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Liebau J, Laatsch BF, Rusnak J, Gunderson K, Finke B, Bargender K, Narkiewicz-Jodko A, Weeks K, Williams MT, Shulgina I, Musier-Forsyth K, Bhattacharyya S, Hati S. Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase Via Crowding and Confinement Effects. Biochemistry 2024; 63:1621-1635. [PMID: 38607680 DOI: 10.1021/acs.biochem.3c00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular environments. A recent study with PEG crowders revealed decreased catalytic activity of Escherichia coli prolyl-tRNA synthetase (Ec ProRS), where the smaller molecular weight PEGs had the maximum impact. The molecular mechanism of the crowding effects of PEGs is not clearly understood. PEG may impact protein conformation and dynamics, thus its function. In the present study, the effects of PEG molecules of various molecular weights and concentrations on the conformation and dynamics of Ec ProRS were investigated using a combined experimental and computational approach including intrinsic tryptophan fluorescence spectroscopy, atomic force microscopy, and atomistic molecular dynamic simulations. Results of the present study suggest that lower molecular weight PEGs in the dilute regime have modest effects on the conformational dynamics of Ec ProRS but impact the catalytic function primarily via the excluded volume effect; they form large clusters blocking the active site pocket. In contrast, the larger molecular weight PEGs in dilute to semidilute regimes have a significant impact on the protein's conformational dynamics; they wrap on the protein surface through noncovalent interactions. Thus, lower-molecular-weight PEG molecules impact protein dynamics and function via crowding effects, whereas larger PEGs induce confinement effects. These results have implications for the development of inhibitors for protein targets in a crowded cellular environment.
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Affiliation(s)
- Jessica Liebau
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Bethany F Laatsch
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Joshua Rusnak
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Keegan Gunderson
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Brianna Finke
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Kassandra Bargender
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Alex Narkiewicz-Jodko
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Katelyn Weeks
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Murphi T Williams
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Irina Shulgina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
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2
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Li N, Ma J, Fu H, Yang Z, Xu C, Li H, Zhao Y, Zhao Y, Chen S, Gou L, Zhang X, Zhang S, Li M, Hou X, Zhang L, Lu Y. Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401150. [PMID: 38582512 DOI: 10.1002/advs.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Indexed: 04/08/2024]
Abstract
The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.
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Affiliation(s)
- Na Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hang Fu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325011, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Haihong Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Ximiao Hou
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
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3
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Singh A, Gupta M, Rastogi H, Khare K, Chowdhury PK. Deeper Insights into Mixed Crowding through Enzyme Activity, Dynamics, and Crowder Diffusion. J Phys Chem B 2024; 128:5293-5309. [PMID: 38808573 DOI: 10.1021/acs.jpcb.4c00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Given the fact that the cellular interior is crowded by many different kinds of macromolecules, it is important that in vitro studies be carried out in the presence of mixed crowder systems. In this regard, we have used binary crowders formed by the combination of some of the commonly used crowding agents, namely, Ficoll 70, Dextran 70, Dextran 40, and PEG 8000 (PEG 8), to study how these affect enzyme activity, dynamics, and crowder diffusion. The enzyme chosen is AK3L1, an isoform of adenylate kinase. To investigate its dynamics, we have carried out three single point mutations (A74C, A132C, and A209C) with the cysteine residues being labeled with a coumarin-based solvatochromic probe [CPM: (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin)]. Both enzyme activity and dynamics decreased in the binary mixtures as compared with the sum of the individual crowders, suggesting a reduction in excluded volume (in the mixture). To gain deeper insights into the binary mixtures, fluorescence correlation spectroscopy studies were carried out using fluorescein isothiocyanate-labeled Dextran 70 and tetramethylrhodamine-labeled AK3L1 as the diffusion probes. Diffusion in binary mixtures was observed to be much more constrained (relative to the sum of the individual crowders) for the labeled enzyme as compared to the labeled crowder showing different environments being faced by the two species. This was further confirmed during imaging of the phase-separated droplets formed in the binary mixtures having PEG as one of the crowding agents. The interior of these droplets was found to be rich in crowders and densely packed, as shown by confocal and digital holographic microscopy images, with the enzymes predominantly residing outside these droplets, that is, in the relatively less crowded regions. Taken together, our data provide important insights into various aspects of the simplest form of mixed crowding, that is, composed of just two components, and also hint at the enhanced complexity that the cellular interior presents toward having a detailed and comprehensive understanding of the same.
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Affiliation(s)
- Arvind Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Kedar Khare
- Optics and Photonics Centre, 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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4
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Quaye JA, Wood KE, Snelgrove C, Ouedraogo D, Gadda G. An active site mutation induces oxygen reactivity in D-arginine dehydrogenase: A case of superoxide diverting protons. J Biol Chem 2024; 300:107381. [PMID: 38762175 PMCID: PMC11193025 DOI: 10.1016/j.jbc.2024.107381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024] Open
Abstract
Enzymes are potent catalysts that increase biochemical reaction rates by several orders of magnitude. Flavoproteins are a class of enzymes whose classification relies on their ability to react with molecular oxygen (O2) during catalysis using ionizable active site residues. Pseudomonas aeruginosa D-arginine dehydrogenase (PaDADH) is a flavoprotein that oxidizes D-arginine for P. aeruginosa survival and biofilm formation. The crystal structure of PaDADH reveals the interaction of the glutamate 246 (E246) side chain with the substrate and at least three other active site residues, establishing a hydrogen bond network in the active site. Additionally, E246 likely ionizes to facilitate substrate binding during PaDADH catalysis. This study aimed to investigate how replacing the E246 residue with leucine affects PaDADH catalysis and its ability to react with O2 using steady-state kinetics coupled with pH profile studies. The data reveal a gain of O2 reactivity in the E246L variant, resulting in a reduced flavin semiquinone species and superoxide (O2•-) during substrate oxidation. The O2•- reacts with active site protons, resulting in an observed nonstoichiometric slope of 1.5 in the enzyme's log (kcat/Km) pH profile with D-arginine. Adding superoxide dismutase results in an observed correction of the slope to 1.0. This study demonstrates how O2•- can alter the slopes of limbs in the pH profiles of flavin-dependent enzymes and serves as a model for correcting nonstoichiometric slopes in elucidating reaction mechanisms of flavoproteins.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Kendall E Wood
- Biology Department, Morehouse College, Atlanta, Georgia, USA
| | - Claire Snelgrove
- The Gwinnett School of Mathematics, Science, and Technology, Lawrenceville, Georgia, USA
| | - Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Department of Biology, Georgia State University, Atlanta, Georgia, USA; Department of the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
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5
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Coricello A, Nardone AJ, Lupia A, Gratteri C, Vos M, Chaptal V, Alcaro S, Zhu W, Takagi Y, Richards NGJ. Cryo-EM and Molecular Dynamics Simulations Reveal Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.16.541009. [PMID: 37292727 PMCID: PMC10245805 DOI: 10.1101/2023.05.16.541009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
How motions in enzymes might be linked to catalytic function is of considerable general interest. Recent advances in X-ray crystallography and cryogenic electron microscopy offer the promise of elucidating functionally relevant motions in proteins that are not easily amenable to study by other biophysical methods. Here we use 3D variability analysis (3DVA) on cryo-EM maps for wild type (WT) human asparagine synthetase (ASNS) and the R142I ASNS variant to identify conformational changes in the Arg-142 side chain, which mediates the formation of a catalytically relevant intramolecular tunnel. Our 3DVA results for WT ASNS are consistent with independent molecular dynamics (MD) simulations on a model generated from the X-ray structure of human ASNS. Moreover, MD simulations of computational models for the ASNS/β-aspartyl-AMP/MgPPi and R142I/β-aspartyl-AMP/MgPPi ternary complexes, suggest that the structural integrity of the tunnel is impaired in the R142I variant when β-aspartyl-AMP is present in the synthetase active site. The kinetic properties of the R142I ASNS variant support the proposed function of Arg-142. These studies illustrate the power of cryo-EM to identify localized motions and dissect the conformational landscape of large proteins. When combined with MD simulations, 3DVA is a powerful approach to understanding how conformational dynamics might regulate function in multi-domain enzymes possessing multiple active sites.
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Affiliation(s)
- Adriana Coricello
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Present address: Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - Alanya J Nardone
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Antonio Lupia
- Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Present address: Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, 09042 Cagliari, Italy
| | - Carmen Gratteri
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Matthijn Vos
- NanoImaging Core Facility, Centre de Resources et Recherches Technologiques, Institut Pasteur, 75015 Paris, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, 69367 Lyon, France
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Wen Zhu
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Yuichiro Takagi
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
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6
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Ray D, Das S, Raucci U. Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations. J Chem Inf Model 2024; 64:3953-3958. [PMID: 38607669 DOI: 10.1021/acs.jcim.4c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
The rate constants of enzyme-catalyzed reactions (kcat) are often approximated from the barrier height of the reactive step. We introduce an enhanced sampling QM/MM approach that directly calculates the kinetics of enzymatic reactions, without introducing the transition-state theory assumptions, and takes into account the dynamical equilibrium between the reactive and non-reactive conformations of the enzyme/substrate complex. Our computed kcat values are in order-of-magnitude agreement with the experimental data for two representative enzymatic reactions.
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Affiliation(s)
- Dhiman Ray
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
| | - Sudip Das
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
| | - Umberto Raucci
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
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7
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Sridhar S, Kiema T, Schmitz W, Widersten M, Wierenga RK. Structural enzymology studies with the substrate 3S-hydroxybutanoyl-CoA: bifunctional MFE1 is a less efficient dehydrogenase than monofunctional HAD. FEBS Open Bio 2024; 14:655-674. [PMID: 38458818 PMCID: PMC10988713 DOI: 10.1002/2211-5463.13786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/08/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
Multifunctional enzyme, type-1 (MFE1) catalyzes the second and third step of the β-oxidation cycle, being, respectively, the 2E-enoyl-CoA hydratase (ECH) reaction (N-terminal part, crotonase fold) and the NAD+-dependent, 3S-hydroxyacyl-CoA dehydrogenase (HAD) reaction (C-terminal part, HAD fold). Structural enzymological properties of rat MFE1 (RnMFE1) as well as of two of its variants, namely the E123A variant (a glutamate of the ECH active site is mutated into alanine) and the BCDE variant (without domain A of the ECH part), were studied, using as substrate 3S-hydroxybutanoyl-CoA. Protein crystallographic binding studies show the hydrogen bond interactions of 3S-hydroxybutanoyl-CoA as well as of its 3-keto, oxidized form, acetoacetyl-CoA, with the catalytic glutamates in the ECH active site. Pre-steady state binding experiments with NAD+ and NADH show that the kon and koff rate constants of the HAD active site of monomeric RnMFE1 and the homologous human, dimeric 3S-hydroxyacyl-CoA dehydrogenase (HsHAD) for NAD+ and NADH are very similar, being the same as those observed for the E123A and BCDE variants. However, steady state and pre-steady state kinetic data concerning the HAD-catalyzed dehydrogenation reaction of the substrate 3S-hydroxybutanoyl-CoA show that, respectively, the kcat and kchem rate constants for conversion into acetoacetyl-CoA by RnMFE1 (and its two variants) are about 10 fold lower as when catalyzed by HsHAD. The dynamical properties of dehydrogenases are known to be important for their catalytic efficiency, and it is discussed that the greater complexity of the RnMFE1 fold correlates with the observation that RnMFE1 is a slower dehydrogenase than HsHAD.
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Affiliation(s)
- Shruthi Sridhar
- Faculty of Biochemistry and Molecular MedicineUniversity of OuluFinland
| | | | - Werner Schmitz
- Theodor Boveri Institute of Biosciences (Biocenter)University of WürzburgGermany
| | | | - Rik K. Wierenga
- Faculty of Biochemistry and Molecular MedicineUniversity of OuluFinland
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8
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McFarlane NR, Harvey JN. Exploration of biochemical reactivity with a QM/MM growing string method. Phys Chem Chem Phys 2024; 26:5999-6007. [PMID: 38293892 DOI: 10.1039/d3cp05772k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
In this work, we have implemented the single-ended growing string method using a hybrid internal/Cartesian coordinate scheme within our in-house QM/MM package, QoMMMa, representing the first implementation of the growing string method in the QM/MM framework. The goal of the implementation was to facilitate generation of QM/MM reaction pathways with minimal user input, and also to improve the quality of the pathways generated as compared to the widely used adiabatic mapping approach. We have validated the algorithm against a reaction which has been studied extensively in previous computational investigations - the Claisen rearrangement catalysed by chorismate mutase. The nature of the transition state and the height of the barrier was predicted well using our algorithm, where more than 88% of the pathways generated were deemed to be of production quality. Directly compared to using adiabatic mapping, we found that while our QM/MM single-ended growing string method is slightly less efficient, it readily produces reaction pathways with fewer discontinuites and thus minimises the need for involved remapping of unsatisfactory energy profiles.
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Affiliation(s)
- Neil R McFarlane
- Department of Chemistry, KU Leuven, B-3001 Leuven, Celestijnenlaan 200f, 2404, Belgium.
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001 Leuven, Celestijnenlaan 200f, 2404, Belgium.
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9
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Juretić D, Bonačić Lošić Ž. Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation. ENTROPY (BASEL, SWITZERLAND) 2024; 26:151. [PMID: 38392406 PMCID: PMC10888251 DOI: 10.3390/e26020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.
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Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, Šetalište Ivana Meštrovića 45, 21000 Split, Croatia
- Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
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10
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Ostermeier L, Ascani M, Gajardo-Parra N, Sadowski G, Held C, Winter R. Leveraging liquid-liquid phase separation and volume modulation to regulate the enzymatic activity of formate dehydrogenase. Biophys Chem 2024; 304:107128. [PMID: 37922819 DOI: 10.1016/j.bpc.2023.107128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
Engineering of reaction media is an exciting alternative for modulating kinetic properties of biocatalytic reactions. We addressed the combined effect of an aqueous two-phase system (ATPS) and high hydrostatic pressure on the kinetics of the Candida boidinii formate dehydrogenase-catalyzed oxidation of formate to CO2. Pressurization was found to lead to an increase of the binding affinity (decrease of KM, respectively) and a decrease of the turnover number, kcat. The experimental approach was supported using thermodynamic modeling with the electrolyte Perturbed-Chain Statistical Associating Fluid Theory (ePC-SAFT) equation of state to predict the liquid-liquid phase separation and the molecular crowding effect of the ATPS on the kinetic properties. The ePC-SAFT was able to quantitatively predict the KM-values of the substrate in both phases at 1 bar as well as up to a pressure of 1000 bar. The framework presented enables significant advances in bioprocess engineering, including the design of processes with significantly fewer experiments and trial-and-error approaches.
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Affiliation(s)
- Lena Ostermeier
- Department of Chemistry and Chemical, Biology, Physical Chemistry I, TU Dortmund University, 44227 Dortmund, Germany
| | - Moreno Ascani
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Nicolás Gajardo-Parra
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Gabriele Sadowski
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Christoph Held
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
| | - Roland Winter
- Department of Chemistry and Chemical, Biology, Physical Chemistry I, TU Dortmund University, 44227 Dortmund, Germany.
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11
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Quaye J, Ouedraogo D, Gadda G. Targeted Mutation of a Non-catalytic Gating Residue Increases the Rate of Pseudomonas aeruginosa d-Arginine Dehydrogenase Catalytic Turnover. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71. [PMID: 37933126 PMCID: PMC10655190 DOI: 10.1021/acs.jafc.3c05328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
Commercial food and l-amino acid industries rely on bioengineered d-amino acid oxidizing enzymes to detect and remove d-amino acid contaminants. However, the bioengineering of enzymes to generate faster biological catalysts has proven difficult as a result of the failure to target specific kinetic steps that limit enzyme turnover, kcat, and the poor understanding of loop dynamics critical for catalysis. Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) oxidizes most d-amino acids and is a good candidate for application in the l-amino acid and food industries. The side chain of the loop L2 E246 residue located at the entrance of the PaDADH active site pocket potentially favors the closed active site conformation and secures the substrate upon binding. This study used site-directed mutagenesis, steady-state, and rapid reaction kinetics to generate the glutamine, glycine, and leucine variants and investigate whether increasing the rate of product release could translate to an increased enzyme turnover rate. Upon E246 mutation to glycine, there was an increased rate of d-arginine turnover kcat from 122 to 500 s-1. Likewise, the kcat values increased 2-fold for the glutamine or leucine variants. Thus, we have engineered a faster biocatalyst for industrial applications by selectively increasing the rate of the PaDADH product release.
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Affiliation(s)
- Joanna
Afokai Quaye
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
| | - Daniel Ouedraogo
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
| | - Giovanni Gadda
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Department
of Biology, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Center
for Diagnostics and Therapeutics, Georgia
State University, Atlanta, Georgia 30302-3965, United States
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12
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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13
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Rivoire O. How Flexibility Can Enhance Catalysis. PHYSICAL REVIEW LETTERS 2023; 131:088401. [PMID: 37683166 DOI: 10.1103/physrevlett.131.088401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change induced by substrate binding can overcome this limitation, ultimately enabling barrier-free catalysis. The model is deliberately minimal, but the principle it illustrates is general and consistent with unique features of proteins as well as with previous informal proposals to explain the superiority of enzymes over other classes of catalysts. Implementing the discriminative switch suggested by the model could help overcome limitations currently encountered in the design of artificial catalysts.
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Affiliation(s)
- Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, and Gulliver, CNRS, ESPCI, Université Paris Sciences et Lettres, 75005 Paris, France
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14
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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15
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Li W, Kohne M, Warncke K. Reactivity Tracking of an Enzyme Progress Coordinate. J Phys Chem Lett 2023; 14:7157-7164. [PMID: 37540029 PMCID: PMC10440813 DOI: 10.1021/acs.jpclett.3c01464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
The reactivity of individual solvent-coupled protein configurations is used to track and resolve the progress coordinate for the core reaction sequence of substrate radical rearrangement and hydrogen atom transfer in the ethanolamine ammonia-lyase (EAL) enzyme from Salmonella enterica. The first-order decay of the substrate radical intermediate is the monitored reaction. Heterogeneous confinement from sucrose hydrates in the mesophase solvent surrounding the cryotrapped protein introduces distributed kinetics in the non-native decay of the substrate radical pair capture substate, which arise from an ensemble of configurational microstates. Reaction rates increase by >103-fold across the distribution to approach that for the native enabled substate for radical rearrangement, which reacts with monotonic kinetics. The native progress coordinate thus involves a collapse of the configuration space to generate optimized reactivity. Reactivity tracking reveals fundamental features of solvent-protein-reaction configurational coupling and leads to a model that refines the ensemble paradigm of enzyme catalysis for strongly adiabatic chemical steps.
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Affiliation(s)
- Wei Li
- Department
of Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Meghan Kohne
- Department
of Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Kurt Warncke
- Department
of Physics, Emory University, Atlanta, Georgia 30322, United States
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16
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Steyn-Ross ML, Steyn-Ross DA, Prentice EJ, Walker EJ, Arcus VL. Evidence for a short-lived resonance state in enzyme catalysis via rate-equation convolution. Phys Rev E 2023; 107:064407. [PMID: 37464627 DOI: 10.1103/physreve.107.064407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/30/2023] [Indexed: 07/20/2023]
Abstract
At the cellular level, all biological function relies on enzymes to provide catalytic acceleration of essential biochemical processes driving cellular metabolism. The enzyme is presumed to lower the activation energy barrier separating reactants from products, but the precise mechanism remains unresolved. Here we examine the temperature dependence of the enzyme-catalyzed dissociation of p-nitrophenyl-α-D-glucopyranoside (pNPG), a chromogenic analog for maltose, isomaltose, and sucrose disaccharide sugars, into p-nitrophenol (pNP) and glucose (monosaccharide). The enzymes of interest are the wild type and mutant forms of glucosidase MalL produced by the probiotic bacterium Bacillus subtilis. The per-enzyme production rates k(T) for the pNPG→ glucose reaction all show a characteristic temperature profile with an Arrhenius-like (approximately exponential) slow acceleration at low temperatures, rising through a point of inflexion to reach a maximum, then turning over to decline steeply towards zero production at high temperatures. This asymmetric profile is found to be well fitted by convolving an exponential growth function f(T) with a Gaussian temperature distribution g(T) to produce an exponentially modified Gaussian function h(T). To give a physical interpretation of the convolution components, we make the temperature mapping Θ≡T_{ref}-T where T_{ref} marks the temperature at which a given mutant becomes fully denatured (unfolded) and therefore inactive, then convert the convolution components to probability density functions which obey the convolution theorem of statistics. Working in Θ space, we identify f(Θ) as the density function for an Arrhenius-like transition from ground-state A to metastable-state B, and g(Θ) as the Gaussian distribution of offset-temperature fluctuations for the metastable state. By mapping the standard thermodynamic relations for temperature and energy fluctuations to the enzyme frame of reference, we are able to derive an expression for the lifetime for the metastable B state. For the 15 enzyme experiments, we obtain a mean value 〈Δt〉≳(29.0±1.3)×10^{-15}s, in remarkably good agreement with the ∼30-fs estimate for the period of glycosidic bond oscillations extracted from published infrared spectroscopy. We suggest that the metastable B state provides a low-energy target that has the effect of lowering the activation energy barrier by presenting an alternative axis for the reaction coordinate.
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Affiliation(s)
| | | | | | - Emma J Walker
- School of Science, University of Waikato, Hamilton, New Zealand
| | - V L Arcus
- School of Science, University of Waikato, Hamilton, New Zealand
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17
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Abstract
Debate has been simmering for some years regarding the importance of internal thermal motions of enzymes to catalysis. Recent developments in protein design may bring resolution of the more contentious points a little closer.
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Affiliation(s)
- Jeremy R. H. Tame
- Protein Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama, 230-0045 Japan
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18
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Gazizov AS, Smolobochkin AV, Rizbayeva TS, Vatsadze SZ, Burilov AR, Sinyashin OG, Alabugin IV. "Stereoelectronic Deprotection of Nitrogen": Recovering Nucleophilicity with a Conformational Change. J Org Chem 2023. [PMID: 37216317 DOI: 10.1021/acs.joc.3c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Ureas are often thought of as "double amides" due to the obvious structural similarity of these functional groups. The main structural feature of an amide is its planarity, which is responsible for the conjugation between the nitrogen atom and carbonyl moiety and the decrease of amide nucleophilicity. Consequently, since amides are poor nucleophiles, ureas are often thought of as poor nucleophiles as well. Herein, we demonstrate that ureas can be distinctly different from amides. These differences can be amplified by rotation around one of the ureas' C-N bonds, which switches off the amide resonance and recovers the nucleophilicity of one of the nitrogen atoms. This conformational change can be further facilitated by the judicious introduction of steric bulk to disfavor the planar conformation. This change in reactivity is an example of "stereoelectronic deprotection," a concept when the desired reactivity of a functional group is produced by a conformational change rather than a chemical modification. This concept may be used complementarily to the traditional protecting groups. We also demonstrate both the viability and the utility of this concept by the synthesis of unusual 2-oxoimidazolium salts possessing quaternary nitrogen atoms at the urea moiety.
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Affiliation(s)
- Almir S Gazizov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russian Federation
| | - Andrey V Smolobochkin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russian Federation
| | - Tanzilya S Rizbayeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russian Federation
| | - Sergey Z Vatsadze
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp., Moscow 119991, Russian Federation
| | - Alexander R Burilov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russian Federation
| | - Oleg G Sinyashin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russian Federation
| | - Igor V Alabugin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russian Federation
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee Fl 32306, United States
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19
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Feehan R, Copeland M, Franklin MW, Slusky JSG. MAHOMES II: A webserver for predicting if a metal binding site is enzymatic. Protein Sci 2023; 32:e4626. [PMID: 36916762 PMCID: PMC10044107 DOI: 10.1002/pro.4626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023]
Abstract
Recent advances have enabled high-quality computationally generated structures for proteins with no solved crystal structures. However, protein function data remains largely limited to experimental methods and homology mapping. Since structure determines function, it is natural that methods capable of using computationally generated structures for functional annotations need to be advanced. Our laboratory recently developed a method to distinguish between metalloenzyme and nonenzyme sites. Here we report improvements to this method by upgrading our physicochemical features to alleviate the need for structures with sub-angstrom precision and using machine learning to reduce training data labeling error. Our improved classifier identifies protein bound metal sites as enzymatic or nonenzymatic with 94% precision and 92% recall. We demonstrate that both adjustments increased predictive performance and reliability on sites with sub-angstrom variations. We constructed a set of predicted metalloprotein structures with no solved crystal structures and no detectable homology to our training data. Our model had an accuracy of 90%-97.5% depending on the quality of the predicted structures included in our test. Finally, we found the physicochemical trends that drove this model's successful performance were local protein density, second shell ionizable residue burial, and the pocket's accessibility to the site. We anticipate that our model's ability to correctly identify catalytic metal sites could enable identification of new enzymatic mechanisms and improve de novo metalloenzyme design success rates.
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Affiliation(s)
- Ryan Feehan
- Center for Computational BiologyThe University of Kansas, 2030 Becker Dr66047LawrenceKansasUSA
| | - Matthew Copeland
- Center for Computational BiologyThe University of Kansas, 2030 Becker Dr66047LawrenceKansasUSA
| | - Meghan W. Franklin
- Center for Computational BiologyThe University of Kansas, 2030 Becker Dr66047LawrenceKansasUSA
| | - Joanna S. G. Slusky
- Center for Computational BiologyThe University of Kansas, 2030 Becker Dr66047LawrenceKansasUSA
- Department of Molecular Biosciences|The University of Kansas, Ave. Lawrence KS 66045‐31011200SunnysideKansasUSA
- Present address:
Generate BiomedicinesSomervilleMassachusettsUSA
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20
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Deng H, Qin M, Liu Z, Yang Y, Wang Y, Yao L. Engineering the Active Site Lid Dynamics to Improve the Catalytic Efficiency of Yeast Cytosine Deaminase. Int J Mol Sci 2023; 24:ijms24076592. [PMID: 37047565 PMCID: PMC10095239 DOI: 10.3390/ijms24076592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
Conformational dynamics is important for enzyme catalysis. However, engineering dynamics to achieve a higher catalytic efficiency is still challenging. In this work, we develop a new strategy to improve the activity of yeast cytosine deaminase (yCD) by engineering its conformational dynamics. Specifically, we increase the dynamics of the yCD C-terminal helix, an active site lid that controls the product release. The C-terminal is extended by a dynamical single α-helix (SAH), which improves the product release rate by up to ~8-fold, and the overall catalytic rate kcat by up to ~2-fold. It is also shown that the kcat increase is due to the favorable activation entropy change. The NMR H/D exchange data indicate that the conformational dynamics of the transition state analog complex increases as the helix is extended, elucidating the origin of the enhanced catalytic entropy. This study highlights a novel dynamics engineering strategy that can accelerate the overall catalysis through the entropy-driven mechanism.
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Affiliation(s)
- Hanzhong Deng
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Qin
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Ying Yang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Yefei Wang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Lishan Yao
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
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21
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Feehan R, Copeland M, Franklin MW, Slusky JSG. MAHOMES II: A webserver for predicting if a metal binding site is enzymatic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531790. [PMID: 36945603 PMCID: PMC10028950 DOI: 10.1101/2023.03.08.531790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Recent advances have enabled high-quality computationally generated structures for proteins with no solved crystal structures. However, protein function data remains largely limited to experimental methods and homology mapping. Since structure determines function, it is natural that methods capable of using computationally generated structures for functional annotations need to be advanced. Our laboratory recently developed a method to distinguish between metalloenzyme and non-enzyme sites. Here we report improvements to this method by upgrading our physicochemical features to alleviate the need for structures with sub-angstrom precision and using machine learning to reduce training data labeling error. Our improved classifier identifies protein bound metal sites as enzymatic or non-enzymatic with 94% precision and 92% recall. We demonstrate that both adjustments increased predictive performance and reliability on sites with sub-angstrom variations. We constructed a set of predicted metalloprotein structures with no solved crystal structures and no detectable homology to our training data. Our model had an accuracy of 90 - 97.5% depending on the quality of the predicted structures included in our test. Finally, we found the physicochemical trends that drove this model's successful performance were local protein density, second shell ionizable residue burial, and the pocket's accessibility to the site. We anticipate that our model's ability to correctly identify catalytic metal sites could enable identification of new enzymatic mechanisms and improve de novo metalloenzyme design success rates. Significance statement Identification of enzyme active sites on proteins with unsolved crystallographic structures can accelerate discovery of novel biochemical reactions, which can impact healthcare, industrial processes, and environmental remediation. Our lab has developed an ML tool for predicting sites on computationally generated protein structures as enzymatic and non-enzymatic. We have made our tool available on a webserver, allowing the scientific community to rapidly search previously unknown protein function space.
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Affiliation(s)
- Ryan Feehan
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Matthew Copeland
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Meghan W. Franklin
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Joanna S. G. Slusky
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave. Lawrence KS 66045-3101
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22
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Ouedraogo D, Souffrant M, Yao XQ, Hamelberg D, Gadda G. Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d-Arginine Dehydrogenase. Biochemistry 2023; 62:1070-1081. [PMID: 36795942 PMCID: PMC9996824 DOI: 10.1021/acs.biochem.2c00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Numerous studies demonstrate that enzymes undergo multiple conformational changes during catalysis. The malleability of enzymes forms the basis for allosteric regulation: residues located far from the active site can exert long-range dynamical effects on the active site residues to modulate catalysis. The structure of Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) shows four loops (L1, L2, L3, and L4) that span the substrate and the FAD-binding domains. Loop L4 comprises residues 329-336, spanning over the flavin cofactor. The I335 residue on loop L4 is ∼10 Å away from the active site and ∼3.8 Å from N(1)-C(2)═O atoms of the flavin. In this study, we used molecular dynamics and biochemical techniques to investigate the effect of the mutation of I335 to histidine on the catalytic function of PaDADH. Molecular dynamics showed that the conformational dynamics of PaDADH are shifted to a more closed conformation in the I335H variant. In agreement with an enzyme that samples more in a closed conformation, the kinetic data of the I335H variant showed a 40-fold decrease in the rate constant of substrate association (k1), a 340-fold reduction in the rate constant of substrate dissociation from the enzyme-substrate complex (k2), and a 24-fold decrease in the rate constant of product release (k5), compared to that of the wild-type. Surprisingly, the kinetic data are consistent with the mutation having a negligible effect on the reactivity of the flavin. Altogether, the data indicate that the residue at position 335 has a long-range dynamical effect on the catalytic function in PaDADH.
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Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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23
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Zhang A, Zhuang X, Liu J, Huang J, Lin L, Tang Y, Zhao S, Li R, Wang B, Fang B, Hong W. Catalytic cycle of formate dehydrogenase captured by single-molecule conductance. Nat Catal 2023. [DOI: 10.1038/s41929-023-00928-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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24
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Bernard DN, Narayanan C, Hempel T, Bafna K, Bhojane PP, Létourneau M, Howell EE, Agarwal PK, Doucet N. Conformational exchange divergence along the evolutionary pathway of eosinophil-associated ribonucleases. Structure 2023; 31:329-342.e4. [PMID: 36649708 PMCID: PMC9992247 DOI: 10.1016/j.str.2022.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/24/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023]
Abstract
The evolutionary role of conformational exchange in the emergence and preservation of function within structural homologs remains elusive. While protein engineering has revealed the importance of flexibility in function, productive modulation of atomic-scale dynamics has only been achieved on a finite number of distinct folds. Allosteric control of unique members within dynamically diverse structural families requires a better appreciation of exchange phenomena. Here, we examined the functional and structural role of conformational exchange within eosinophil-associated ribonucleases. Biological and catalytic activity of various EARs was performed in parallel to mapping their conformational behavior on multiple timescales using NMR and computational analyses. Despite functional conservation and conformational seclusion to a specific domain, we show that EARs can display similar or distinct motional profiles, implying divergence rather than conservation of flexibility. Comparing progressively more distant enzymes should unravel how this subfamily has evolved new functions and/or altered their behavior at the molecular level.
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Affiliation(s)
- David N Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Chitra Narayanan
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada; Department of Chemistry, New Jersey City University, Jersey City, NJ 07305, USA
| | - Tim Hempel
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany; Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Khushboo Bafna
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Purva Prashant Bhojane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, 1045 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.
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25
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Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023; 9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.
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26
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Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatische C4-Epimerisierung von UDP-Glucuronsäure: präzise gesteuerte Rotation eines transienten 4-Ketointermediats für eine invertierende Reaktion ohne Decarboxylierung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202211937. [PMID: 38515538 PMCID: PMC10952283 DOI: 10.1002/ange.202211937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Indexed: 03/23/2024]
Abstract
AbstractUDP‐Glucuronsäure(UDP‐GlcA)‐4‐Epimerase repräsentiert eine wichtige Fragestellung in der Enzymkatalyse: die Balance zwischen konformativer Flexibilität und genauer Positionierung. Das Enzym koordiniert die C4‐Oxidation des Substrats durch NAD+ mit der Rotation eines leicht decarboxylierbaren β‐Ketosäure‐Intermediats im aktiven Zentrum zur Ermöglichung der stereoinvertierenden Reduktion der Ketogruppe durch NADH. Wir zeigen hier die nur schwer erfassbare Rotationskoordinate des 4‐Ketointermediats. Distorsion des Zuckerrings in eine Boot‐Konformation erzeugt torsionale Mobilität in der Bindungstasche des Enzyms. Die Endpunkte der Rotation zeigen den 4‐Ketozucker in einer unverformten 4C1‐Sesselkonformation. Die äquatorial positionierte Carboxylatgruppe ist ungünstig für die 4‐Ketozucker‐Decarboxylierung. Varianten der Epimerase zeigen Decarboxylierung, wenn sie die Bindung mit der Carboxylatgruppe im entgegengesetzten Rotationsisomer des Substrats entfernen. R185A/D‐Substitutionen wandeln die Epimerase in UDP‐Xylose‐Synthasen um, welche UDP‐GlcA in stereospezifischen, konfigurationserhaltenden Reaktionen decarboxylieren.
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Affiliation(s)
- Annika J. E. Borg
- Institut für Biotechnologie und BioprozesstechnikTechnische Universität GrazPetersgasse 12/18010GrazÖsterreich
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
- Derzeitige Adresse: Nostrum BiodiscoveryAv. De Josep Tarradellas, 8–1008029BarcelonaSpanien
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Passeig Lluís Companys, 2308010BarcelonaSpanien
| | - Bernd Nidetzky
- Institut für Biotechnologie und BioprozesstechnikTechnische Universität GrazPetersgasse 12/18010GrazÖsterreich
- Austrian Center of Industrial Biotechnology (acib)Krenngasse 378010GrazÖsterreich
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27
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Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatic C4-Epimerization of UDP-Glucuronic Acid: Precisely Steered Rotation of a Transient 4-Keto Intermediate for an Inverted Reaction without Decarboxylation. Angew Chem Int Ed Engl 2023; 62:e202211937. [PMID: 36308301 PMCID: PMC10107529 DOI: 10.1002/anie.202211937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
UDP-glucuronic acid (UDP-GlcA) 4-epimerase illustrates an important problem regarding enzyme catalysis: balancing conformational flexibility with precise positioning. The enzyme coordinates the C4-oxidation of the substrate by NAD+ and rotation of a decarboxylation-prone β-keto acid intermediate in the active site, enabling stereoinverting reduction of the keto group by NADH. We reveal the elusive rotational landscape of the 4-keto intermediate. Distortion of the sugar ring into boat conformations induces torsional mobility in the enzyme's binding pocket. The rotational endpoints show that the 4-keto sugar has an undistorted 4 C1 chair conformation. The equatorially placed carboxylate group disfavors decarboxylation of the 4-keto sugar. Epimerase variants lead to decarboxylation upon removal of the binding interactions with the carboxylate group in the opposite rotational isomer of the substrate. Substitutions R185A/D convert the epimerase into UDP-xylose synthases that decarboxylate UDP-GlcA in stereospecific, configuration-retaining reactions.
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Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Present address: Nostrum Biodiscovery, Av. De Josep Tarradellas, 8-10, 08029, Barcelona, Spain
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria.,Austrian Center of Industrial Biotechnology (acib), Krenngasse 37, 8010, Graz, Austria
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28
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Yang Y, Fu Y, Wu S, Zhao L, Qin C, Wang X, Su Z. Endohedral Functionalization for Structural Transformation of Polyoxovanadate-Based Metal-Organic Cube. Inorg Chem 2023; 62:648-652. [PMID: 36583537 DOI: 10.1021/acs.inorgchem.2c03635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Functionalized internal modifications of metal-organic polyhedra (MOPs) can endow properties and functions different from the original ones. Until now, there have been only a few examples of endohedral modifications of polyoxovanadate-based MOPs. Herein, an efficient coordination-driven strategy was chosen for the inner modification of two metal-organic cubes (MOCs) with different sizes, VMOC-1 and VMOC-4, constructed from polyoxovanadate clusters [V6O6(OCH3)9(SO4)(CO2)3]2- SBU and tetradentate ligands. Pyridinophosphonic acid with potential coordination capability was introduced to replace the sulfate of the hexavanadate cluster and graft the pyridine functional group inside the cage. The introduction of pyridylphosphate in the VMOC-4 system gave a cubic cage with a pyridyl endo-modified isomer. Interestingly, the smaller cubic cage VMOC-1 was induced to undergo structural transformation to obtain VMOC-py-1. The organic dyes adsorption of VMOC-py-1 and VMOC-1 showed that the endomodified structure could adsorb larger and more dyes, compared to the original cube.
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Affiliation(s)
- Yang Yang
- Key Lab of Polyoxometalate Science of Ministry of Education, National & Local United Engineering Laboratory for Power Battery, Northeast Normal University, Changchun 130024, People's Republic of China
| | - Yaomei Fu
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, 262700, China
| | - Shuangxue Wu
- Key Lab of Polyoxometalate Science of Ministry of Education, National & Local United Engineering Laboratory for Power Battery, Northeast Normal University, Changchun 130024, People's Republic of China
| | - Liang Zhao
- Key Lab of Polyoxometalate Science of Ministry of Education, National & Local United Engineering Laboratory for Power Battery, Northeast Normal University, Changchun 130024, People's Republic of China
| | - Chao Qin
- Key Lab of Polyoxometalate Science of Ministry of Education, National & Local United Engineering Laboratory for Power Battery, Northeast Normal University, Changchun 130024, People's Republic of China
| | - Xinlong Wang
- Key Lab of Polyoxometalate Science of Ministry of Education, National & Local United Engineering Laboratory for Power Battery, Northeast Normal University, Changchun 130024, People's Republic of China
| | - Zhongmin Su
- College of Science, Hainan University, Haikou 570228, China
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29
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Sharma H, Raju B, Narendra G, Motiwale M, Sharma B, Verma H, Silakari O. QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update. ChemistrySelect 2023. [DOI: 10.1002/slct.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Himani Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Baddipadige Raju
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Gera Narendra
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Mohit Motiwale
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Bhavna Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Himanshu Verma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Om Silakari
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
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30
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Persichetti JR, Jiang Y, Hudson PS, O'Brien EP. Modeling Ensembles of Enzyme Reaction Pathways with Hi-MSM Reveals the Importance of Accounting for Pathway Diversity. J Phys Chem B 2022; 126:9748-9758. [PMID: 36383711 DOI: 10.1021/acs.jpcb.2c04496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Conventional quantum mechanical-molecular mechanics (QM/MM) simulation approaches for modeling enzyme reactions often assume that there is one dominant reaction pathway and that this pathway can be sampled starting from an X-ray structure of the enzyme. These assumptions reduce computational cost; however, their validity has not been extensively tested. This is due in part to the lack of a rigorous formalism for integrating disparate pathway information from dynamical QM/MM calculations. Here, we present a way to model ensembles of reaction pathways efficiently using a divide-and-conquer strategy through Hierarchical Markov State Modeling (Hi-MSM). This approach allows information on multiple, distinct pathways to be incorporated into a chemical kinetic model, and it allows us to test these two assumptions. Applying Hi-MSM to the reaction carried out by dihydrofolate reductase (DHFR) we find (i) there are multiple, distinct pathways significantly contributing to the overall flux of the reaction that the conventional approach does not identify and (ii) that the conventional approach does not identify the dominant reaction pathway. Thus, both assumptions underpinning the conventional approach are violated. Since DHFR is a relatively small enzyme, and configuration space scales exponentially with protein size, accounting for multiple reaction pathways is likely to be necessary for most enzymes.
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31
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Rajasekaran VV, Ghosh A, Kundu S, Mondal D, Paululat T, Schmittel M. Synchronizing Two Distinct Nano-Circular Sliding Motions in Six-Component Machinery for Double Catalysis. Angew Chem Int Ed Engl 2022; 61:e202212473. [PMID: 36197751 PMCID: PMC9828345 DOI: 10.1002/anie.202212473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Indexed: 11/05/2022]
Abstract
The heteroleptic multi-component double slider-on-deck system DS3 exhibits tight coupling of motional speed of two distinct nano-circular sliders (k298 =77 and 41 kHz) despite a 2.2 nm separation. In comparison, the single sliders in DS1 and DS2 move at vastly different speed (k298 =1.1 vs. 350 kHz). Synchronization of the motions in DS3 remains even when one slows the movement of the faster slider using small molecular brake pads. In contrast to the individual DS1 and DS2 systems, DS3 is a powerful catalyst for a two-step reaction by using the motion of both sliders to drive two catalytic processes.
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Affiliation(s)
- Vishnu Verman Rajasekaran
- Center of Micro and Nanochemistry and (Bio)TechnologyOrganische Chemie IUniversity of SiegenAdolf-Reichwein Str. 257068SiegenGermany
| | - Amit Ghosh
- Center of Micro and Nanochemistry and (Bio)TechnologyOrganische Chemie IUniversity of SiegenAdolf-Reichwein Str. 257068SiegenGermany
| | - Sohom Kundu
- Center of Micro and Nanochemistry and (Bio)TechnologyOrganische Chemie IUniversity of SiegenAdolf-Reichwein Str. 257068SiegenGermany
| | - Debabrata Mondal
- Center of Micro and Nanochemistry and (Bio)TechnologyOrganische Chemie IUniversity of SiegenAdolf-Reichwein Str. 257068SiegenGermany
| | - Thomas Paululat
- Center of Micro and Nanochemistry and (Bio)TechnologyOrganische Chemie IIUniversity of SiegenAdolf-Reichwein Str. 257068SiegenGermany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and (Bio)TechnologyOrganische Chemie IUniversity of SiegenAdolf-Reichwein Str. 257068SiegenGermany
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32
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Yabukarski F, Doukov T, Pinney MM, Biel JT, Fraser JS, Herschlag D. Ensemble-function relationships to dissect mechanisms of enzyme catalysis. SCIENCE ADVANCES 2022; 8:eabn7738. [PMID: 36240280 PMCID: PMC9565801 DOI: 10.1126/sciadv.abn7738] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 08/30/2022] [Indexed: 05/27/2023]
Abstract
Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.
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Affiliation(s)
- Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Margaux M. Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Justin T. Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
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33
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Toledo-González Y, Sotiropoulos JM, Bécart D, Guichard G, Carbonnière P. Insight into Substrate Recognition by Urea-Based Helical Foldamer Catalysts Using a DFT Global Optimization Approach. J Org Chem 2022; 87:10726-10735. [PMID: 35917494 DOI: 10.1021/acs.joc.2c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptides and foldamers have recently gained increasing attention as chiral catalysts to achieve challenging (asymmetric) transformations. We previously reported that short helically folded aliphatic oligoureas in combination with achiral Brønsted bases are effective H-bonding catalysts for C-C bond-forming reactions─i.e., the conjugate addition of 1,3-dicarbonyl pronucleophiles to nitroalkenes─with high reactivity and selectivity and at remarkably low chiral catalyst/substrate molar ratios. This theoretical investigation at the density functional theory level of theory, aims to both analyze how the substrates of the reaction interact with the foldamer catalyst and rationalize a chain-length dependence effect on the catalytic properties. We confirm that the first two ureas are the only H-bond donors available to interact with external molecules. Moreover, each urea site interacts with one of the two reactants allowing a short distance between the two reacting carbons, thus facilitating the conjugated addition. Additionally, it was observed that the molecular recognition and catalyst-substrate interactions are mainly governed by electrostatic interactions but not orbital interactions (see from NBO if this is finally true). On these grounds, an electrostatic potential (ESP) analysis showed an important internal charge separation in the catalyst, the positive ESP region being concentrated around the first two ureas, with its area extending as the number of residues increases.
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Affiliation(s)
| | | | - Diane Bécart
- Université Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Gilles Guichard
- Université Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Philippe Carbonnière
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, 5254 Pau, France
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34
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Gao S, Klinman JP. Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts. Curr Opin Struct Biol 2022; 75:102434. [PMID: 35872562 PMCID: PMC9901422 DOI: 10.1016/j.sbi.2022.102434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 02/08/2023]
Abstract
With the growing acceptance of the contribution of protein conformational ensembles to enzyme catalysis and regulation, research in the field of protein dynamics has shifted toward an understanding of the atomistic properties of protein dynamical networks and the mechanisms and time scales that control such behavior. A full description of an enzymatic reaction coordinate is expected to extend beyond the active site and include site-specific networks that communicate with the protein/water interface. Advances in experimental tools for the spatial resolution of thermal activation pathways are being complemented by biophysical methods for visualizing dynamics in real time. An emerging multidimensional model integrates the impacts of bound substrate/effector on the distribution of protein substates that are in rapid equilibration near room temperature with reaction-specific protein embedded heat transfer conduits.
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Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, CA, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, United States. https://twitter.com/S_H_Gao
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, CA, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, United States; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, United States.
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35
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Quaye JA, Ball J, Gadda G. Kinetic solvent viscosity effects uncover an internal isomerization of the enzyme-substrate complex in Pseudomonas aeruginosa PAO1 NADH:Quinone oxidoreductase. Arch Biochem Biophys 2022; 727:109342. [PMID: 35777523 DOI: 10.1016/j.abb.2022.109342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/02/2022]
Abstract
NAD(P)H:quinone oxidoreductases (NQOs) play an essential protective role as antioxidants in the detoxification of quinones in both Prokaryotes and Eukaryotes. NQO from Pseudomonas aeruginosa PAO1 uses FMN to catalyze the two-electron reduction of various quinones with NADH. In this study, steady-state kinetics, kinetic solvent viscosity effects, and rapid reaction kinetics were used to determine which kinetic steps control the overall turnover of the enzyme with benzoquinone or juglone. The rate constant for flavin reduction (kred) at pH 6.0 was 12.9 ± 0.3 s-1, and the Kd for NADH was at least an order of magnitude lower than 90 μM. With benzoquinone, the kcat value was 11.7 ± 0.3 s-1, consistent with flavin reduction being almost entirely rate-limiting for overall turnover. With juglone, a kcat value of 10.0 ± 0.5 s-1 was recorded. The normalized plot of the relative solvent viscosity effects on the kcat values established that hydride transfer from NADH to the FMN and quinol product release, with a calculated rate constant (kP-rel) of 52 s-1, are partially rate-limiting for the overall turnover of NQO. Kinetic solvent viscosity effects with glucose or sucrose revealed a hyperbolic dependence on the kcat and kcat/Km values with benzoquinone or juglone, respectively, consistent with the presence of a solvent-sensitive internal isomerization of the enzyme-substrate complex (ES). The data demonstrate opposing effects of benzoquinone and juglone on the equilibrium of the NQO ES isomerization with glucose or sucrose. Thus, our study demonstrates how quinol substrate properties alter the equilibrium of NQO ES isomerization.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA
| | - Jacob Ball
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA.
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36
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Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B 12-dependent ethanolamine ammonia-lyase. Methods Enzymol 2022; 669:229-259. [PMID: 35644173 DOI: 10.1016/bs.mie.2021.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Coenzyme B12 (adenosylcobalamin) -dependent ethanolamine ammonia-lyase (EAL) is the signature enzyme in ethanolamine utilization metabolism associated with microbiome homeostasis and disease conditions in the human gut. The enzyme conducts a complex choreography of bond-making/bond-breaking steps that rearrange substrate to products through a radical mechanism, with themes common to other coenzyme B12-dependent and radical enzymes. The methods presented are targeted to test the hypothesis that particular, select protein and coupled solvent configurational fluctuations contribute to enzyme function. The general approach is to correlate enzyme function with an introduced perturbation that alters the properties (for example, degree of concertedness, or collectiveness) of protein and coupled solvent dynamics. Methods for sample preparation and low-temperature kinetic measurements by using temperature-step reaction initiation and time-resolved, full-spectrum electron paramagnetic resonance spectroscopy are detailed. A framework for interpretation of results obtained in ensemble systems under conditions of statistical equilibrium within the reacting, globally unstable state is presented. The temperature-dependence of the first-order rate constants for decay of the cryotrapped paramagnetic substrate radical state in EAL, through the chemical step of radical rearrangement, displays a piecewise-continuous Arrhenius dependence from 203 to 295K, punctuated by a kinetic bifurcation over 219-220K. The results reveal the obligatory contribution of a class of select collective protein and coupled solvent fluctuations to the interconversion of two resolved, sequential configurational substates, on the decay time scale. The select class of collective fluctuations also contributes to the chemical step. The methods and analysis are generally applicable to other coenzyme B12-dependent and related radical enzymes.
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37
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Rapp C, Nidetzky B. Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate. ACS Catal 2022; 12:6816-6830. [PMID: 35747200 PMCID: PMC9207888 DOI: 10.1021/acscatal.2c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/12/2022] [Indexed: 11/29/2022]
Abstract
![]()
Transient oxidation–reduction
through hydride transfer with
tightly bound NAD coenzyme is used by a large class of sugar nucleotide
epimerases to promote configurational inversion of carbon stereocenters
in carbohydrate substrates. A requirement for the epimerases to coordinate
hydride abstraction and re-addition with substrate rotation in the
binding pocket poses a challenge for dynamical protein conformational
selection linked to enzyme catalysis. Here, we studied the thermophilic
C2 epimerase from Thermodesulfatator atlanticus (TaCPa2E) in combination with a slow CDP-glucose
substrate (kcat ≈ 1.0 min–1; 60 °C) to explore the sensitivity of the enzymatic hydride
transfer toward environmental fluctuations affected by temperature
(20–80 °C). We determined noncompetitive primary kinetic
isotope effects (KIE) due to 2H at the glucose C2 and showed
that a normal KIE on the kcat (Dkcat) reflects isotope sensitivity of
the hydrogen abstraction to enzyme-NAD+ in a rate-limiting
transient oxidation. The Dkcat peaked at 40 °C was 6.1 and decreased to 2.1 at low (20 °C)
and 3.3 at high temperature (80 °C). The temperature profiles
for kcat with the 1H and 2H substrate showed a decrease in the rate below a dynamically
important breakpoint (∼40 °C), suggesting an equilibrium
shift to an impaired conformational landscape relevant for catalysis
in the low-temperature region. Full Marcus-like model fits of the
rate and KIE profiles provided evidence for a high-temperature reaction
via low-frequency conformational sampling associated with a broad
distribution of hydride donor–acceptor distances (long-distance
population centered at 3.31 ± 0.02 Å), only poorly suitable
for quantum mechanical tunneling. Collectively, dynamical characteristics
of TaCPa2E-catalyzed hydride transfer during transient
oxidation of CDP-glucose reveal important analogies to mechanistically
simpler enzymes such as alcohol dehydrogenase and dihydrofolate reductase.
A loose-fit substrate (in TaCPa2E) resembles structural
variants of these enzymes by extensive dynamical sampling to balance
conformational flexibility and catalytic efficiency.
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Affiliation(s)
- Christian Rapp
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria
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38
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Clayton J, Ellis-Guardiola K, Mahoney BJ, Soule J, Clubb RT, Wereszczynski J. Directed inter-domain motions enable the IsdH Staphylococcus aureus receptor to rapidly extract heme from human hemoglobin. J Mol Biol 2022; 434:167623. [DOI: 10.1016/j.jmb.2022.167623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/07/2022] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
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Rastogi H, Chowdhury PK. Correlating the Local and Global Dynamics of an Enzyme in the Crowded Milieu. J Phys Chem B 2022; 126:3208-3223. [PMID: 35442681 DOI: 10.1021/acs.jpcb.1c09759] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymes are dynamic biological macromolecules, with their catalytic function(s) being largely influenced by the changes in local fluctuations of amino acid side chains as well as global structural modulations that the enzyme undergoes. Such local and global motions can be highly affected inside the crowded physiological interior of the cell. Here, we have addressed the role of dynamic structural flexibility in affecting the activation energy barrier of a flexible multidomain enzyme adenylate kinase (AK3L1, UniProtKB: Q9UIJ7). Activation energy profiles of both local (at three different sites along the polypeptide backbone) and global dynamics of the enzyme have been monitored using solvation studies on the subnanosecond time scale and tryptophan quenching studies over the temperature range of 278-323 K, respectively, under crowded conditions (Ficoll 70, Dextran 40, Dextran 70, and PEG 8). This study not only provides the site-specific mapping of dynamics but reveals that the activation energies associated with these local motions undergo a significant decrease in the presence of macromolecular crowders, providing new insights into how crowding affects internal protein dynamics. The crowded scenario also aids in enhancing the coupling between the local and global motions of the enzyme. Moreover, select portions/regions of the enzyme when taken together can well mirror the overall dynamics of the biomolecule, showing possible energy hotspots along the polypeptide backbone.
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Affiliation(s)
- Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India 110016
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India 110016
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40
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Iyengar SM, Barnsley KK, Xu R, Prystupa A, Ondrechen MJ. Electrostatic fingerprints of catalytically active amino acids in enzymes. Protein Sci 2022; 31:e4291. [PMID: 35481659 PMCID: PMC8994506 DOI: 10.1002/pro.4291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 11/06/2022]
Abstract
The computed electrostatic and proton transfer properties are studied for 20 enzymes that represent all six major enzyme commission classes and a variety of different folds. The properties of aspartate, glutamate, and lysine residues that have been previously experimentally determined to be catalytically active are reported. The catalytic aspartate and glutamate residues studied here are strongly coupled to at least one other aspartate or glutamate residue and often to multiple other carboxylate residues with intrinsic pKa differences less than 1 pH unit. Sometimes these catalytic acidic residues are also coupled to a histidine residue, such that the intrinsic pKa of the acidic residue is higher than that of the histidine. All catalytic lysine residues studied here are strongly coupled to tyrosine or cysteine residues, wherein the intrinsic pKa of the anion-forming residue is higher than that of the lysine. Some catalytic lysines are also coupled to other lysines with intrinsic pKa differences within 1 pH unit. Some evidence of the possible types of interactions that facilitate nucleophilicity is discussed. The interactions reported here provide important clues about how side chain functional groups that are weak Brønsted acids or bases for the free amino acid in solution can achieve catalytic potency and become strong acids, bases or nucleophiles in the enzymatic environment.
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Affiliation(s)
- Suhasini M. Iyengar
- Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts USA
| | - Kelly K. Barnsley
- Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts USA
| | - Rholee Xu
- Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts USA
| | - Aleksandr Prystupa
- Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts USA
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts USA
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41
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Stein RL. Mechanisms of macromolecular reactions. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:11. [PMID: 35303191 DOI: 10.1007/s40656-022-00492-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
During the past two decades, philosophers of biology have increasingly turned their attention to mechanisms of biological phenomena. Through analyses of mechanistic proposals advanced by biologists, the goal of these philosophers is to understand what a mechanism is and how mechanisms explain. These analyses have generally focused on mechanistic proposals for phenomenon that occur at the cellular or sub-cellular level, such as synapse firing, protein synthesis, or metabolic pathway operation. Little is said about the mechanisms of the macromolecular reactions that underpin these phenomena. These reactions comprise a diverse family of reaction types, and include protein folding, macromolecular complex formation, receptor-ligand interactions, and enzyme catalysis. In this paper, I develop an account of mechanism that focuses exclusively on macromolecular reactions. I begin by reviewing how mechanism is understood in enzymology, and how mechanistic concepts of enzymology apply to macromolecular reactions in general. We will see that the mechanism of a macromolecular reaction is most accurately described as a progression of reaction intermediates, where the evolution of intermediates, from one to the next, is characterized by an energetic coupling between chemistry and protein dynamics. I then make the case that this description necessitates a grounding in a process ontology. To describe the mechanism by which a macromolecular reaction occurs is to describe a process.
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42
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Winston DS, Gorman SD, Boehr DD. Conformational transitions in yeast chorismate mutase important for allosteric regulation as identified by nuclear magnetic resonance spectroscopy. J Mol Biol 2022; 434:167531. [DOI: 10.1016/j.jmb.2022.167531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
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43
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Wang Q, Wu Q, Ye T, Wang X, Qiu H, Xie J, Wang Y, Zhou S, Wu W. Reversible Regulating the Substrate Specificity of Enzymes in Microgels by a Phase Transition in Polymer Networks. ACS Macro Lett 2022; 11:26-32. [PMID: 35574802 DOI: 10.1021/acsmacrolett.1c00687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here, we report a distinct approach for regulating the substrate specificity of enzymes immobilized in microgels by a phase transition in polymer networks. The finding is demonstrated on glucose oxidase that is immobilized in thermoresponsive poly(N-isopropylacrylamide)-based microgels. Laser light scattering and enzymatic oxidation tests indicate that the broadened specificity appears at low temperatures, at which the gel matrix is in the relatively swollen state relative to its state at microgel synthesis temperature; upon heating to the relative higher temperatures, the gel matrix is not able to shrink further that offers a tight space in which the enzyme resides to retain high glucose specificity. It is proposed that polymer phase transition in the gel matrix mainly alter protein gates that control passage of substrates into active sites, making them open or close to a certain extent that enable reversible regulating the substrate specificity. The finding is also observed on bulk gels under a rational design, making it of potential interest in enzymatic biofuel cell applications.
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Affiliation(s)
- Qiangwei Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qingshi Wu
- College of Chemical Engineering and Materials Science, Quanzhou Normal University, Quanzhou, Fujian 362000, China
| | - Ting Ye
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiaofei Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Huijuan Qiu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Jianda Xie
- School of Materials Science and Engineering, Xiamen University of Technology, Xiamen, Fujian 361024, China
| | - Yusong Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shiming Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weitai Wu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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44
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Mixed component metal-organic frameworks: Heterogeneity and complexity at the service of application performances. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214273] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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45
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Monza E, Gil V, Lucas MF. Computational Enzyme Design at Zymvol. Methods Mol Biol 2022; 2397:249-259. [PMID: 34813068 DOI: 10.1007/978-1-0716-1826-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Directed evolution is the most recognized methodology for enzyme engineering. The main drawback resides in its random nature and in the limited sequence exploration; both require screening of thousands (if not millions) of variants to achieve a target function. Computer-driven approaches can limit laboratorial screening to a few hundred candidates, enabling and accelerating the development of industrial enzymes. In this book chapter, the technology adopted at Zymvol is described. An overview of the current development and future directions in the company is also provided.
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Affiliation(s)
- Emanuele Monza
- Zymvol Biomodeling SL, Carrer Roc Boronat 117, Barcelona, Spain.
| | - Victor Gil
- Zymvol Biomodeling SL, Carrer Roc Boronat 117, Barcelona, Spain
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46
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Laureanti JA, Su Q, Shaw WJ. A protein scaffold enables hydrogen evolution for a Ni-bisdiphosphine complex. Dalton Trans 2021; 50:15754-15759. [PMID: 34704584 DOI: 10.1039/d1dt03295j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An artificial metalloenzyme acting as a functional biomimic of hydrogenase enzymes was activated by assembly via covalent attachment of the molecular complex, [Ni(PNglycineP)2]2-, within a structured protein scaffold. Electrocatalytic H2 production was observed from pH 3.0 to 10.0 for the artificial enzyme, while no electrocatalytic activity was observed for similar [Ni(PNP)2]2+ systems.
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Affiliation(s)
- Joseph A Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Qiwen Su
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Wendy J Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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47
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Correspondence insights into the role of genes in cell functionality. Comments on "The gene: An appraisal" by K. Baverstock. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:152-160. [PMID: 34624359 DOI: 10.1016/j.pbiomolbio.2021.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/21/2022]
Abstract
One of the most important goals of the post-genomic era is to understand the different sources of molecular information that regulate the functional and structural architecture of cells. In this regard, Prof. K. Baverstock underscores in his recent article "The gene: An appraisal" (Baverstock, 2021) that genes are not the leading elements in cellular functionality, inheritance and evolution. As a consequence, the theory of evolution based on the Neo-Darwinian synthesis, is inadequate for today's scientific evidence. Conversely, the author contends that life processes viewed on the basis of thermodynamics, complex system dynamics and self-organization provide a new framework for the foundations of Biology. I consider it necessary to comment on some essential aspects of this relevant work, and here I present a short overview of the main non-genetic sources of biomolecular order and complexity that underline the molecular dynamics and functionality of cells. These sources generate different processes of complexity, which encompasses from the most elementary levels of molecular activity to the emergence of systemic behaviors, and the information necessary to sustain them is not contained in the genome.
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48
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Theisen FF, Staby L, Tidemand FG, O'Shea C, Prestel A, Willemoës M, Kragelund BB, Skriver K. Quantification of Conformational Entropy Unravels Effect of Disordered Flanking Region in Coupled Folding and Binding. J Am Chem Soc 2021; 143:14540-14550. [PMID: 34473923 DOI: 10.1021/jacs.1c04214] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Intrinsic disorder (ID) constitutes a new dimension to the protein structure-function relationship. The ability to undergo conformational changes upon binding is a key property of intrinsically disordered proteins and remains challenging to study using conventional methods. A 1994 paper by R. S. Spolar and M. T. Record presented a thermodynamic approach for estimating changes in conformational entropy based on heat capacity changes, allowing quantification of residues folding upon binding. Here, we adapt the method for studies of intrinsically disordered proteins. We integrate additional data to provide a broader experimental foundation for the underlying relations and, based on >500 protein-protein complexes involving disordered proteins, reassess a key relation between polar and nonpolar surface area changes, previously determined using globular protein folding. We demonstrate the improved suitability of the adapted method to studies of the folded αα-hub domain RST from radical-induced cell death 1, whose interactome is characterized by ID. From extensive thermodynamic data, quantifying the conformational entropy changes upon binding, and comparison to the NMR structure, the adapted method improves accuracy for ID-based studies. Furthermore, we apply the method, in conjunction with NMR, to reveal hitherto undetected effects of interaction-motif context. Thus, inclusion of the disordered context of the DREB2A RST-binding motif induces structuring of the binding motif, resulting in major enthalpy-entropy compensation in the interaction interface. This study, also evaluating additional interactions, demonstrates the strength of the ID-adapted Spolar-Record thermodynamic approach for dissection of structural features of ID-based interactions, easily overlooked in traditional studies, and for translation of these into mechanistic knowledge.
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Affiliation(s)
| | | | - Frederik Grønbæk Tidemand
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
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49
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Rodriguez-Rivera FP, Levi SM. Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms. ACS CENTRAL SCIENCE 2021; 7:1117-1125. [PMID: 34345664 PMCID: PMC8323112 DOI: 10.1021/acscentsci.1c00389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Indexed: 06/13/2023]
Abstract
Diverging from traditional target inhibition, proteasomal protein degradation approaches have emerged as novel therapeutic modalities that embody distinct pharmacological profiles and can access previously undrugged targets. Small molecule degraders have the potential to catalytically destroy target proteins at substoichiometric concentrations, thus lowering administered doses and extending pharmacological effects. With this mechanistic premise, research efforts have advanced the development of small molecule degraders that benefit from stable and increased affinity ternary complexes. However, a holistic framework that evaluates different degradation modes from a catalytic perspective, including focusing on kinetically favored degradation mechanisms, is lacking. In this Outlook, we introduce the concept of an induced cooperativity spectrum as a unifying framework to mechanistically understand catalytic degradation profiles. This framework is bolstered by key examples of published molecular degraders extending from molecular glues to bivalent degraders. Critically, we discuss remaining challenges and future opportunities in drug discovery to rationally design and phenotypically screen for efficient degraders.
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Affiliation(s)
- Frances P. Rodriguez-Rivera
- Discovery
Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Samuel M. Levi
- Pfizer
Worldwide Research and Development, Pfizer,
Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
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50
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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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