1
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Okafor SU, Pinto G, Brdecka M, Smith W, Lewis TWR, Gutierrez M, Bellert DJ. Hydrogen tunneling with an atypically small KIE measured in the mediated decomposition of the Co(CH 3COOH) + complex. Phys Chem Chem Phys 2024. [PMID: 39470007 DOI: 10.1039/d4cp02722a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2024]
Abstract
Quantum mechanical tunneling (QMT) is a well-documented phenomenon in the C-H bond activation mechanism and is commonly identified by large KIE values. Herein we present surprising findings in the kinetic study of hydrogen tunneling in the Co+ mediated decomposition of acetic acid and its perdeuterated isotopologue, conducted with the energy resolved single photon initiated dissociative rearrangement reaction (SPIDRR) technique. Following laser activation, the reaction proceeds along parallel product channels Co(CH4O)+ + CO and Co(C2H2O)+ + H2O. An energetic threshold is observed in the energy dependence of the unimolecular microcanonical rate constants, k(E). This is interpreted as the reacting population surmounting a rate-limiting Eyring barrier in the reaction's potential energy surface. Measurements of the heavier isotopologue's reaction kinetics supports this interpretation. Kinetic signatures measured at energies below the Eyring barrier are attributed to H/D QMT. The below-the-barrier tunneling kinetics presents an unusually linear energy dependence and a staggeringly small tunneling KIE of ∼1.4 over a wide energy range. We explain this surprising observation in terms of a narrow tunneling barrier, wherein the electronic structure of the Co+ metal plays a pivotal role in enhanced reactivity by promoting efficient tunneling. These results suggest that hydrogen tunneling could play important functions in transition metal chemistry, such as that found in enzymatic mechanisms, even if small KIE values are measured.
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Affiliation(s)
| | | | | | - William Smith
- Baylor University, 1311 S 5th St, Waco, TX 76706, USA.
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2
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Harding-Larsen D, Funk J, Madsen NG, Gharabli H, Acevedo-Rocha CG, Mazurenko S, Welner DH. Protein representations: Encoding biological information for machine learning in biocatalysis. Biotechnol Adv 2024; 77:108459. [PMID: 39366493 DOI: 10.1016/j.biotechadv.2024.108459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 09/19/2024] [Accepted: 09/29/2024] [Indexed: 10/06/2024]
Abstract
Enzymes offer a more environmentally friendly and low-impact solution to conventional chemistry, but they often require additional engineering for their application in industrial settings, an endeavour that is challenging and laborious. To address this issue, the power of machine learning can be harnessed to produce predictive models that enable the in silico study and engineering of improved enzymatic properties. Such machine learning models, however, require the conversion of the complex biological information to a numerical input, also called protein representations. These inputs demand special attention to ensure the training of accurate and precise models, and, in this review, we therefore examine the critical step of encoding protein information to numeric representations for use in machine learning. We selected the most important approaches for encoding the three distinct biological protein representations - primary sequence, 3D structure, and dynamics - to explore their requirements for employment and inductive biases. Combined representations of proteins and substrates are also introduced as emergent tools in biocatalysis. We propose the division of fixed representations, a collection of rule-based encoding strategies, and learned representations extracted from the latent spaces of large neural networks. To select the most suitable protein representation, we propose two main factors to consider. The first one is the model setup, which is influenced by the size of the training dataset and the choice of architecture. The second factor is the model objectives such as consideration about the assayed property, the difference between wild-type models and mutant predictors, and requirements for explainability. This review is aimed at serving as a source of information and guidance for properly representing enzymes in future machine learning models for biocatalysis.
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Affiliation(s)
- David Harding-Larsen
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Jonathan Funk
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Niklas Gesmar Madsen
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Hani Gharabli
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Carlos G Acevedo-Rocha
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Ditte Hededam Welner
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Bygning 220, 2800 Kgs. Lyngby, Denmark.
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3
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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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4
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Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
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5
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Patrick J, Pettersson P, Mäler L. Lipid- and substrate-induced conformational and dynamic changes in a glycosyltransferase involved in E. coli LPS synthesis revealed by 19F and 31P NMR. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184209. [PMID: 37558175 DOI: 10.1016/j.bbamem.2023.184209] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/03/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023]
Abstract
WaaG is a glycosyltransferase (GT) involved in the synthesis of the bacterial cell wall, and in Escherichia coli it catalyzes the transfer of a glucose moiety from the donor substrate UDP-glucose onto the nascent lipopolysaccharide (LPS) molecule which when completed constitutes the major component of the bacterium's outermost defenses. Similar to other GTs of the GT-B fold, having two Rossman-like domains connected by a short linker, WaaG is believed to undergo complex inter-domain motions as part of its function to accommodate the nascent LPS and UDP-glucose in the catalytic site located in the cleft between the two domains. As the nascent LPS is bulky and membrane-bound, WaaG is a peripheral membrane protein, adding to the complexity of studying the enzyme in a biologically relevant environment. Using specific 5-fluoro-Trp labelling of native and inserted tryptophans and 19F NMR we herein studied the dynamic interactions of WaaG with lipids using bicelles, and with the donor substrate. Line-shape changes when bicelles are added to WaaG show that the dynamic behavior is altered when binding to the model membrane, while a chemical shift change indicates an altered environment around a tryptophan located in the C-terminal domain of WaaG upon interaction with UDP-glucose or UDP. A lipid-bound paramagnetic probe was used to confirm that the membrane interaction is mediated by a loop region located in the N-terminal domain. Furthermore, the hydrolysis of the donor substrate by WaaG was quantified by 31P NMR.
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Affiliation(s)
- Joan Patrick
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Department of Chemistry, Umeå University, Umeå, Sweden.
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6
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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7
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Markin CJ, Mokhtari DA, Du S, Doukov T, Sunden F, Cook JA, Fordyce PM, Herschlag D. Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology. Proc Natl Acad Sci U S A 2023; 120:e2219074120. [PMID: 37428919 PMCID: PMC10629569 DOI: 10.1073/pnas.2219074120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/14/2023] [Indexed: 07/12/2023] Open
Abstract
Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active-site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues that reduced catalysis had little or no impact on TSA binding and many even increased tungstate affinity. These disparate effects can be accounted for by a model in which distal mutations alter the enzyme's conformational landscape, increasing the occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this ensemble model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity (but not more likely to impact catalysis), presumably due to increased conformational flexibility that allows previously disfavored microstates to increase in occupancy. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration of distal residues that shape the enzyme's conformational landscape and fine-tune active-site residues. Biologically, the evolution of extensive communication between the active site and remote residues to aid catalysis may have provided the foundation for allostery to make it a highly evolvable trait.
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Affiliation(s)
- Craig J. Markin
- Department of Biochemistry, Stanford University, Stanford, CA94305
| | | | - Siyuan Du
- Department of Biochemistry, Stanford University, Stanford, CA94305
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Light Source, Stanford Linear Accelerator Centre National Accelerator Laboratory, Menlo Park, CA94025
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, CA94305
| | - Jordan A. Cook
- Department of Biochemistry, Stanford University, Stanford, CA94305
| | - Polly M. Fordyce
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94110
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
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8
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Waheed SO, Varghese A, DiCastri I, Kaski B, LaRouche C, Fields GB, Karabencheva-Christova TG. Mechanism of the Early Catalytic Events in the Collagenolysis by Matrix Metalloproteinase-1. Chemphyschem 2023; 24:e202200649. [PMID: 36161746 DOI: 10.1002/cphc.202200649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/23/2022] [Indexed: 02/04/2023]
Abstract
Metalloproteinase-1 (MMP-1) catalyzed collagen degradation is essential for a wide variety of normal physiological processes, while at the same time contributing to several diseases in humans. Therefore, a comprehensive understanding of this process is of great importance. Although crystallographic and spectroscopic studies provided fundamental information about the structure and function of MMP-1, the precise mechanism of collagen degradation especially considering the complex and flexible structure of the substrate, remains poorly understood. In addition, how the protein environment dynamically reorganizes at the atomic scale into a catalytically active state capable of collagen hydrolysis remains unknown. In this study, we applied experimentally-guided multiscale molecular modeling methods including classical molecular dynamics (MD), well-tempered (WT) classical metadynamics (MetD), combined quantum mechanics/molecular mechanics (QM/MM) MD and QM/MM MetD simulations to explore and characterize the early catalytic events of MMP-1 collagenolysis. Importantly the study provided a complete atomic and dynamic description of the transition from the open to the closed form of the MMP-1•THP complex. Notably, the formation of catalytically active Michaelis complex competent for collagen cleavage was characterized. The study identified the changes in the coordination state of the catalytic zinc(II) associated with the conformational transformation and the formation of catalytically productive ES complex. Our results confirm the essential role of the MMP-1 catalytic domain's α-helices (hA, hB and hC) and the linker region in the transition to the catalytically competent ES complex. Overall, the results provide unique mechanistic insight into the conformational transformations and associated changes in the coordination state of the catalytic zinc(II) that would be important for the design of effective MMP-1 inhibitors.
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Affiliation(s)
- Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Isabella DiCastri
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Brenden Kaski
- Department of Kinesiology and Integrative Physiology, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Ciara LaRouche
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Gregg B Fields
- Department of Chemistry & Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, Florida, 33458, USA
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9
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Galmés MÀ, Nödling AR, He K, Luk LYP, Świderek K, Moliner V. Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases. Chem Sci 2022; 13:4779-4787. [PMID: 35655887 PMCID: PMC9067594 DOI: 10.1039/d2sc00778a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics strategy based on combining the best electrostatic properties of enzymes with activity in a common reaction is presented. The computational protocol has been applied to the re-design of the protein scaffold of an existing promiscuous esterase from Bacillus subtilis Bs2 to enhance its secondary amidase activity. After the alignment of Bs2 with a non-homologous amidase Candida antarctica lipase B (CALB) within rotation quaternions, a relevant spatial aspartate residue of the latter was transferred to the former as a means to favor the electrostatics of transition state formation, where a clear separation of charges takes place. Deep computational insights, however, revealed a significant conformational change caused by the amino acid replacement, provoking a shift in the pK a of the inserted aspartate and counteracting the anticipated catalytic effect. This prediction was experimentally confirmed with a 1.3-fold increase in activity. The good agreement between theoretical and experimental results, as well as the linear correlation between the electrostatic properties and the activation energy barriers, suggest that the presented computational-based investigation can transform in an enzyme engineering approach.
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Affiliation(s)
- Miquel À Galmés
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
| | - Alexander R Nödling
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Kaining He
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Louis Y P Luk
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Katarzyna Świderek
- Department of Physical and Analytical Chemistry, Universitat Jaume I 12071 Castellón Spain +34 964728070
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
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10
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Gonzalez NA, Li BA, McCully ME. The stability and dynamics of computationally designed proteins. Protein Eng Des Sel 2022; 35:gzac001. [PMID: 35174855 PMCID: PMC9214642 DOI: 10.1093/protein/gzac001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Protein stability, dynamics and function are intricately linked. Accordingly, protein designers leverage dynamics in their designs and gain insight to their successes and failures by analyzing their proteins' dynamics. Molecular dynamics (MD) simulations are a powerful computational tool for quantifying both local and global protein dynamics. This review highlights studies where MD simulations were applied to characterize the stability and dynamics of designed proteins and where dynamics were incorporated into computational protein design. First, we discuss the structural basis underlying the extreme stability and thermostability frequently observed in computationally designed proteins. Next, we discuss examples of designed proteins, where dynamics were not explicitly accounted for in the design process, whose coordinated motions or active site dynamics, as observed by MD simulation, enhanced or detracted from their function. Many protein functions depend on sizeable or subtle conformational changes, so we finally discuss the computational design of proteins to perform a specific function that requires consideration of motion by multi-state design.
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Affiliation(s)
- Natali A Gonzalez
- Department of Biology, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA
| | - Brigitte A Li
- Department of Biology, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA
| | - Michelle E McCully
- Department of Biology, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA
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11
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Chen D, Li Y, Li X, Savidge T, Qian Y, Fan X. Factors determining the enzyme catalytic power caused by noncovalent interactions: Charge alterations in enzyme active sites. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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12
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Bozovic O, Jankovic B, Hamm P. Using azobenzene photocontrol to set proteins in motion. Nat Rev Chem 2021; 6:112-124. [PMID: 37117294 DOI: 10.1038/s41570-021-00338-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 02/06/2023]
Abstract
Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, it is possible to change binding affinities, control allostery or manipulate complex biological processes, for example. Additionally, owing to their intrinsically fast photoisomerization, azobenzene photoswitches can serve as triggers that initiate out-of-equilibrium processes. Such switching of the activity initiates a cascade of conformational events that can be accessed with time-resolved methods. In this Review, we show how the potency of azobenzene photoswitching can be combined with transient spectroscopic techniques to disclose the order of events and experimentally observe biomolecular interactions in real time. This strategy will further our understanding of how a protein can accommodate, adapt and readjust its structure to answer an incoming signal, revealing more of the dynamical character of proteins.
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13
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Prah A, Mavri J, Stare J. An electrostatic duel: subtle differences in the catalytic performance of monoamine oxidase A and B isoenzymes elucidated at the residue level using quantum computations. Phys Chem Chem Phys 2021; 23:26459-26467. [PMID: 34806105 DOI: 10.1039/d1cp03993h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The origin of the immense catalytic power of enzymes remains one of the biggest unresolved questions in biochemistry, with electrostatics being one of the main contenders. Herein, we report results that not only confirm that electrostatics is the driving force behind enzyme catalysis, but also that it is capable of tuning subtle differences in the catalytic performance between structurally similar enzymes, as demonstrated using the example of isoenzymes, monoamine oxidases A and B. Using our own computationally efficient multiscale model [A. Prah, et al., ACS Catal., 2019, 9, 1231] we analyzed the rate-limiting step of the reaction between phenylethylamine and both isoenzymes and deduced that the electrostatic environment provided by isoenzyme B has a perceivably higher catalytic influence on all the considered parameters of the reaction (energy barrier, charge transfer, dipole moment, and HOMO-LUMO gap). This is in full agreement with the available experimental kinetic data and with our own simulations of the reaction in question. In-depth analysis of individual amino acid contributions of both isoenzymes to the barrier (based on the interaction between the electric field provided by the enzyme and the dipole moment of the reacting moiety) shows that the majority of the difference between the isoenzymes can be attributed to a small number of sizable differences between the aligned amino acid pairs, whereas in most of the pairs the difference in contribution to the barrier is vanishingly small. These results suggest that electrostatics largely controls the substrate selectivity of enzymes and validates our approach as being capable of discerning fine nuances in the selectivity of structurally related isoenzymes.
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Affiliation(s)
- Alja Prah
- Theory Department, National Institute of Chemistry, Slovenia. .,University of Ljubljana, Faculty of Pharmacy, Slovenia
| | - Janez Mavri
- Theory Department, National Institute of Chemistry, Slovenia.
| | - Jernej Stare
- Theory Department, National Institute of Chemistry, Slovenia.
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14
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Rumfeldt J, Kurttila M, Takala H, Ihalainen JA. The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV-vis absorption spectroscopy study. Photochem Photobiol Sci 2021; 20:1173-1181. [PMID: 34460093 DOI: 10.1007/s43630-021-00090-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
Solvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation state of the biliverdin chromophore from Deinococcus radiodurans bacteriophytchrome, and thus, the pH of the surrounding solution, is determined. The observed absorbance changes are related to the solvent access of the chromophore binding pocket, gated by the hairpin extension. We therefore propose a model with an "open" (solvent-exposed, deprotonation-active on a (sub)second time-scale) state and a "closed" (solvent-gated, deprotonation inactive) state, where the hairpin fluctuates slowly between these conformations thereby controlling the deprotonation process of the chromophore on a minute time scale. When the connection between the hairpin and the biliverdin surroundings is destabilized by a point mutation, the amplitude of the deprotonation phase increases considerably. In the absence of the extension, the chromophore deprotonates essentially without any "gating". Hence, we introduce a straightforward method to study the stability and fluctuation of the phytochrome hairpin in its photostationary state. This approach can be extended to other chromophore-protein systems where absorption changes reflect dynamic processes of the protein.
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Affiliation(s)
- Jessica Rumfeldt
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Moona Kurttila
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Heikki Takala
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
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15
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Adesina AS, Luk LYP, Allemann RK. Cryo-kinetics Reveal Dynamic Effects on the Chemistry of Human Dihydrofolate Reductase. Chembiochem 2021; 22:2410-2414. [PMID: 33876533 PMCID: PMC8360168 DOI: 10.1002/cbic.202100017] [Citation(s) in RCA: 1] [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: 01/13/2021] [Revised: 04/16/2021] [Indexed: 12/03/2022]
Abstract
Effects of isotopic substitution on the rate constants of human dihydrofolate reductase (HsDHFR), an important target for anti-cancer drugs, have not previously been characterized due to its complex fast kinetics. Here, we report the results of cryo-measurements of the kinetics of the HsDHFR catalyzed reaction and the effects of protein motion on catalysis. Isotopic enzyme labeling revealed an enzyme KIE (kHLE /kHHE ) close to unity above 0 °C; however, the enzyme KIE was increased to 1.72±0.15 at -20 °C, indicating that the coupling of protein motions to the chemical step is minimized under optimal conditions but enhanced at non-physiological temperatures. The presented cryogenic approach provides an opportunity to probe the kinetics of mammalian DHFRs, thereby laying the foundation for characterizing their transition state structure.
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Affiliation(s)
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
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16
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Uversky VN, Giuliani A. Networks of Networks: An Essay on Multi-Level Biological Organization. Front Genet 2021; 12:706260. [PMID: 34234818 PMCID: PMC8255927 DOI: 10.3389/fgene.2021.706260] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/31/2021] [Indexed: 01/01/2023] Open
Abstract
The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the macromolecule and systemic effect as allosteric behavior. Similar pictures can be drawn for structure and function of cells, organs, tissues, and ecological systems. The majority of biologists are used to think that causally relevant events originate from the lower level (the molecular one) in the form of perturbations, that “climb up” the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such causative model, stemming from the usual genotype-phenotype distinction, is not the only one. As a matter of fact, one can observe top-down, bottom-up, as well as middle-out perturbation/control trajectories. The recent complex network studies allow to go further the pure qualitative observation of the existence of both non-linear and non-bottom-up processes and to uncover the deep nature of multi-level organization. Here, taking as paradigm protein structural and interaction networks, we review some of the most relevant results dealing with between networks communication shedding light on the basic principles of complex system control and dynamics and offering a more realistic frame of causation in biology.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
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17
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Xin X, Li C, Gao D, Wang D. Catalytic Descriptors to Investigate Catalytic Power in the Reaction of Haloalkane Dehalogenase Enzyme with 1,2-Dichloroethane. Int J Mol Sci 2021; 22:ijms22115854. [PMID: 34072602 PMCID: PMC8197811 DOI: 10.3390/ijms22115854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Enzymes play a fundamental role in many biological processes. We present a theoretical approach to investigate the catalytic power of the haloalkane dehalogenase reaction with 1,2-dichloroethane. By removing the three main active-site residues one by one from haloalkane dehalogenase, we found two reactive descriptors: one descriptor is the distance difference between the breaking bond and the forming bond, and the other is the charge difference between the transition state and the reactant complex. Both descriptors scale linearly with the reactive barriers, with the three-residue case having the smallest barrier and the zero-residue case having the largest. The results demonstrate that, as the number of residues increases, the catalytic power increases. The predicted free energy barriers using the two descriptors of this reaction in water are 23.1 and 24.2 kcal/mol, both larger than the ones with any residues, indicating that the water solvent hinders the reactivity. Both predicted barrier heights agree well with the calculated one at 25.2 kcal/mol using a quantum mechanics and molecular dynamics approach, and also agree well with the experimental result at 26.0 kcal/mol. This study shows that reactive descriptors can also be used to describe and predict the catalytic performance for enzyme catalysis.
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18
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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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19
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Ramirez-Mondragon CA, Nguyen ME, Milicaj J, Hassan BA, Tucci FJ, Muthyala R, Gao J, Taylor EA, Sham YY. Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics. Int J Mol Sci 2021; 22:ijms22094619. [PMID: 33924837 PMCID: PMC8124905 DOI: 10.3390/ijms22094619] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022] Open
Abstract
It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site triggers an open-to-closed conformation transition, necessary for their catalytic functions. Herein, we describe microsecond molecular dynamics simulations of two distantly related glycosyltransferases that are part of the GT-B structural superfamily, HepI and GtfA. Simulations were performed using the open and closed conformations of these unbound proteins, respectively, and we sought to identify the major dynamical modes and communication networks that interconnect the open and closed structures. We provide the first reported evidence within the scope of our simulation parameters that the interconversion between open and closed conformations is a hierarchical multistep process which can be a conserved feature of enzymes of the same structural superfamily. Each of these motions involves of a collection of smaller molecular reorientations distributed across both domains, highlighting the complexities of protein dynamic involved in the interconversion process. Additionally, dynamic cross-correlation analysis was employed to explore the potential effect of distal residues on the catalytic efficiency of HepI. Multiple distal nonionizable residues of the C-terminal domain exhibit motions anticorrelated to positively charged residues in the active site in the N-terminal domain involved in substrate binding. Mutations of these residues resulted in a reduction in negatively correlated motions and an altered enzymatic efficiency that is dominated by lower Km values with kcat effectively unchanged. The findings suggest that residues with opposing conformational motions involved in the opening and closing of the bidomain HepI protein can allosterically alter the population and conformation of the “closed” state, essential to the formation of the Michaelis complex. The stabilization effects of these mutations likely equally influence the energetics of both the ground state and the transition state of the catalytic reaction, leading to the unaltered kcat. Our study provides new insights into the role of conformational dynamics in glycosyltransferase’s function and new modality to modulate enzymatic efficiency.
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Affiliation(s)
- Carlos A. Ramirez-Mondragon
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; (C.A.R.-M.); (M.E.N.); (J.G.)
| | - Megin E. Nguyen
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; (C.A.R.-M.); (M.E.N.); (J.G.)
| | - Jozafina Milicaj
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA; (J.M.); (B.A.H.); (F.J.T.)
| | - Bakar A. Hassan
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA; (J.M.); (B.A.H.); (F.J.T.)
| | - Frank J. Tucci
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA; (J.M.); (B.A.H.); (F.J.T.)
| | - Ramaiah Muthyala
- Department of Experimental and Clinical Pharmacology, College Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Jiali Gao
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; (C.A.R.-M.); (M.E.N.); (J.G.)
- Department of Chemistry, University of Minnesota, Minneapolis, Minneapolis, MN 55455, USA
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Erika A. Taylor
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA; (J.M.); (B.A.H.); (F.J.T.)
- Correspondence: (E.A.T.); (Y.Y.S.); Tel.: +1-(860)-685-2739 (E.A.T.); +1-(612)-625-6255 (Y.Y.S.); Fax: +1-(860)-685-2211 (E.A.T.); +1-(612)-625-5149 (Y.Y.S.)
| | - Yuk Y. Sham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; (C.A.R.-M.); (M.E.N.); (J.G.)
- Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (E.A.T.); (Y.Y.S.); Tel.: +1-(860)-685-2739 (E.A.T.); +1-(612)-625-6255 (Y.Y.S.); Fax: +1-(860)-685-2211 (E.A.T.); +1-(612)-625-5149 (Y.Y.S.)
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20
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Quinn TR, Steussy CN, Haines BE, Lei J, Wang W, Sheong FK, Stauffacher CV, Huang X, Norrby PO, Helquist P, Wiest O. Microsecond timescale MD simulations at the transition state of PmHMGR predict remote allosteric residues. Chem Sci 2021; 12:6413-6418. [PMID: 34084441 PMCID: PMC8115266 DOI: 10.1039/d1sc00102g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Understanding the mechanisms of enzymatic catalysis requires a detailed understanding of the complex interplay of structure and dynamics of large systems that is a challenge for both experimental and computational approaches. More importantly, the computational demands of QM/MM simulations mean that the dynamics of the reaction can only be considered on a timescale of nanoseconds even though the conformational changes needed to reach the catalytically active state happen on a much slower timescale. Here we demonstrate an alternative approach that uses transition state force fields (TSFFs) derived by the quantum-guided molecular mechanics (Q2MM) method that provides a consistent treatment of the entire system at the classical molecular mechanics level and allows simulations at the microsecond timescale. Application of this approach to the second hydride transfer transition state of HMG-CoA reductase from Pseudomonas mevalonii (PmHMGR) identified three remote residues, R396, E399 and L407, (15-27 Å away from the active site) that have a remote dynamic effect on enzyme activity. The predictions were subsequently validated experimentally via site-directed mutagenesis. These results show that microsecond timescale MD simulations of transition states are possible and can predict rather than just rationalize remote allosteric residues.
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Affiliation(s)
- Taylor R Quinn
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA .,Early TDE Discovery, Early Oncology, Oncology R&D, AstraZeneca Boston USA
| | - Calvin N Steussy
- Department of Biological Sciences, Purdue Center for Cancer Research, Purdue University West Lafayette IN 47907 USA
| | - Brandon E Haines
- Department of Chemistry, Westmont College Santa Barbara CA 93108 USA
| | - Jinping Lei
- Department of Chemistry, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China.,School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 China
| | - Wei Wang
- Department of Chemistry, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Fu Kit Sheong
- Department of Chemistry, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue Center for Cancer Research, Purdue University West Lafayette IN 47907 USA
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Per-Ola Norrby
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA .,Data Science and Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg Pepparedsleden 1 SE-431 83 Mölndal Sweden
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA .,Lab of Computational Chemistry and Drug Design, School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School Shenzhen China
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21
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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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22
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Mukherjee P, Chandra Singh P. Experimental insight into enzyme catalysis and dynamics: A review on applications of state of art spectroscopic methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 122:33-62. [PMID: 32951815 DOI: 10.1016/bs.apcsb.2020.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are dynamic in nature and understanding their activity depends on exploring their overall structural fluctuation as well as transformation at the active site in free state as well as turnover conditions. In this chapter, the application of several different spectroscopy techniques viz. single molecule spectroscopy, ultrafast spectroscopy and Raman spectroscopy in the context of enzyme dynamics and catalysis are discussed. The importance of such studies are significant in the understanding of new discoveries of drugs, cure for some lethal diseases, gene modification as well as in industrial applications.
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Affiliation(s)
- Puspal Mukherjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
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23
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Acceleration of catalysis in dihydrofolate reductase by transient, site-specific photothermal excitation. Proc Natl Acad Sci U S A 2021; 118:2014592118. [PMID: 33468677 DOI: 10.1073/pnas.2014592118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the role of protein dynamics in chemical catalysis in the enzyme dihydrofolate reductase (DHFR), using a pump-probe method that employs pulsed-laser photothermal heating of a gold nanoparticle (AuNP) to directly excite a local region of the protein structure and transient absorbance to probe the effect on enzyme activity. Enzyme activity is accelerated by pulsed-laser excitation when the AuNP is attached close to a network of coupled motions in DHFR (on the FG loop, containing residues 116-132, or on a nearby alpha helix). No rate acceleration is observed when the AuNP is attached away from the network (distal mutant and His-tagged mutant) with pulsed excitation, or for any attachment site with continuous wave excitation. We interpret these results within an energy landscape model in which transient, site-specific addition of energy to the enzyme speeds up the search for reactive conformations by activating motions that facilitate this search.
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24
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Sevink GJA, Liwo JA, Asinari P, MacKernan D, Milano G, Pagonabarraga I. Unfolding the prospects of computational (bio)materials modeling. J Chem Phys 2020; 153:100901. [PMID: 32933271 DOI: 10.1063/5.0019773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this perspective communication, we briefly sketch the current state of computational (bio)material research and discuss possible solutions for the four challenges that have been increasingly identified within this community: (i) the desire to develop a unified framework for testing the consistency of implementation and physical accuracy for newly developed methodologies, (ii) the selection of a standard format that can deal with the diversity of simulation data and at the same time simplifies data storage, data exchange, and data reproduction, (iii) how to deal with the generation, storage, and analysis of massive data, and (iv) the benefits of efficient "core" engines. Expressed viewpoints are the result of discussions between computational stakeholders during a Lorentz center workshop with the prosaic title Workshop on Multi-scale Modeling and are aimed at (i) improving validation, reporting and reproducibility of computational results, (ii) improving data migration between simulation packages and with analysis tools, (iii) popularizing the use of coarse-grained and multi-scale computational tools among non-experts and opening up these modern computational developments to an extended user community.
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Affiliation(s)
- G J Agur Sevink
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jozef Adam Liwo
- Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Pietro Asinari
- Department of Energy, Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Turin, Italy
| | - Donal MacKernan
- UCD School of Physics, University College Dublin, Dublin 4, Ireland
| | - Giuseppe Milano
- Theoretical Physical Chemistry, Organic Materials Modeling, Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan Yonezawa, Yamagata-ken 992-8510, Japan
| | - Ignacio Pagonabarraga
- CECAM Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne (EPFL), Batochime, Avenue Forel 2, Lausanne CH-1015, Switzerland
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25
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Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis. Catalysts 2020. [DOI: 10.3390/catal10060684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The catalytic role of near attack conformations (NACs), molecular states that lie on the pathway between the ground state (GS) and transition state (TS) of a chemical reaction, is not understood completely. Using a computational approach that combines Bürgi–Dunitz theory with all-atom molecular dynamics simulations, the role of NACs in catalyzing the first stages of HIV-1 protease peptide hydrolysis was previously investigated using a substrate that represents the recognized SP1-NC cleavage site of the HIV-1 Gag polyprotein. NACs were found to confer no catalytic effect over the uncatalyzed reaction there ( Δ Δ G N ‡ ∼ 0 kcal/mol). Here, using the same approach, the role of NACs across multiple substrates that each represent a further recognized cleavage site is investigated. Overall rate enhancement varies by | Δ Δ G ‡ | ∼ 12–15 kcal/mol across this set, and although NACs contribute a small and approximately constant barrier to the uncatalyzed reaction (< Δ G N ‡ u > = 4.3 ± 0.3 kcal/mol), they are found to contribute little significant catalytic effect ( | Δ Δ G N ‡ | ∼ 0–2 kcal/mol). Furthermore, no correlation is exhibited between NAC contributions and the overall energy barrier ( R 2 = 0.01). However, these small differences in catalyzed NAC contributions enable rates to match those required for the kinetic order of processing. Therefore, NACs may offer an alternative and subtle mode compared to non-NAC contributions for fine-tuning reaction rates during complex evolutionary sequence selection processes—in this case across cleavable polyproteins whose constituents exhibit multiple functions during the virus life-cycle.
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26
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Liebau J, Tersa M, Trastoy B, Patrick J, Rodrigo-Unzueta A, Corzana F, Sparrman T, Guerin ME, Mäler L. Unveiling the activation dynamics of a fold-switch bacterial glycosyltransferase by 19F NMR. J Biol Chem 2020; 295:9868-9878. [PMID: 32434931 PMCID: PMC7380196 DOI: 10.1074/jbc.ra120.014162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/19/2020] [Indexed: 11/06/2022] Open
Abstract
Fold-switch pathways remodel the secondary structure topology of proteins in response to the cellular environment. It is a major challenge to understand the dynamics of these folding processes. Here, we conducted an in-depth analysis of the α-helix–to–β-strand and β-strand–to–α-helix transitions and domain motions displayed by the essential mannosyltransferase PimA from mycobacteria. Using 19F NMR, we identified four functionally relevant states of PimA that coexist in dynamic equilibria on millisecond-to-second timescales in solution. We discovered that fold-switching is a slow process, on the order of seconds, whereas domain motions occur simultaneously but are substantially faster, on the order of milliseconds. Strikingly, the addition of substrate accelerated the fold-switching dynamics of PimA. We propose a model in which the fold-switching dynamics constitute a mechanism for PimA activation.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Montse Tersa
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Beatriz Trastoy
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Joan Patrick
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ane Rodrigo-Unzueta
- Departamento de Bioquímica and Instituto Biofisika, Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Bizkaia, Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, Logroño, Spain
| | | | - Marcelo E Guerin
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain .,Departamento de Bioquímica and Instituto Biofisika, Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden .,Department of Chemistry, Umeå University, Umeå, Sweden
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27
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Magalhães RP, Fernandes HS, Sousa SF. Modelling Enzymatic Mechanisms with QM/MM Approaches: Current Status and Future Challenges. Isr J Chem 2020. [DOI: 10.1002/ijch.202000014] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rita P. Magalhães
- UCIBIO@REQUIMTE, BioSIMDepartamento de Biomedicina, Faculdade de Medicina da Universidade do Porto Alameda Professor Hernâni Monteiro 4200-319 Porto Portugal
| | - Henriques S. Fernandes
- UCIBIO@REQUIMTE, BioSIMDepartamento de Biomedicina, Faculdade de Medicina da Universidade do Porto Alameda Professor Hernâni Monteiro 4200-319 Porto Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE, BioSIMDepartamento de Biomedicina, Faculdade de Medicina da Universidade do Porto Alameda Professor Hernâni Monteiro 4200-319 Porto Portugal
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28
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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29
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Scott AF, Luk LY, Tuñón I, Moliner V, Allemann RK. Heavy Enzymes and the Rational Redesign of Protein Catalysts. Chembiochem 2019; 20:2807-2812. [PMID: 31016852 PMCID: PMC6900096 DOI: 10.1002/cbic.201900134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Indexed: 11/21/2022]
Abstract
An unsolved mystery in biology concerns the link between enzyme catalysis and protein motions. Comparison between isotopically labelled "heavy" dihydrofolate reductases and their natural-abundance counterparts has suggested that the coupling of protein motions to the chemistry of the catalysed reaction is minimised in the case of hydride transfer. In alcohol dehydrogenases, unnatural, bulky substrates that induce additional electrostatic rearrangements of the active site enhance coupled motions. This finding could provide a new route to engineering enzymes with altered substrate specificity, because amino acid residues responsible for dynamic coupling with a given substrate present as hotspots for mutagenesis. Detailed understanding of the biophysics of enzyme catalysis based on insights gained from analysis of "heavy" enzymes might eventually allow routine engineering of enzymes to catalyse reactions of choice.
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Affiliation(s)
- Alan F. Scott
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Louis Y.‐P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Iñaki Tuñón
- Departament de Química FísicaUniversitat de Valencia46100BurjassotSpain
| | - Vicent Moliner
- Department of Physical and Analytical ChemistryUniversitat Jaume IAvenida de Vicent Sos Baynat, s/n12071CastellonSpain
| | - Rudolf K. Allemann
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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30
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Hanževački M, Banhatti RD, Čondić-Jurkić K, Smith AS, Smith DM. Exploring Reactive Conformations of Coenzyme A during Binding and Unbinding to Pyruvate Formate-Lyase. J Phys Chem A 2019; 123:9345-9356. [PMID: 31580071 DOI: 10.1021/acs.jpca.9b06913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme that converts pyruvate and coenzyme A (CoA) into formate and acetyl-CoA in two half-reactions. Recently, we showed that the acetylation of the PFL active site in the first half-reaction induces subtle conformational changes, leading to the opening of a potential channel for CoA entry. Entry of CoA into the active site is crucial for the second half-reaction, involving the acetyl transfer to CoA, and the completion of the catalytic cycle. Using steered molecular dynamics (SMD) simulations, performed on acetylated and nonacetylated monomeric PFL model systems, we first of all investigate the possible entry/exit pathways of CoA with respect to the active site through the previously identified channel. We then perform umbrella sampling simulations on multiple snapshots from SMD trajectories as well as unrestrained molecular dynamics simulations starting from the final structures obtained from entry SMD, with a view to identifying possible bound states of CoA in the near vicinity of the active site. Detailed study of the unrestrained dissociation processes reveals the presence of stable and reactive bound states of CoA close to the active site, one of which is in an ideal position for triggering the second half-reaction. Examination of the spatial distributions associated with the reactive bound states allows us to discuss the free energy barriers. Umbrella sampling, performed on snapshots from unrestrained dynamics confirms the above findings. The significance of the results for the catalysis are discussed for both acetylated and nonacetylated systems.
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Affiliation(s)
- Marko Hanževački
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,PULS Group, Department of Physics, Interdisciplinary Center for Nanostructured Films , Friedrich-Alexander-Universität Erlangen-Nürnberg , Cauerstraße 3 , 91058 Erlangen , Germany
| | - Radha Dilip Banhatti
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Karmen Čondić-Jurkić
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Ana-Sunčana Smith
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,PULS Group, Department of Physics, Interdisciplinary Center for Nanostructured Films , Friedrich-Alexander-Universität Erlangen-Nürnberg , Cauerstraße 3 , 91058 Erlangen , Germany
| | - David M Smith
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
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31
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Cui DS, Lipchock JM, Brookner D, Loria JP. Uncovering the Molecular Interactions in the Catalytic Loop That Modulate the Conformational Dynamics in Protein Tyrosine Phosphatase 1B. J Am Chem Soc 2019; 141:12634-12647. [PMID: 31339043 DOI: 10.1021/jacs.9b04470] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Active-site loops are integral to the function of numerous enzymes. They enable substrate and product binding and release, sequester reaction intermediates, and recruit catalytic groups. Here, we examine the catalytic loop in the enzyme protein tyrosine phosphatase 1B (PTP1B). PTP1B has a mobile so-called WPD loop (named for its three N-terminal residues) that initiates the dephosphorylation of phosphor-tyrosine substrates upon loop closure. We have combined X-ray crystallography, solution NMR, and pre-steady-state kinetics experiments on wild-type and five WPD loop mutants to identify the relationships between the loop structure, dynamics, and function. The motions of the WPD loop are modulated by the formation of weak molecular interactions, where perturbations of these interactions modulate the conformational equilibrium landscape. The point mutants in the WPD loop alter the loop equilibrium position from a predominantly open state (P185A) to 50:50 (F182A), 35:65 (P188A), and predominantly closed states (T177A and P188A). Surprisingly, there is no correlation between the observed catalytic rates in the loop mutants and changes to the WPD loop equilibrium position. Rather, we observe a strong correlation between the rate of dephosphorylation of the phosphocysteine enzyme intermediate and uniform millisecond motions, not only within the loop but also in the adjacent α-helical domain of PTP1B. Thus, the control of loop motion and thereby catalytic activity is dispersed and resides within not only the loop sequence but also the surrounding protein architecture. This has broad implications for the general mechanistic understanding of enzyme reactions and the role that flexible loops play in the catalytic cycle.
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Affiliation(s)
- Danica S Cui
- Department of Chemistry , Yale University , New Haven , Connecticut 06511 , United States
| | - James Michael Lipchock
- Department of Chemistry , Washington College , Chestertpwm , Maryland 21620 , United States
| | - Dennis Brookner
- Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06511 , United States
| | - J Patrick Loria
- Department of Chemistry , Yale University , New Haven , Connecticut 06511 , United States.,Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06511 , United States
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32
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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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33
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Genna V, Marcia M, De Vivo M. A Transient and Flexible Cation-π Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases. J Am Chem Soc 2019; 141:10770-10776. [PMID: 31251587 DOI: 10.1021/jacs.9b03663] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metal-dependent DNA and RNA nucleases are enzymes that cleave nucleic acids with great efficiency and precision. These enzyme-mediated hydrolytic reactions are fundamental for the replication, repair, and storage of genetic information within the cell. Here, extensive classical and quantum-based free-energy molecular simulations show that a cation-π interaction is transiently formed in situ at the metal core of Bacteriophage-λ Exonuclease (Exo-λ), during catalysis. This noncovalent interaction (Lys131-Tyr154) triggers nucleophile activation for nucleotide excision. Then, our simulations also show the oscillatory dynamics and swinging of the newly formed cation-π dyad, whose conformational change may favor proton release from the cationic Lys131 to the bulk solution, thus restoring the precatalytic protonation state in Exo-λ. Altogether, we report on the novel mechanistic character of cation-π interactions for catalysis. Structural and bioinformatic analyses support that flexible orientation and transient formation of mobile cation-π interactions may represent a common catalytic strategy to promote nucleic acid hydrolysis in DNA and RNA nucleases.
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 , Genoa , Italy
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble , 71 Avenue des Martyrs , Grenoble 38042 , France
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 , Genoa , Italy
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34
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Prah A, Frančišković E, Mavri J, Stare J. Electrostatics as the Driving Force Behind the Catalytic Function of the Monoamine Oxidase A Enzyme Confirmed by Quantum Computations. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04045] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Alja Prah
- Theory Department, National Institute of Chemistry, 1001 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Eric Frančišković
- Theory Department, National Institute of Chemistry, 1001 Ljubljana, Slovenia
| | - Janez Mavri
- Theory Department, National Institute of Chemistry, 1001 Ljubljana, Slovenia
| | - Jernej Stare
- Theory Department, National Institute of Chemistry, 1001 Ljubljana, Slovenia
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35
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Uversky VN. Protein intrinsic disorder and structure-function continuum. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:1-17. [DOI: 10.1016/bs.pmbts.2019.05.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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36
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Tuñón I, Williams IH. The transition state and cognate concepts. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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37
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Kulkarni Y, Kamerlin SCL. Computational physical organic chemistry using the empirical valence bond approach. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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Wei WJ, Qian HX, Wang WJ, Liao RZ. Computational Understanding of the Selectivities in Metalloenzymes. Front Chem 2018; 6:638. [PMID: 30622942 PMCID: PMC6308299 DOI: 10.3389/fchem.2018.00638] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/07/2018] [Indexed: 01/26/2023] Open
Abstract
Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.
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Affiliation(s)
| | | | | | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, China
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39
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
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40
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Roca M, Ruiz-Pernía JJ, Castillo R, Oliva M, Moliner V. Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase. Phys Chem Chem Phys 2018; 20:25722-25737. [PMID: 30280169 DOI: 10.1039/c8cp04244f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial topics. In the present work, the hydride transfer step in the formate dehydrogenase (FDH EC 1.2.1.2) enzyme is studied by means of molecular dynamic (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials in order to explore any correlation between dynamics, tunnelling effects and the rate constant. The temperature dependence of the kinetic isotope effects (KIEs), which is one of the few tests that can be studied by experiments and simulations to shed light on this debate, has been computed and the results have been compared with previous experimental data. The classical mechanical free energy barrier and the number of recrossing trajectories seem to be temperature-independent while the quantum vibrational corrections and the tunnelling effects are slightly temperature-dependent over the interval of 5-45 °C. The computed primary KIEs are in very good agreement with previous experimental data, being almost temperature-independent within the standard deviations. The modest dependence on the temperature is due to just the quantum vibrational correction contribution. These results, together with the analysis of the evolution of the collective variables such as the electrostatic potential or the electric field created by the protein on the key atoms involved in the reaction, confirm that while the protein is well preorganised, some changes take place along the reaction that favour the hydride transfer and the product release. Coordinates defining these movements are, in fact, part of the real reaction coordinate.
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Affiliation(s)
- Maite Roca
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | | | - Raquel Castillo
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Mónica Oliva
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
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41
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Uversky VN. Flexibility of the "rigid" classics or rugged bottom of the folding funnels of myoglobin, lysozyme, RNase A, chymotrypsin, cytochrome c, and carboxypeptidase A1. INTRINSICALLY DISORDERED PROTEINS 2018; 5:e1355205. [PMID: 30250772 DOI: 10.1080/21690707.2017.1355205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/08/2017] [Indexed: 10/18/2022]
Abstract
The abilities to crystalize of a globular protein and to solve its crystal structure seem to represent triumph of the lock-and-key model of protein functionality, where the presence of unique 3D structure resembling aperiodic crystal is considered as a prerequisite for a given protein to possess specific biologic activity. The history of protein crystallography has its roots in first crystal structures of myoglobin, lysozyme, RNase A, chymotrypsin, cytochrome c, and carboxypeptidase A1 solved more than 50 y ago. This article briefly considers extensive structural information currently available for these proteins and shows that the bottoms of their folding funnels (i.e., the lowest parts of their potential energy landscapes) are not smoothed but rugged. In other words, these crystallization classics are characterized by significant conformational flexibility and are not rigid (immobile) crystal-like entities.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
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42
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Molecular modeling of conformational dynamics and its role in enzyme evolution. Curr Opin Struct Biol 2018; 52:50-57. [PMID: 30205262 DOI: 10.1016/j.sbi.2018.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
Abstract
With increasing computational power, biomolecular simulations have become an invaluable tool for understanding enzyme mechanisms and the origins of enzyme catalysis. More recently, computational studies have started to focus on understanding how enzyme activity itself evolves, both in terms of enhancing the native or new activities on existing enzyme scaffolds, or completely de novo on previously non-catalytic scaffolds. In this context, both experiment and molecular modeling provided strong evidence for an important role of conformational dynamics in the evolution of enzyme functions. This contribution will present a brief overview of the current state of the art for computationally exploring enzyme conformational dynamics in enzyme evolution, and, using several showcase studies, illustrate the ways molecular modeling can be used to shed light on how enzyme function evolves, at the most fundamental molecular level.
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43
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Riel AMS, Decato DA, Sun J, Massena CJ, Jessop MJ, Berryman OB. The intramolecular hydrogen bonded-halogen bond: a new strategy for preorganization and enhanced binding. Chem Sci 2018; 9:5828-5836. [PMID: 30079195 PMCID: PMC6050591 DOI: 10.1039/c8sc01973h] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/13/2018] [Indexed: 01/02/2023] Open
Abstract
Natural and synthetic molecules use weak noncovalent forces to preorganize structure and enable remarkable function. Herein, we introduce the intramolecular hydrogen bonded-halogen bond (HB-XB) as a novel method to preorganize halogen bonding (XBing) molecules, while generating a polarization-enhanced XB. Positioning a fluoroaniline between two iodopyridinium XB donors engendered intramolecular hydrogen bonding (HBing) to the electron-rich belt of both XB donors. NMR solution studies established the efficacy of the HB-XB. The receptor with HB-XBs (G2XB) displayed a nearly 9-fold increase in halide binding over control receptors. Gas-phase density functional theory conformational analysis indicated that the amine stabilizes the bidentate conformation. Furthermore, gas-phase interaction energies showed that the bidentate HB-XBs of G2XBme2+ are more than 3.2 kcal mol-1 stronger than the XBs in a control without the intramolecular HB. Additionally, crystal structures confirm that HB-XBs form tighter contacts with I- and Br- and produce receptors that are more planar. Collectively the results establish the intramolecular HB-XB as a tractable strategy to preorganize XB molecules and regulate XB strength.
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Affiliation(s)
| | - Daniel A Decato
- University of Montana , 32 Campus Drive , Missoula , MT , USA .
| | - Jiyu Sun
- University of Montana , 32 Campus Drive , Missoula , MT , USA .
| | - Casey J Massena
- University of Montana , 32 Campus Drive , Missoula , MT , USA .
| | - Morly J Jessop
- University of Montana , 32 Campus Drive , Missoula , MT , USA .
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44
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Petrović D, Risso VA, Kamerlin SCL, Sanchez-Ruiz JM. Conformational dynamics and enzyme evolution. J R Soc Interface 2018; 15:20180330. [PMID: 30021929 PMCID: PMC6073641 DOI: 10.1098/rsif.2018.0330] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022] Open
Abstract
Enzymes are dynamic entities, and their dynamic properties are clearly linked to their biological function. It follows that dynamics ought to play an essential role in enzyme evolution. Indeed, a link between conformational diversity and the emergence of new enzyme functionalities has been recognized for many years. However, it is only recently that state-of-the-art computational and experimental approaches are revealing the crucial molecular details of this link. Specifically, evolutionary trajectories leading to functional optimization for a given host environment or to the emergence of a new function typically involve enriching catalytically competent conformations and/or the freezing out of non-competent conformations of an enzyme. In some cases, these evolutionary changes are achieved through distant mutations that shift the protein ensemble towards productive conformations. Multifunctional intermediates in evolutionary trajectories are probably multi-conformational, i.e. able to switch between different overall conformations, each competent for a given function. Conformational diversity can assist the emergence of a completely new active site through a single mutation by facilitating transition-state binding. We propose that this mechanism may have played a role in the emergence of enzymes at the primordial, progenote stage, where it was plausibly promoted by high environmental temperatures and the possibility of additional phenotypic mutations.
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Affiliation(s)
- Dušan Petrović
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain
| | | | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain
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45
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Jones HBL, Crean RM, Matthews C, Troya AB, Danson MJ, Bull SD, Arcus VL, van der Kamp MW, Pudney CR. Uncovering the Relationship between the Change in Heat Capacity for Enzyme Catalysis and Vibrational Frequency through Isotope Effect Studies. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Vickery L. Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton 3240, New Zealand
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
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Cerqueira NMFSA, Fernandes PA, Ramos MJ. Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation. Chemphyschem 2018; 19:669-689. [DOI: 10.1002/cphc.201700339] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 09/22/2017] [Indexed: 01/12/2023]
Affiliation(s)
- N. M. F. S. A. Cerqueira
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - P. A. Fernandes
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - M. J. Ramos
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
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47
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Klinman JP, Offenbacher AR, Hu S. Origins of Enzyme Catalysis: Experimental Findings for C-H Activation, New Models, and Their Relevance to Prevailing Theoretical Constructs. J Am Chem Soc 2017; 139:18409-18427. [PMID: 29244501 PMCID: PMC5812730 DOI: 10.1021/jacs.7b08418] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C-H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases. The data necessitate a reformulation of the dominant textbook definition of biological catalysis. A multidimensional model emerges that incorporates a range of protein motions that can be parsed into a combination of global stochastic conformational thermal fluctuations and local donor-acceptor distance sampling. These motions are needed to achieve a high degree of precision with regard to internuclear distances, geometries, and charges within the active site. The available model also suggests a physical framework for understanding the empirical enthalpic barrier in enzyme-catalyzed processes. We conclude by addressing the often conflicting interface between computational and experimental chemists, emphasizing the need for computation to predict experimental results in advance of their measurement.
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Affiliation(s)
- Judith P Klinman
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Adam R Offenbacher
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Shenshen Hu
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
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48
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Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P. Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis. J Phys Chem B 2017; 121:10828-10840. [DOI: 10.1021/acs.jpcb.7b09129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vojtěch Mlýnský
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via
Bonomea 265, 34136 Trieste, Italy
| | - Petra Kührová
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
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49
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Li J, Xie Y, Wang R, Fang Z, Fang W, Zhang X, Xiao Y. Mechanism of salt-induced activity enhancement of a marine-derived laccase, Lac15. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:225-236. [PMID: 28875401 DOI: 10.1007/s00249-017-1251-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/07/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
Abstract
Laccase (benzenediol: oxygen oxidoreductases, EC1.10.3.2) is a multi-copper oxidase capable of oxidizing a variety of phenolic and other aromatic organic compounds. The catalytic power of laccase makes it an attractive candidate for potential applications in many areas of industry including biodegradation of organic pollutants and synthesis of novel drugs. Most laccases are vulnerable to high salt and have limited applications. However, some laccases are not only tolerant to but also activated by certain concentrations of salt and thus have great application potential. The mechanisms of salt-induced activity enhancement of laccases are unclear as yet. In this study, we used dynamic light scattering, size exclusion chromatography, analytical ultracentrifugation, intrinsic fluorescence emission, circular dichroism, ultraviolet-visible light absorption, and an enzymatic assay to investigate the potential correlation between the structure and activity of the marine-derived laccase, Lac15, whose activity is promoted by low concentrations of NaCl. The results showed that low concentrations of NaCl exert little influence on the protein structure, which was partially folded in the absence of the salt; moreover, the partially folded rather than the fully folded state seemed to be favorable for enzyme activity, and this partially folded state was distinctive from the so-called 'molten globule' occasionally observed in active enzymes. More data indicated that salt might promote laccase activity through mechanisms involving perturbation of specific local sites rather than a change in global structure. Potential binding sites for chloride ions and their roles in enzyme activity promotion are proposed.
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Affiliation(s)
- Jie Li
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Yanan Xie
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Rui Wang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Wei Fang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Xuecheng Zhang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China. .,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China. .,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China.
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China. .,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China. .,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China.
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50
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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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