many enzymatic reactions. From a chemical
perspective, close to the TS, enzymatic systems seem to stiffen, restricting
motions orthogonal to the chemical coordinate and enabling dynamics
along the reaction coordinate to occur selectively. Studies of how
enzymes evolved to support those efficient dynamics at various time
scales are still in their infancy, and further experiments and calculations
are needed to reveal these phenomena in both enzymes and uncatalyzed
reactions.
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Affiliation(s)
- Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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49
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Abstract
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The active
site of an enzyme is surrounded by a fluctuating environment of protein
and solvent conformational states, and a realistic calculation of
chemical reaction rates and kinetic isotope effects of enzyme-catalyzed
reactions must take account of this environmental diversity. Ensemble-averaged
variational transition state theory with multidimensional tunneling
(EA-VTST/MT) was developed as a way to carry out such calculations.
This theory incorporates ensemble averaging, quantized vibrational
energies, energy, tunneling, and recrossing of transition state dividing
surfaces in a systematic way. It has been applied successfully to
a number of hydrogen-, proton-, and hydride-transfer reactions. The
theory also exposes the set of effects that should be considered in
reliable rate constants calculations. We first review the basic
theory and the steps in the calculation. A key role is played by the
generalized free energy of activation profile, which is obtained by
quantizing the classical potential of mean force as a function of
a reaction coordinate because the one-way flux through the transition
state dividing surface can be written in terms of the generalized
free energy of activation. A recrossing transmission coefficient accounts
for the difference between the one-way flux through the chosen transition
state dividing surface and the net flux, and a tunneling transmission
coefficient converts classical motion along the reaction coordinate
to quantum mechanical motion. The tunneling calculation is multidimensional,
accounting for the change in vibrational frequencies along the tunneling
path and shortening of the tunneling path with respect to the minimum
energy path (MEP), as promoted by reaction-path curvature. The generalized
free energy of activation and the transmission coefficients both involve
averaging over an ensemble of reaction paths and conformations, and
this includes the coupling of protein motions to the rearrangement
of chemical bonds in a statistical mechanically correct way. The standard
deviations of the transmissions coefficients provide information on
the diversity of the distribution of reaction paths, barriers, and
protein conformations along the members of an ensemble of reaction
paths passing through the transition state. We first illustrate
the theory by discussing the application to both wild-type and mutant Escherichia coli dihydrofolate reductase and hyperthermophilic Thermotoga maritima dihydrofolate reductase (DHFR); DHFR
is of special interest because the protein conformational changes
have been widely studied. Then we present shorter discussions of several
other applications of EA-VTST/MT to transfer of protons, hydrogen
atoms, and hydride ions and their deuterated analogs. Systems discussed
include hydride transfer in alcohol dehydrogenase, xylose isomerase,
and thymidylate synthase, proton transfer in methylamine dehydrogenase,
hydrogen atom transfer in methylmalonyl-CoA mutase, and nucleophilic
substitution in haloalkane dehalogenase and two-dimensional potentials
of mean force for potentially coupled proton and hydride transfer
in the β-oxidation of butyryl-coenzyme A catalyzed by short-chain
acyl-CoA dehydrogenase and in the pyruvate to lactate transformation
catalyzed by lactate dehydrogenase.
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Affiliation(s)
- Laura Masgrau
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
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50
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Hanoian P, Liu CT, Hammes-Schiffer S, Benkovic S. Perspectives on electrostatics and conformational motions in enzyme catalysis. Acc Chem Res 2015; 48:482-9. [PMID: 25565178 PMCID: PMC4334233 DOI: 10.1021/ar500390e] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Enzymes
are essential for all living organisms, and their effectiveness as
chemical catalysts has driven more than a half century of research
seeking to understand the enormous rate enhancements they provide.
Nevertheless, a complete understanding of the factors that govern
the rate enhancements and selectivities of enzymes remains elusive,
due to the extraordinary complexity and cooperativity that are the
hallmarks of these biomolecules. We have used a combination of site-directed
mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear
magnetic resonance (NMR), vibrational and fluorescence spectroscopies,
resonance energy transfer, and computer simulations to study the implications
of conformational motions and electrostatic interactions on enzyme
catalysis in the enzyme dihydrofolate reductase (DHFR). We have
demonstrated that modest equilibrium conformational changes are functionally
related to the hydride transfer reaction. Results obtained for mutant
DHFRs illustrated that reductions in hydride transfer rates are correlated
with altered conformational motions, and analysis of the evolutionary
history of DHFR indicated that mutations appear to have occurred to
preserve both the hydride transfer rate and the associated conformational
changes. More recent results suggested that differences in local electrostatic
environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination
of primary and solvent kinetic isotope effects, we demonstrated that
the reaction mechanism is consistent across a broad pH range, and
computer simulations suggested that deprotonation of the active site
Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into
the ecDHFR active site provided an experimental tool
for interrogating these microenvironments and for investigating changes
in electrostatics along the DHFR catalytic cycle. Complementary molecular
dynamics simulations in conjunction with mixed quantum mechanical/molecular
mechanical calculations accurately reproduced the vibrational frequency
shifts in these probes and provided atomic-level insight into the
residues influencing these changes. Our findings indicate that conformational
and electrostatic changes are intimately related and functionally
essential. This approach can be readily extended to the study of other
enzyme systems to identify more general trends in the relationship
between conformational fluctuations and electrostatic interactions.
These results are relevant to researchers seeking to design novel
enzymes as well as those seeking to develop therapeutic agents that
function as enzyme inhibitors.
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Affiliation(s)
- Philip Hanoian
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - C. Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stephen Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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