51
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Rastogi H, Chowdhury PK. Understanding enzyme behavior in a crowded scenario through modulation in activity, conformation and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140699. [PMID: 34298166 DOI: 10.1016/j.bbapap.2021.140699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 01/25/2023]
Abstract
Macromolecular crowding, inside the physiological interior, modulates the energy landscape of biological macromolecules in multiple ways. Amongst these, enzymes occupy a special place and hence understanding the function of the same in the crowded interior is of utmost importance. In this study, we have investigated the manner in which the multidomain enzyme, AK3L1 (PDB ID: 1ZD8), an isoform of adenylate kinase, has its features affected in presence of commonly used crowders (PEG 8, Dextran 40, Dextran 70, and Ficoll 70). Michaelis Menten plots reveal that the crowders in general enhance the activity of the enzyme, with the Km and Vmax values showing significant variations. Ficoll 70, induced the maximum activity for AK3L1 at 100 g/L, beyond which the activity reduced. Ensemble FRET studies were performed to provide insights into the relative domain (LID and CORE) displacements in presence of the crowders. Solvation studies reveal that the protein matrix surrounding the probe CPM (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin) gets restricted in presence of the crowders, with Ficoll 70 providing the maximum rigidity, the same being linked to the decrease in the activity of the enzyme. Through our multipronged approach, we have observed a distinct correlation between domain displacement, enzyme activity and associated dynamics. Thus, keeping in mind the complex nature of enzyme activity and the surrounding bath of dense soup that the biological entity remains immersed in, indeed more such approaches need to be undertaken to have a better grasp of the "enzymes in the crowd".
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Affiliation(s)
- Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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52
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Ojeda-May P, Mushtaq AU, Rogne P, Verma A, Ovchinnikov V, Grundström C, Dulko-Smith B, Sauer UH, Wolf-Watz M, Nam K. Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions. Biochemistry 2021; 60:2246-2258. [PMID: 34250801 PMCID: PMC8297476 DOI: 10.1021/acs.biochem.1c00221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Enzymes employ a wide range of protein motions to achieve efficient catalysis of
chemical reactions. While the role of collective protein motions in substrate binding,
product release, and regulation of enzymatic activity is generally understood, their
roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations,
enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are
combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the
roles of catalytic residues in catalysis and the conformational change in the enzyme.
This study reveals that the motions in the active site, which occur on a time scale of
picoseconds to nanoseconds, link the catalytic reaction to the slow conformational
dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In
particular, substantial conformational rearrangement occurs in the active site following
the catalytic reaction. This rearrangement not only affects the reaction barrier but
also promotes a more open conformation of the enzyme after the reaction, which then
results in an accelerated opening of the enzyme compared to that of the reactant state.
The results illustrate a linkage between enzymatic catalysis and collective protein
motions, whereby the disparate time scales between the two processes are bridged by a
cascade of intermediate-scale motion of catalytic residues modulating the free energy
landscapes of the catalytic and conformational change processes.
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Affiliation(s)
- Pedro Ojeda-May
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden.,High Performance Computing Centre North (HPC2N), Umeå University, Umeå SE-90187, Sweden
| | | | - Per Rogne
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | - Apoorv Verma
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | | | - Beata Dulko-Smith
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Uwe H Sauer
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | | | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
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53
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Feehan R, Franklin MW, Slusky JSG. Machine learning differentiates enzymatic and non-enzymatic metals in proteins. Nat Commun 2021; 12:3712. [PMID: 34140507 PMCID: PMC8211803 DOI: 10.1038/s41467-021-24070-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/02/2021] [Indexed: 11/09/2022] Open
Abstract
Metalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. Because of the physicochemical similarities between the active sites of metalloenzymes and inactive metal binding sites, it is challenging to differentiate between them. Yet distinguishing these two classes is critical for the identification of both native and designed enzymes. Because of similarities between catalytic and non-catalytic metal binding sites, finding physicochemical features that distinguish these two types of metal sites can indicate aspects that are critical to enzyme function. In this work, we develop the largest structural dataset of enzymatic and non-enzymatic metalloprotein sites to date. We then use a decision-tree ensemble machine learning model to classify metals bound to proteins as enzymatic or non-enzymatic with 92.2% precision and 90.1% recall. Our model scores electrostatic and pocket lining features as more important than pocket volume, despite the fact that volume is the most quantitatively different feature between enzyme and non-enzymatic sites. Finally, we find our model has overall better performance in a side-to-side comparison against other methods that differentiate enzymatic from non-enzymatic sequences. We anticipate that our model's ability to correctly identify which metal sites are responsible for enzymatic activity could enable identification of new enzymatic mechanisms and de novo enzyme design.
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Affiliation(s)
- Ryan Feehan
- Center for Computational Biology, The University of Kansas, Lawrence, KS, USA
| | - Meghan W Franklin
- Center for Computational Biology, The University of Kansas, Lawrence, KS, USA
| | - Joanna S G Slusky
- Center for Computational Biology, The University of Kansas, Lawrence, KS, USA.
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA.
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54
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Mittal N, Ojanguren A, Niederberger M, Lizundia E. Degradation Behavior, Biocompatibility, Electrochemical Performance, and Circularity Potential of Transient Batteries. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004814. [PMID: 34194934 PMCID: PMC8224425 DOI: 10.1002/advs.202004814] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/02/2021] [Indexed: 05/08/2023]
Abstract
Transient technology seeks the development of materials, devices, or systems that undergo controlled degradation processes after a stable operation period, leaving behind harmless residues. To enable externally powered fully transient devices operating for longer periods compared to passive devices, transient batteries are needed. Albeit transient batteries are initially intended for biomedical applications, they represent an effective solution to circumvent the current contaminant leakage into the environment. Transient technology enables a more efficient recycling as it enhances material retrieval rates, limiting both human and environmental exposures to the hazardous pollutants present in conventional batteries. Little efforts are focused to catalog and understand the degradation characteristics of transient batteries. As the energy field is a property-driven science, not only electrochemical performance but also their degradation behavior plays a pivotal role in defining the specific end-use applications. The state-of-the-art transient batteries are critically reviewed with special emphasis on the degradation mechanisms, transiency time, and biocompatibility of the released degradation products. The potential of transient batteries to change the current paradigm that considers batteries as harmful waste is highlighted. Overall, transient batteries are ready for takeoff and hold a promising future to be a frontrunner in the uptake of circular economy concepts.
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Affiliation(s)
- Neeru Mittal
- Laboratory for Multifunctional MaterialsDepartment of MaterialsETH ZürichVladimir‐Prelog‐Weg 5Zürich8093Switzerland
| | - Alazne Ojanguren
- Laboratory for Multifunctional MaterialsDepartment of MaterialsETH ZürichVladimir‐Prelog‐Weg 5Zürich8093Switzerland
| | - Markus Niederberger
- Laboratory for Multifunctional MaterialsDepartment of MaterialsETH ZürichVladimir‐Prelog‐Weg 5Zürich8093Switzerland
| | - Erlantz Lizundia
- Laboratory for Multifunctional MaterialsDepartment of MaterialsETH ZürichVladimir‐Prelog‐Weg 5Zürich8093Switzerland
- Life Cycle Thinking GroupDepartment of Graphic Design and Engineering ProjectsFaculty of Engineering in BilbaoUniversity of the Basque Country (UPV/EHU)Bilbao48013Spain
- BCMaterialsBasque Center for MaterialsApplications and NanostructuresUPV/EHU Science ParkLeioa48940Spain
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55
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Breijyeh Z, Karaman R. Enzyme Models-From Catalysis to Prodrugs. Molecules 2021; 26:molecules26113248. [PMID: 34071328 PMCID: PMC8198240 DOI: 10.3390/molecules26113248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
Enzymes are highly specific biological catalysts that accelerate the rate of chemical reactions within the cell. Our knowledge of how enzymes work remains incomplete. Computational methodologies such as molecular mechanics (MM) and quantum mechanical (QM) methods play an important role in elucidating the detailed mechanisms of enzymatic reactions where experimental research measurements are not possible. Theories invoked by a variety of scientists indicate that enzymes work as structural scaffolds that serve to bring together and orient the reactants so that the reaction can proceed with minimum energy. Enzyme models can be utilized for mimicking enzyme catalysis and the development of novel prodrugs. Prodrugs are used to enhance the pharmacokinetics of drugs; classical prodrug approaches focus on alternating the physicochemical properties, while chemical modern approaches are based on the knowledge gained from the chemistry of enzyme models and correlations between experimental and calculated rate values of intramolecular processes (enzyme models). A large number of prodrugs have been designed and developed to improve the effectiveness and pharmacokinetics of commonly used drugs, such as anti-Parkinson (dopamine), antiviral (acyclovir), antimalarial (atovaquone), anticancer (azanucleosides), antifibrinolytic (tranexamic acid), antihyperlipidemia (statins), vasoconstrictors (phenylephrine), antihypertension (atenolol), antibacterial agents (amoxicillin, cephalexin, and cefuroxime axetil), paracetamol, and guaifenesin. This article describes the works done on enzyme models and the computational methods used to understand enzyme catalysis and to help in the development of efficient prodrugs.
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56
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Coulther TA, Ko J, Ondrechen MJ. Amino acid interactions that facilitate enzyme catalysis. J Chem Phys 2021; 154:195101. [PMID: 34240918 DOI: 10.1063/5.0041156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Interactions in enzymes between catalytic and neighboring amino acids and how these interactions facilitate catalysis are examined. In examples from both natural and designed enzymes, it is shown that increases in catalytic rates may be achieved through elongation of the buffer range of the catalytic residues; such perturbations in the protonation equilibria are, in turn, achieved through enhanced coupling of the protonation equilibria of the active ionizable residues with those of other ionizable residues. The strongest coupling between protonation states for a pair of residues that deprotonate to form an anion (or a pair that accept a proton to form a cation) is achieved when the difference in the intrinsic pKas of the two residues is approximately within 1 pH unit. Thus, catalytic aspartates and glutamates are often coupled to nearby acidic residues. For an anion-forming residue coupled to a cation-forming residue, the elongated buffer range is achieved when the intrinsic pKa of the anion-forming residue is higher than the intrinsic pKa of the (conjugate acid of the) cation-forming residue. Therefore, the high pKa, anion-forming residues tyrosine and cysteine make good coupling partners for catalytic lysine residues. For the anion-cation pairs, the optimum difference in intrinsic pKas is a function of the energy of interaction between the residues. For the energy of interaction ε expressed in units of (ln 10)RT, the optimum difference in intrinsic pKas is within ∼1 pH unit of ε.
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Affiliation(s)
- Timothy A Coulther
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jaeju Ko
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705, USA
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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57
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De la Fuente IM, Martínez L, Carrasco-Pujante J, Fedetz M, López JI, Malaina I. Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior. Front Genet 2021; 12:644615. [PMID: 34093645 PMCID: PMC8176287 DOI: 10.3389/fgene.2021.644615] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Nutrition, CEBAS-CSIC Institute, Murcia, Spain
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
- Basque Center of Applied Mathematics (BCAM), Bilbao, Spain
| | - Jose Carrasco-Pujante
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Maria Fedetz
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada, Spain
| | - José I. López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
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58
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Zhu S, Gao B, Peigneur S, Tytgat J. How a Scorpion Toxin Selectively Captures a Prey Sodium Channel: The Molecular and Evolutionary Basis Uncovered. Mol Biol Evol 2021; 37:3149-3164. [PMID: 32556211 DOI: 10.1093/molbev/msaa152] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The growing resistance of insects to chemical pesticides is reducing the effectiveness of conventional methods for pest control and thus, the development of novel insecticidal agents is imperative. Scorpion toxins specific for insect voltage-gated sodium channels (Navs) have been considered as one of the most promising insecticide alternatives due to their host specificity, rapidly evoked toxicity, biodegradability, and the lack of resistance. However, they have not been developed for uses in agriculture and public health, mainly because of a limited understanding of their molecular and evolutionary basis controlling their phylogenetic selectivity. Here, we show that the traditionally defined insect-selective scorpion toxin LqhIT2 specifically captures a prey Nav through a conserved trapping apparatus comprising a three-residue-formed cavity and a structurally adjacent leucine. The former serves as a detector to recognize and bind a highly exposed channel residue conserved in insects and spiders, two major prey items for scorpions; and the latter subsequently seizes the "moving" voltage sensor via hydrophobic interactions to reduce activation energy for channel opening, demonstrating its action in an enzyme-like manner. Based on the established toxin-channel interaction model in combination with toxicity assay, we enlarged the toxic spectrum of LqhIT2 to spiders and certain other arthropods. Furthermore, we found that genetic background-dependent cavity shapes determine the species selectivity of LqhIT2-related toxins. We expect that the discovery of the trapping apparatus will improve our understanding of the evolution and design principle of Nav-targeted toxins from a diversity of arthropod predators and accelerate their uses in pest control.
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Affiliation(s)
- Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Steve Peigneur
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Jan Tytgat
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Leuven, Belgium
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59
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Zhang Y, Wu Y, Wu Y, Chang Y, Liu M. CRISPR-Cas systems: From gene scissors to programmable biosensors. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116210] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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60
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Galdadas I, Qu S, Oliveira ASF, Olehnovics E, Mack AR, Mojica MF, Agarwal PK, Tooke CL, Gervasio FL, Spencer J, Bonomo RA, Mulholland AJ, Haider S. Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics. eLife 2021; 10:e66567. [PMID: 33755013 PMCID: PMC8060031 DOI: 10.7554/elife.66567] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding allostery in enzymes and tools to identify it offer promising alternative strategies to inhibitor development. Through a combination of equilibrium and nonequilibrium molecular dynamics simulations, we identify allosteric effects and communication pathways in two prototypical class A β-lactamases, TEM-1 and KPC-2, which are important determinants of antibiotic resistance. The nonequilibrium simulations reveal pathways of communication operating over distances of 30 Å or more. Propagation of the signal occurs through cooperative coupling of loop dynamics. Notably, 50% or more of clinically relevant amino acid substitutions map onto the identified signal transduction pathways. This suggests that clinically important variation may affect, or be driven by, differences in allosteric behavior, providing a mechanism by which amino acid substitutions may affect the relationship between spectrum of activity, catalytic turnover, and potential allosteric behavior in this clinically important enzyme family. Simulations of the type presented here will help in identifying and analyzing such differences.
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Affiliation(s)
- Ioannis Galdadas
- University College London, Department of ChemistryLondonUnited Kingdom
| | - Shen Qu
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Ana Sofia F Oliveira
- University of Bristol, Centre for Computational Chemistry, School of ChemistryBristolUnited Kingdom
| | - Edgar Olehnovics
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Andrew R Mack
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Molecular Biology and MicrobiologyClevelandUnited States
| | - Maria F Mojica
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Infectious Diseases, School of MedicineClevelandUnited States
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Catherine L Tooke
- University of Bristol, School of Cellular and Molecular MedicineBristolUnited Kingdom
| | - Francesco Luigi Gervasio
- University College London, Department of ChemistryLondonUnited Kingdom
- University College London, Institute of Structural and Molecular BiologyLondonUnited Kingdom
- University of Geneva, Pharmaceutical SciencesGenevaSwitzerland
| | - James Spencer
- University of Bristol, School of Cellular and Molecular MedicineBristolUnited Kingdom
| | - Robert A Bonomo
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Molecular Biology and MicrobiologyClevelandUnited States
- Case Western Reserve University, Department of Infectious Diseases, School of MedicineClevelandUnited States
- Case Western Reserve University, Department of BiochemistryClevelandUnited States
- Case Western Reserve University, Department of PharmacologyClevelandUnited States
- Case Western Reserve University, Department of Proteomics and BioinformaticsClevelandUnited States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES)ClevelandUnited States
| | - Adrian J Mulholland
- University of Bristol, Centre for Computational Chemistry, School of ChemistryBristolUnited Kingdom
| | - Shozeb Haider
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
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61
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Feehan R, Montezano D, Slusky JSG. Machine learning for enzyme engineering, selection and design. Protein Eng Des Sel 2021; 34:gzab019. [PMID: 34296736 PMCID: PMC8299298 DOI: 10.1093/protein/gzab019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/15/2022] Open
Abstract
Machine learning is a useful computational tool for large and complex tasks such as those in the field of enzyme engineering, selection and design. In this review, we examine enzyme-related applications of machine learning. We start by comparing tools that can identify the function of an enzyme and the site responsible for that function. Then we detail methods for optimizing important experimental properties, such as the enzyme environment and enzyme reactants. We describe recent advances in enzyme systems design and enzyme design itself. Throughout we compare and contrast the data and algorithms used for these tasks to illustrate how the algorithms and data can be best used by future designers.
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Affiliation(s)
- Ryan Feehan
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047-1620, USA
| | - Daniel Montezano
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047-1620, USA
| | - Joanna S G Slusky
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047-1620, USA
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave. Lawrence, KS 66045-7600, USA
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62
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Winkler C, Schrittwieser JH, Kroutil W. Power of Biocatalysis for Organic Synthesis. ACS CENTRAL SCIENCE 2021; 7:55-71. [PMID: 33532569 PMCID: PMC7844857 DOI: 10.1021/acscentsci.0c01496] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 05/05/2023]
Abstract
Biocatalysis, using defined enzymes for organic transformations, has become a common tool in organic synthesis, which is also frequently applied in industry. The generally high activity and outstanding stereo-, regio-, and chemoselectivity observed in many biotransformations are the result of a precise control of the reaction in the active site of the biocatalyst. This control is achieved by exact positioning of the reagents relative to each other in a fine-tuned 3D environment, by specific activating interactions between reagents and the protein, and by subtle movements of the catalyst. Enzyme engineering enables one to adapt the catalyst to the desired reaction and process. A well-filled biocatalytic toolbox is ready to be used for various reactions. Providing nonnatural reagents and conditions and evolving biocatalysts enables one to play with the myriad of options for creating novel transformations and thereby opening new, short pathways to desired target molecules. Combining several biocatalysts in one pot to perform several reactions concurrently increases the efficiency of biocatalysis even further.
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Affiliation(s)
- Christoph
K. Winkler
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße
28, 8010 Graz, Austria
| | - Joerg H. Schrittwieser
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße
28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße
28, 8010 Graz, Austria
- Field
of Excellence BioHealth − University of Graz, 8010 Graz, Austria
- BioTechMed
Graz, 8010 Graz, Austria
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63
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Thompson EJ, Paul A, Iavarone AT, Klinman JP. Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase. J Am Chem Soc 2021; 143:785-797. [PMID: 33395523 DOI: 10.1021/jacs.0c09423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report here on the salient role of protein mobility in accessing conformational landscapes that enable efficient enzyme catalysis. We are focused on yeast enolase, a highly conserved lyase with a TIM barrel domain and catalytic loop, as part of a larger study of the relationship of site selective protein motions to chemical reactivity within superfamilies. Enthalpically hindered variants were developed by replacement of a conserved hydrophobic side chain (Leu 343) with smaller side chains. Leu343 is proximal to the active site base in enolase, and comparative pH rate profiles for the valine and alanine variants indicate a role for side chain hydrophobicity in tuning the pKa of the catalytic base. However, the magnitude of a substrate deuterium isotope effect is almost identical for wild-type (WT) and Leu343Ala, supporting an unchanged rate-determining proton abstraction step. The introduced hydrophobic side chains at position 343 lead to a discontinuous break in both activity and activation energy as a function of side chain volume. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments were performed as a function of time and temperature for WT and Leu343Ala, and provide a spatially resolved map of changes in protein flexibility following mutation. Impacts on protein flexibility are localized to specific networks that arise at the protein-solvent interface and terminate in a loop that has been shown by X-ray crystallography to close over the active site. These interrelated effects are discussed in the context of long-range, solvent-accessible and thermally activated networks that play key roles in tuning the precise distances and interactions among reactants.
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Affiliation(s)
- Emily J Thompson
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Adhayana Paul
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
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Espinoza-Herrera J, Martínez LM, Serna-Saldívar SO, Chuck-Hernández C. Methods for the Modification and Evaluation of Cereal Proteins for the Substitution of Wheat Gluten in Dough Systems. Foods 2021; 10:foods10010118. [PMID: 33429906 PMCID: PMC7826639 DOI: 10.3390/foods10010118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 02/06/2023] Open
Abstract
The substitution of wheat gluten in the food industry is a relevant research area because the only known treatment for celiac disease is abstinence from this protein complex. The use of gluten-free cereals in dough systems has demonstrated that the viscoelastic properties of gluten cannot be achieved without the modification of the protein fraction. The quality of the final product is determined by the ability of the modification to form a matrix similar to that of gluten and to reach this, different methods have been proposed and tested. These procedures can be classified into four main types: chemical, enzymatic, physical, and genetic. This article provides a comprehensive review of the most recent research done in protein modification of cereal and pseudocereals for gluten substitution. The reported effects and methodologies for studying the changes made with each type of modification are described; also, some opportunity areas for future works regarding the study of the effect of protein modifications on gluten-free products are presented.
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65
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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66
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Hjörleifsson JG, Helland R, Magnúsdóttir M, Ásgeirsson B. The high catalytic rate of the cold-active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop. FEBS Open Bio 2020; 11:173-184. [PMID: 33197282 PMCID: PMC7780099 DOI: 10.1002/2211-5463.13041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022] Open
Abstract
The role of surface loops in mediating communication through residue networks is still a relatively poorly understood part in the study of cold adaptation of enzymes, especially in terms of their quaternary interactions. Alkaline phosphatase (AP) from the psychrophilic marine bacterium Vibrio splendidus (VAP) is characterized by an analogous large surface loop in each monomer, referred to as the large loop, that hovers over the active site of the other monomer. It presumably has a role in the high catalytic efficiency of VAP which accompanies its extremely low thermal stability. Here, we designed several different variants of VAP with the aim of removing intersubunit interactions at the dimer interface. Breaking the intersubunit contacts from one residue in particular (Arg336) reduced the temperature stability of the catalytically potent conformation and caused a 40% drop in catalytic rate. The high catalytic rates of enzymes from cold‐adapted organisms are often associated with increased dynamic flexibility. Comparison of the relative B‐factors of the R336L crystal structure to that of the wild‐type confirmed surface flexibility was increased in a loop on the opposite monomer, but not in the large loop. The increase in flexibility resulted in a reduced catalytic rate. The large loop increases the area of the interface between the subunits through its contacts and may facilitate an alternating structural cycle demanded by a half‐of‐sites reaction mechanism through stronger ties, as the dimer oscillates between high affinity (active) or low phosphoryl group affinity (inactive).
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Affiliation(s)
| | - Ronny Helland
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT, The Arctic University of Tromsø, Norway
| | - Manuela Magnúsdóttir
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Bjarni Ásgeirsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
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67
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Carretas-Valdez MI, Moreno-Cordova EN, Ibarra-Hernandez BG, Cinco-Moroyoqui FJ, Castillo-Yañez FJ, Casas-Flores S, Osuna-Amarillas PS, Islas-Osuna MA, Arvizu-Flores AA. Characterization of the trypsin-III from Monterey sardine (Sardinops caeruleus): Insights on the cold-adaptation from the A236N mutant. Int J Biol Macromol 2020; 164:2701-2710. [PMID: 32827617 DOI: 10.1016/j.ijbiomac.2020.08.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
Trypsins (E.C. 3.4.21.4) are digestive enzymes that catalyze the hydrolysis of peptide bonds containing arginine and lysine residues. Some trypsins from fish species are active at temperatures just above freezing, and for that are called cold-adapted enzymes, having many biotechnological applications. In this work, we characterized a recombinant trypsin-III from Monterey sardine (Sardinops caeruleus) and studied the role of a single residue on its cold-adapted features. The A236N mutant from sardine trypsin-III showed higher activation energy for the enzyme-catalyzed reaction, it was more active at higher temperatures, and exhibited a higher thermal stability than the wild-type enzyme, suggesting a key role of this residue. The thermodynamic activation parameters revealed an increase in the activation enthalpy for the A236N mutant, suggesting the existence of more intramolecular contacts during the activation step. Molecular models for both enzymes suggest that a hydrogen-bond involving N236 may contact the C-terminal α-helix to the vicinity of the active site, thus affecting the biochemical and thermodynamic properties of the enzyme.
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Affiliation(s)
- Manuel I Carretas-Valdez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Elena N Moreno-Cordova
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Brisa G Ibarra-Hernandez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Cinco-Moroyoqui
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Castillo-Yañez
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, Col. Lomas 4a sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Pablo S Osuna-Amarillas
- Universidad Estatal de Sonora, Carretera Navojoa-Huatabampo km 5, Navojoa, Sonora 85874, Mexico
| | - Maria A Islas-Osuna
- Centro de Investigación en Alimentación y Desarrollo, Laboratorio de Genética y Biología Molecular de Plantas, Carr. Gustavo Enrique Astiazarán Rosas, N0. 46. Col. La Victoria, Hermosillo, Sonora 83304, Mexico.
| | - Aldo A Arvizu-Flores
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico.
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68
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Matienko L, Mickhailovna ME, Ivanovich BV, Nikolaevich GA. AFM Research in Catalysis and Medicine. CURRENT ORGANOCATALYSIS 2020. [DOI: 10.2174/2213337207999200717171645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
In this study, we show that the AFM method not only allows monitoring the
morphological changes in biological structures fixed on the surface due to H-bonds, but also makes it
possible to study the self-organization of metal complexes by simulating the active center of enzymes
due to intermolecular H-bonds into stable nanostructures; the sizes of which are much smaller than the
studied biological objects. The possible role of intermolecular hydrogen bonds in the formation of stable
supramolecular metal complexes, which are effective catalysts for the oxidation of alkyl arenes to
hydroperoxides by molecular oxygen and mimic the selective active sites of enzymes, was first studied
by AFM.
Methods and Results:
The formation of supramolecular structures due to intermolecular hydrogen
bonds and, possibly, other non-covalent interactions, based on homogenous catalysts and models of
active centers enzymes, heteroligand nickel and iron complexes, was proven by AFM-technique. AFM
studies of supramolecular structures were carried out using NSG30 cantilever with a radius of curvature
of 2 nm, in the tapping mode. To form nanostructures on the surface of a hydrophobic, chemically
modified silicon surface as a substrate, the sample was prepared using a spin-coating process from solutions
of the nickel and iron complexes. The composition and the structure of the complex
Ni2(acac)(OAc)3·NMP·2H2O were determined in earlier works using various methods: mass spectrometry,
UV- and IR-spectroscopy, elemental analysis, and polarography. Self-assembly of supramolecular
structures is due to intermolecular interactions with a certain coordination of these interactions, which
may be a consequence of the properties of the components themselves, the participation of hydrogen
bonds and other non-covalent interactions, as well as the balance of the interaction of these components
with the surface. Using AFM, approaches have been developed for fixing on the surface and quantifying
parameters of cells.
Conclusion:
This study summarizes the authors' achievements in using the atomic force microscopy
(AFM) method to study the role of intermolecular hydrogen bonds (and other non-covalent interactions)
and supramolecular structures in the mechanisms of catalysis. The data obtained from AFM
based on nickel and iron complexes, which are effective catalysts and models of active sites of enzymes,
indicate a high probability of the formation of supramolecular structures in real conditions of
catalytic oxidation, and can bring us closer to understanding enzymes activity. With a sensitive AFM
method, it is possible to observe the self-organization of model systems into stable nanostructures due
to H-bonds and possibly other non-covalent interactions, which can be considered as a step towards
modeling the active sites of enzymes. Methodical approaches of atomic force microscopy for the study
of morphological changes of cells have been developed.
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Affiliation(s)
- Ludmila Matienko
- The Federal State Budget Institution of Science N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, 4 Kosygin str., Moscow, 119334, Russian Federation
| | - Mil Elena Mickhailovna
- The Federal State Budget Institution of Science N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, 4 Kosygin str., Moscow, 119334, Russian Federation
| | - Binyukov Vladimir Ivanovich
- The Federal State Budget Institution of Science N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, 4 Kosygin str., Moscow, 119334, Russian Federation
| | - Goloshchapov Alexandr Nikolaevich
- The Federal State Budget Institution of Science N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, 4 Kosygin str., Moscow, 119334, Russian Federation
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Gao S, Thompson EJ, Barrow SL, Zhang W, Iavarone AT, Klinman JP. Hydrogen-Deuterium Exchange within Adenosine Deaminase, a TIM Barrel Hydrolase, Identifies Networks for Thermal Activation of Catalysis. J Am Chem Soc 2020; 142:19936-19949. [PMID: 33181018 DOI: 10.1021/jacs.0c07866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteins are intrinsically flexible macromolecules that undergo internal motions with time scales spanning femtoseconds to milliseconds. These fluctuations are implicated in the optimization of reaction barriers for enzyme catalyzed reactions. Time, temperature, and mutation dependent hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) has been previously employed to identify spatially resolved, catalysis-linked dynamical regions of enzymes. We now extend this technique to pursue the correlation of protein flexibility and chemical reactivity within the diverse and widespread TIM barrel proteins, targeting murine adenosine deaminase (mADA) that catalyzes the irreversible deamination of adenosine to inosine and ammonia. Following a structure-function analysis of rate and activation energy for a series of mutations at a second sphere phenylalanine positioned in proximity to the bound substrate, the catalytically impaired Phe61Ala with an elevated activation energy (Ea = 7.5 kcal/mol) and the wild type (WT) mADA (Ea = 5.0 kcal/mol) were selected for HDX-MS experiments. The rate constants and activation energies of HDX for peptide segments are quantified and used to assess mutation-dependent changes in local and distal motions. Analyses reveal that approximately 50% of the protein sequence of Phe61Ala displays significant changes in the temperature dependence of HDX behaviors, with the dominant change being an increase in protein flexibility. Utilizing Phe61Ile, which displays the same activation energy for kcat as WT, as a control, we were able to further refine the HDX analysis, highlighting the regions of mADA that are altered in a functionally relevant manner. A map is constructed that illustrates the regions of protein that are proposed to be essential for the thermal optimization of active site configurations that dominate reaction barrier crossings in the native enzyme.
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Affiliation(s)
| | | | | | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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70
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Chen Q, Men D, Sun T, Zhang Y, Yuan Q, Hu T, Hu Z, Wu J, Deng Y, Zhang XE, Wen J. Supreme Catalytic Properties of Enzyme Nanoparticles Based on Ferritin Self-Assembly. ACS APPLIED BIO MATERIALS 2020; 3:7158-7167. [DOI: 10.1021/acsabm.0c00961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qingmei Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Tianyu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yan Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Qianqian Yuan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Taidou Hu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Zhangsheng Hu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jun Wu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, China
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71
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Orville AM. Recent results in time resolved serial femtosecond crystallography at XFELs. Curr Opin Struct Biol 2020; 65:193-208. [PMID: 33049498 DOI: 10.1016/j.sbi.2020.08.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022]
Abstract
Time-resolved serial femtosecond crystallography (tr-SFX) methods exploit slurries of crystalline samples that range in size from hundreds of nanometers to a few tens of micrometers, at near-physiological temperature and pressure, to generate atomic resolution models and probe authentic function with the same experiment. 'Dynamic structural biology' is often used to encompass the research philosophy and techniques. Reaction cycles for tr-SFX studies are initiated by photons or ligand addition/mixing strategies, wherein the latter are potentially generalizable across enzymology. Thus, dynamic structural biology often creates stop-motion molecular movies of macromolecular function. In metal-dependent systems, complementary spectroscopic information can also be collected from the same samples and X-ray pulses, which provides even more detailed mechanistic insights. These types of experimental data also complement quantum mechanical and classical dynamics numerical calculations. Correlated structural-functional results will yield more detailed mechanistic insights and will likely translate into better drugs and treatments impacting human health, and better catalysis for clean energy and agriculture.
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Affiliation(s)
- Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom; Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom.
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72
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Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: Looking beyond a single structure. ChemCatChem 2020; 12:4704-4720. [PMID: 33897908 PMCID: PMC8064270 DOI: 10.1002/cctc.202000665] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 12/23/2022]
Abstract
Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.
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Affiliation(s)
- Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078
- Arium BioLabs, 2519 Caspian Drive, Knoxville, Tennessee 37932
| | - David N. Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Khushboo Bafna
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
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73
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Abstract
Enzymology is concerned with the study of enzyme structure, function, regulation and kinetics. It is an interdisciplinary subject that can be treated as an exclusive sphere of exhaustive inquiry within mathematical, physico-chemical and biological sciences. Hence, teaching of enzymology, in general, and enzyme kinetics, in particular, should be undertaken in an interdisciplinary manner for a holistic appreciation of this subject. Further, analogous examples from everyday life should form an integral component of the teaching for an intuitive grasp of the subject matter. Furthermore, simulation-based appreciation of enzyme kinetics should be preferred over simplifying assumptions and approximations of traditional enzyme kinetics teaching. In this Words of Advice, I outline the domain depth of enzymology across the various disciplines and provide initial ideas on how appropriate analogies can provide firm insights into the subject. Further, I demonstrate how an intuitive feel for the subject can help not only in grasping abstract concepts but also extending it in experimental design and subsequent interpretation. Use of simulations in grasping complex concepts is also advocated given the advantages this medium offers over traditional approaches involving images and molecular models. Furthermore, I discuss the merits of incorporating the historical backdrop of major discoveries in enzymological teaching. We, at AstraZeneca, have experimented with this approach with the desired outcome of generating interest in the subject from people practising diverse disciplines.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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74
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Hu QH, Williams MT, Shulgina I, Fossum CJ, Weeks KM, Adams LM, Reinhardt CR, Musier-Forsyth K, Hati S, Bhattacharyya S. Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase. ACS Catal 2020; 10:10229-10242. [PMID: 34295570 DOI: 10.1021/acscatal.0c02381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from "eukaryotic-like" ProRSs by the presence of an editing domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal, highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic Pro-AMP formation by Enterococcus faecalis ProRS. The energetics of the adenylate formation by the wild-type enzyme was computed and contrasted with variants containing active site mutations, as well as a deletion mutant lacking the INS domain. The combined results revealed that two distinct types of dynamics contribute to the enzyme's catalytic power. One set of motions is intrinsic to the INS domain and leads to conformational preorganization that is essential for catalysis. A second type of motion, stemming from the electrostatic reorganization of active site residues, impacts the height and width of the energy profile and has a critical role in fine tuning the substrate orientation to facilitate reactive collisions. Thus, motions in a distal domain can preorganize the active site of an enzyme to optimize catalysis.
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Affiliation(s)
- Quin H. Hu
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Murphi T. Williams
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Irina Shulgina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Carl J. Fossum
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Katelyn M. Weeks
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Lauren M. Adams
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Clorice R. Reinhardt
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
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75
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Zajac J, Anderson H, Adams L, Wangmo D, Suhail S, Almen A, Berns L, Coerber B, Dawson L, Hunger A, Jehn J, Johnson J, Plack N, Strasser S, Williams M, Bhattacharyya S, Hati S. Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase. Protein J 2020; 39:542-553. [PMID: 32681406 DOI: 10.1007/s10930-020-09910-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes play important roles in many biological processes. Amino acid residues in the active site pocket of an enzyme, which are in direct contact with the substrate(s), are generally believed to be critical for substrate recognition and catalysis. Identifying and understanding how these "catalytic" residues help enzymes achieve enormous rate enhancement has been the focus of many structural and biochemical studies over the past several decades. Recent studies have shown that enzymes are intrinsically dynamic and dynamic coupling between distant structural elements is essential for effective catalysis in modular enzymes. Therefore, distal residues are expected to have impact on enzyme function. However, few studies have investigated the role of distal residues on enzymatic catalysis. In the present study, the effects of distal residue mutations on the catalytic function of an aminoacyl-tRNA synthetase, namely, prolyl-tRNA synthase, were investigated. The present study demonstrates that distal residues significantly contribute to catalysis of the modular Escherichia coli prolyl-tRNA synthetase by maintaining intrinsic protein flexibility.
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Affiliation(s)
- Jonathan Zajac
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Heidi Anderson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Lauren Adams
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Dechen Wangmo
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Shanzay Suhail
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Aimee Almen
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Lauren Berns
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Breanna Coerber
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Logan Dawson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Andrea Hunger
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Julia Jehn
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Joseph Johnson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Naomi Plack
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Steven Strasser
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | - Murphi Williams
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA
| | | | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, USA.
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76
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Kato K, Nakayoshi T, Sato M, Kurimoto E, Oda A. Molecular Dynamics Simulations for Three-Dimensional Structures of Orotate Phosphoribosyltransferases Constructed from a Simplified Amino Acid Set. ACS OMEGA 2020; 5:13069-13076. [PMID: 32548492 PMCID: PMC7288596 DOI: 10.1021/acsomega.0c01012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/19/2020] [Indexed: 05/08/2023]
Abstract
Proteins of modern terrestrial organisms are composed of nearly 20 amino acids; however, the amino acid sets of primitive organisms may have contained fewer than 20 amino acids. Furthermore, the full set of 20 amino acids is not required by some proteins to encode their function. Indeed, simplified variants of Escherichia coli (E. coli) orotate phosphoribosyltransferase (OPRTase) constructed by Akanuma et al. and composed of a limited amino acid set exhibit significant catalytic activity for the growth of E. coli. However, its structural details are currently unclear. Here, we predict the structures of simplified variants of OPRTase using molecular dynamics (MD) simulations and evaluate the accuracy of the MD simulations for simplified proteins. The three-dimensional structure of the wild-type was largely maintained in the simplified variants, but differences in the catalyst loop and C-terminal helix were observed. These results are considered sufficient to elucidate the differences in catalytic activity between the wild-type and simplified OPRTase variants. Thus, using MD simulations to make structural predictions appears to be a useful strategy when investigating non-wild-type proteins composed of reduced amino acid sets.
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Affiliation(s)
- Koichi Kato
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Department
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Tomoki Nakayoshi
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Mizuha Sato
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- .
Phone: +81-52-832-1151
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77
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Zhang J, Balsbaugh JL, Gao S, Ahn NG, Klinman JP. Hydrogen deuterium exchange defines catalytically linked regions of protein flexibility in the catechol O-methyltransferase reaction. Proc Natl Acad Sci U S A 2020; 117:10797-10805. [PMID: 32371482 PMCID: PMC7245127 DOI: 10.1073/pnas.1917219117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human catechol O-methyltransferase (COMT) has emerged as a model for understanding enzyme-catalyzed methyl transfer from S-adenosylmethionine (AdoMet) to small-molecule catecholate acceptors. Mutation of a single residue (tyrosine 68) behind the methyl-bearing sulfonium of AdoMet was previously shown to impair COMT activity by interfering with methyl donor-acceptor compaction within the activated ground state of the wild type enzyme [J. Zhang, H. J. Kulik, T. J. Martinez, J. P. Klinman, Proc. Natl. Acad. Sci. U.S.A. 112, 7954-7959 (2015)]. This predicts the involvement of spatially defined protein dynamical effects that further tune the donor/acceptor distance and geometry as well as the electrostatics of the reactants. Here, we present a hydrogen/deuterium exchange (HDX)-mass spectrometric study of wild type and mutant COMT, comparing temperature dependences of HDX against corresponding kinetic and cofactor binding parameters. The data show that the impaired Tyr68Ala mutant displays similar breaks in Arrhenius plots of both kinetic and HDX properties that are absent in the wild type enzyme. The spatial resolution of HDX below a break point of 15-20 °C indicates changes in flexibility across ∼40% of the protein structure that is confined primarily to the periphery of the AdoMet binding site. Above 20 °C, Tyr68Ala behaves more like WT in HDX, but its rate and enthalpic barrier remain significantly altered. The impairment of catalysis by Tyr68Ala can be understood in the context of a mutationally induced alteration in protein motions that becomes manifest along and perpendicular to the primary group transfer coordinate.
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Affiliation(s)
- Jianyu Zhang
- Department of Chemistry, University of California, Berkeley, CA 94720
- The California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Jeremy L Balsbaugh
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309
| | - Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, CA 94720
- The California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309;
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, CA 94720;
- The California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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78
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De Raffele D, Martí S, Moliner V. Understanding the Directed Evolution of De Novo Retro-Aldolases from QM/MM Studies. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Daria De Raffele
- Departament de Química Física i Analítica; Universitat Jaume I., 12071 Castellón, Spain
| | - Sergio Martí
- 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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79
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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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80
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Abstract
In the 1930s, Lars Onsager published his famous 'reciprocal relations' describing free energy conversion processes. Importantly, these relations were derived on the assumption that the fluxes of the processes involved in the conversion were proportional to the forces (free energy gradients) driving them. For chemical reactions, however, this condition holds only for systems operating close to equilibrium-indeed very close; nominally requiring driving forces to be smaller than k B T. Fairly soon thereafter, however, it was quite inexplicably observed that in at least some biological conversions both the reciprocal relations and linear flux-force dependency appeared to be obeyed no matter how far from equilibrium the system was being driven. No successful explanation of how this 'paradoxical' behaviour could occur has emerged and it has remained a mystery. We here argue, however, that this anomalous behaviour is simply a gift of water, of its viscosity in particular; a gift, moreover, without which life almost certainly could not have emerged. And a gift whose appreciation we primarily owe to recent work by Prof. R. Dean Astumian who, as providence has kindly seen to it, was led to the relevant insights by the later work of Onsager himself.
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Affiliation(s)
- E. Branscomb
- Carl R. Woese Institute for Genomic Biology, and Department of Physics, University of Illinois, 3113 IGB MC 195, 128 W. Gregory Dr., Urbana, IL 61801, USA
| | - M. J. Russell
- NASA Astrobiology Institute, Ames Research Center, Mountain View, CA, USA
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81
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Coines J, Raich L, Rovira C. Modeling catalytic reaction mechanisms in glycoside hydrolases. Curr Opin Chem Biol 2019; 53:183-191. [PMID: 31731209 DOI: 10.1016/j.cbpa.2019.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 01/21/2023]
Abstract
Modeling catalysis in carbohydrate-active enzymes is a daunting challenge because of the high flexibility and diversity of both enzymes and carbohydrates. Glycoside hydrolases (GHs) are an illustrative example, where conformational changes and subtle interactions have been shown to be critical for catalysis. GHs have pivotal roles in industry (e.g. biofuel or detergent production) and biomedicine (e.g. targets for cancer and diabetes), and thus, a huge effort is devoted to unveil their molecular mechanisms. Besides experimental techniques, computational methods have served to provide an in-depth understanding of GH mechanisms, capturing complex reaction coordinates and the conformational itineraries that substrates follow during the whole catalytic pathway, providing a framework that ultimately may assist the engineering of these enzymes and the design of new inhibitors.
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Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain
| | - Lluís Raich
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA) Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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82
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Zaragoza JPT, Nguy A, Minnetian N, Deng Z, Iavarone AT, Offenbacher AR, Klinman JP. Detecting and Characterizing the Kinetic Activation of Thermal Networks in Proteins: Thermal Transfer from a Distal, Solvent-Exposed Loop to the Active Site in Soybean Lipoxygenase. J Phys Chem B 2019; 123:8662-8674. [PMID: 31580070 PMCID: PMC6944211 DOI: 10.1021/acs.jpcb.9b07228] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rate-limiting chemical reaction catalyzed by soybean lipoxygenase (SLO) involves quantum mechanical tunneling of a hydrogen atom from substrate to its active site ferric-hydroxide cofactor. SLO has emerged as a prototypical system for linking the thermal activation of a protein scaffold to the efficiency of active site chemistry. Significantly, hydrogen-deuterium exchange-mass spectrometry (HDX-MS) experiments on wild type and mutant forms of SLO have uncovered trends in the enthalpic barriers for HDX within a solvent-exposed loop (positions 317-334) that correlate well with trends in the corresponding enthalpic barriers for kcat. A model for this behavior posits that collisions between water and loop 317-334 initiate thermal activation at the protein surface that is then propagated 15-34 Å inward toward the reactive carbon of substrate in proximity to the iron catalyst. In this study, we have prepared protein samples containing cysteine residues either at the tip of the loop 317-334 (Q322C) or on a control loop, 586-603 (S596C). Chemical modification of cysteines with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (Badan, BD) provides site-specific probes for the measurement of fluorescence relaxation lifetimes and Stokes shift decays as a function of temperature. Computational studies indicate that surface water structure is likely to be largely preserved in each sample. While both loops exhibit temperature-independent fluorescence relaxation lifetimes as do the Stokes shifts for S596C-BD, the activation enthalpy for the nanosecond solvent reorganization at Q322C-BD (Ea(ksolv) = 2.8(0.9) kcal/mol)) approximates the enthalpy of activation for catalytic C-H activation (Ea(kcat) = 2.3(0.4) kcal/mol). This study establishes and validates the methodology for measuring rates of rapid local motions at the protein/solvent interface of SLO. These new findings, when combined with previously published correlations between protein motions and the rate-limiting hydride transfer in a thermophilic alcohol dehydrogenase, provide experimental evidence for thermally induced "protein quakes" as the origin of enthalpic barriers in catalysis.
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Affiliation(s)
- Jan Paulo T. Zaragoza
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Andy Nguy
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Natalie Minnetian
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Zhenyu Deng
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - Judith P. Klinman
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, United States
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83
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Hester KP, Bhattarai K, Jiang H, Agarwal PK, Pope C. Engineering Dynamic Surface Peptide Networks on Butyrylcholinesterase G117H for Enhanced Organophosphosphorus Anticholinesterase Catalysis. Chem Res Toxicol 2019; 32:1801-1810. [PMID: 31411024 DOI: 10.1021/acs.chemrestox.9b00146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The single residue mutation of butyrylcholinesterase (BChEG117H) hydrolyzes a number of organophosphosphorus (OP) anticholinesterases. Whereas other BChE active site/proximal mutations have been investigated, none are sufficiently active to be prophylactically useful. In a fundamentally different computer simulations driven strategy, we identified a surface peptide loop (residues 278-285) exhibiting dynamic motions during catalysis and modified it via residue insertions. We evaluated these loop mutants using computer simulations, substrate kinetics, resistance to inhibition, and enzyme reactivation assays using both the choline ester and OP substrates. A slight but significant increase in reactivation was noted with paraoxon with one of the mutants, and changes in KM and catalytic efficiency were noted in others. Simulations suggested weaker interactions between OP versus choline substrates and the active site of all engineered versions of the enzyme. The results indicate that an improvement of OP anticholinesterase hydrolysis through surface loop engineering may be a more effective strategy in an enzyme with higher intrinsic OP compound hydrolase activity.
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Affiliation(s)
- Kirstin P Hester
- Department of Physiological Sciences , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Krishna Bhattarai
- Department of Entomology and Plant Pathology , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Haobo Jiang
- Department of Entomology and Plant Pathology , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Arium BioLabs , 2519 Caspian Drive , Knoxville , Tennessee 37932 , United States
| | - Carey Pope
- Department of Physiological Sciences , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
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84
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Bessman MJ. A cryptic activity in the Nudix hydrolase superfamily. Protein Sci 2019; 28:1494-1500. [PMID: 31173659 PMCID: PMC6635765 DOI: 10.1002/pro.3666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022]
Abstract
The Nudix hydrolase superfamily is identified by a conserved cassette of 23 amino acids, and it is characterized by its pyrophosphorylytic activity on a wide variety of nucleoside diphosphate derivatives. Of the 13 members of the family in Escherichia coli, only one, Orf180, has not been identified with a substrate, although a host of nucleoside diphosphate compounds has been tested. Several reports have noted a strong similarity in the three-dimensional structure of the unrelated enzyme, isopentenyl diphosphate isomerase (IDI) to the Nudix structure, and the report that a Nudix enzyme was involved in the synthesis of geraniol, a product of the two substrates of IDI, prompted an investigation of whether the IDI substrates, isopentenyl diphosphate (IPP), and dimethylallyl diphosphate (DAPP) could be substrates of Orf180. This article demonstrates that Orf180 does have a very low activity on IPP, DAPP, and geranyl pyrophosphate (GPP). However, several of the other Nudix enzymes with established nucleoside diphosphate substrates hydrolyze these compounds at substantial rates. In fact, some Nudix hydrolases have higher activities on IPP, DAPP, and GPP than on their signature nucleoside diphosphate derivatives.
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Affiliation(s)
- Maurice J. Bessman
- Department of BiologyJohns Hopkins UniversityBaltimoreMaryland21218‐2684
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85
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Al-Ayoubi SR, Schummel PH, Cisse A, Seydel T, Peters J, Winter R. Osmolytes modify protein dynamics and function of tetrameric lactate dehydrogenase upon pressurization. Phys Chem Chem Phys 2019; 21:12806-12817. [PMID: 31165827 DOI: 10.1039/c9cp02310k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present a study of the combined effects of natural cosolvents (TMAO, glycine, urea) and pressure on the activity of the tetrameric enzyme lactate dehydrogenase (LDH). To this end, high-pressure stopped-flow methodology in concert with fast UV/Vis spectroscopic detection of product formation was applied. To reveal possible pressure effects on the stability and dynamics of the enzyme, FTIR spectroscopic and neutron scattering measurements were carried out. In neat buffer solution, the catalytic turnover number of the enzyme, kcat, increases up to 1000 bar, the pressure range where dissociation of the tetrameric species to dimers sets in. Accordingly, we obtain a negative activation volume, ΔV# = -45.3 mL mol-1. Further, the enzyme substrate complex has a larger volume compared to the enzyme and substrate in the unbound state. The neutron scattering data show that changes in the fast internal dynamics of the enzyme are not responsible for the increase of kcat upon compression. Whereas the magnitude of kcat is similar in the presence of the osmolytes, the pressure of deactivation is modulated by the addition of cosolvents. TMAO and glycine increase the pressure of deactivation, and in accordance with the observed stabilizing effect both cosolvents exhibit against denaturation and/or dissociation of proteins. While urea does not markedly affect the magnitude of the Michaelis constant, KM, both 1 M TMAO and 1 M glycine exhibit smaller KM values of about 0.07 mM and 0.05 mM below about 1 kbar. Such positive effect on the substrate affinity could be rationalized by the effect the two cosolutes impose on the thermodynamic activities of the reactants, which reflect changes in water-mediated intermolecular interactions. Our data show that the intracellular milieu, i.e., the solution conditions that have evolved, may be sufficient to maintain enzymatic activity under extreme environmental conditions, including the whole pressure range encountered on Earth.
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Affiliation(s)
- Samy R Al-Ayoubi
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
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86
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Effects of Random Mutagenesis and In Vivo Selection on the Specificity and Stability of a Thermozyme. Catalysts 2019. [DOI: 10.3390/catal9050440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Factors that give enzymes stability, activity, and substrate recognition result from the combination of few weak molecular interactions, which can be difficult to study through rational protein engineering approaches. We used irrational random mutagenesis and in vivo selection to test if a β-glycosidase from the thermoacidophile Saccharolobus solfataricus (Ssβ-gly) could complement an Escherichia coli strain unable to grow on lactose. The triple mutant of Ssβ-gly (S26L, P171L, and A235V) was more active than the wild type at 85 °C, inactivated at this temperature almost 300-fold quicker, and showed a 2-fold higher kcat on galactosides. The three mutations, which were far from the active site, were analyzed to test their effect at the structural level. Improved activity on galactosides was induced by the mutations. The S26L and P171L mutations destabilized the enzyme through the removal of a hydrogen bond and increased flexibility of the peptide backbone, respectively. However, the flexibility added by S26L mutation improved the activity at T > 60 °C. This study shows that random mutagenesis and biological selection allowed the identification of residues that are critical in determining thermal activity, stability, and substrate recognition.
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87
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Vidal C, Tomás-Gamasa M, Gutiérrez-González A, Mascareñas JL. Ruthenium-Catalyzed Redox Isomerizations inside Living Cells. J Am Chem Soc 2019; 141:5125-5129. [PMID: 30892889 PMCID: PMC6497367 DOI: 10.1021/jacs.9b00837] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 01/22/2023]
Abstract
Tailored ruthenium(IV) complexes can catalyze the isomerization of allylic alcohols into saturated carbonyl derivatives under physiologically relevant conditions, and even inside living mammalian cells. The reaction, which involves ruthenium-hydride intermediates, is bioorthogonal and biocompatible, and can be used for the "in cellulo" generation of fluorescent and bioactive probes. Overall, our research reveals a novel metal-based tool for cellular intervention, and comes to further demonstrate the compatibility of organometallic mechanisms with the complex environment of cells.
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Affiliation(s)
| | | | - Alejandro Gutiérrez-González
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José L. Mascareñas
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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88
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Abstract
![]()
The enormous rate accelerations observed
for many enzyme catalysts
are due to strong stabilizing interactions between the protein and
reaction transition state. The defining property of these catalysts
is their specificity for binding the transition state with a much
higher affinity than substrate. Experimental results are presented
which show that the phosphodianion-binding energy of phosphate monoester
substrates is used to drive conversion of their protein catalysts
from flexible and entropically rich ground states to stiff and catalytically
active Michaelis complexes. These results are generalized to other
enzyme-catalyzed reactions. The existence of many enzymes in flexible,
entropically rich, and inactive ground states provides a mechanism
for utilization of ligand-binding energy to mold these catalysts into
stiff and active forms. This reduces the substrate-binding energy
expressed at the Michaelis complex, while enabling the full and specific
expression of large transition-state binding energies. Evidence is
presented that the complexity of enzyme conformational changes increases
with increases in the enzymatic rate acceleration. The requirement
that a large fraction of the total substrate-binding energy be utilized
to drive conformational changes of floppy enzymes is proposed to favor
the selection and evolution of protein folds with multiple flexible
unstructured loops, such as the TIM-barrel fold. The effect of protein
motions on the kinetic parameters for enzymes that undergo ligand-driven
conformational changes is considered. The results of computational
studies to model the complex ligand-driven conformational change in
catalysis by triosephosphate isomerase are presented.
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Affiliation(s)
- John P Richard
- Department of Chemistry , SUNY, University at Buffalo , Buffalo , New York 14260-3000 , United States
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