1
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Andrews KG, Piskorz TK, Horton PN, Coles SJ. Enzyme-like Acyl Transfer Catalysis in a Bifunctional Organic Cage. J Am Chem Soc 2024; 146:17887-17897. [PMID: 38914009 DOI: 10.1021/jacs.4c03560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Amide-based organic cage cavities are, in principle, ideal enzyme active site mimics. Yet, cage-promoted organocatalysis has remained elusive, in large part due to synthetic accessibility of robust and functional scaffolds. Herein, we report the acyl transfer catalysis properties of robust, hexaamide cages in organic solvent. Cage structural variation reveals that esterification catalysis with an acyl anhydride acyl carrier occurs only in bifunctional cages featuring internal pyridine motifs and two crucial antipodal carboxylic acid groups. 1H NMR data and X-ray crystallography show that the acyl carrier is rapidly activated inside the cavity as a covalent mixed-anhydride intermediate with an internal hydrogen bond. Michaelis-Menten (saturation) kinetics suggest weak binding (KM = 0.16 M) of the alcohol pronucleophile close to the internal anhydride. Finally, activation and delivery of the alcohol to the internal anhydride by the second carboxylic acid group forms ester product and releases the cage catalyst. Eyring analysis indicates a strong enthalpic stabilization of the transition state (5.5 kcal/mol) corresponding to a rate acceleration of 104 over background acylation, and an ordered, associative rate-determining attack by the alcohol, supported by DFT calculations. We conclude that internal bifunctional organocatalysis specific to the cage structural design is responsible for the enhancement over the background reaction. These results pave the way for organic-phase enzyme mimicry in self-assembled cavities with the potential for cavity elaboration to enact selective acylations.
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Affiliation(s)
- Keith G Andrews
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, U.K
- Department of Chemistry, Durham University, Lower Mount Joy, South Rd, Durham DH1 3LE, U.K
| | - Tomasz K Piskorz
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, U.K
| | - Peter N Horton
- UK National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Simon J Coles
- UK National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, U.K
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2
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Bahrami F, Zhao Y. Rational Design and Synthesis of an Artificial Enzyme for S N2 Reactions through Micellar Imprinting. Org Lett 2024; 26:73-77. [PMID: 38135651 PMCID: PMC11097202 DOI: 10.1021/acs.orglett.3c03666] [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] [Indexed: 12/24/2023]
Abstract
The rational design of catalysts with enzyme-like properties is an elusive goal of chemists despite tremendous interest. Molecular imprinting inside surfactant micelles, followed by postmodification, creates a tailored active site in a water-soluble polymeric "artificial enzyme" for the benzylation of 4-nitrophenol. The reaction happens under neutral conditions with excellent substrate selectivity. Similar to many enzymes, electrostatics play vital roles in catalysis and can be tuned through different bases introduced into the active site.
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Affiliation(s)
- Foroogh Bahrami
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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3
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Luo M, Lan F, Li W, Chen S, Zhang L, Situ B, Li B, Liu C, Pan W, Gao Z, Zhang Y, Zheng L. Design strategies and advanced applications of primer exchange reactions in biosensing: A review. Anal Chim Acta 2023; 1283:341824. [PMID: 37977767 DOI: 10.1016/j.aca.2023.341824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 11/19/2023]
Abstract
Early disease diagnosis relies on the sensitive detection and imaging of biomarkers. Signal amplification is one of the most commonly used methods to improve detection sensitivity. Primer exchange reaction (PER) is a novel signal amplification technique that has garnered attention because of its simple and sensitive features. The classical PER involves a single catalytic hairpin, which enables the attachment of custom sequences to the primer chain, generating a long repeat sequence that can bind numerous signaling molecules and achieve powerful signal amplification. Currently, numerous PER-based signal amplification strategies are available that can improve detection sensitivity and promote the development of the signal amplification field. This review focuses on the mechanism of typical PER, the diversification of PER, and PER-based biosensors for various targets. Finally, the challenges and prospects of PER development are discussed.
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Affiliation(s)
- Min Luo
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Fei Lan
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Wenbin Li
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Siting Chen
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Lifeng Zhang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Bo Situ
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Bo Li
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Chunchen Liu
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Weilun Pan
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Zhuowei Gao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Ye Zhang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Lei Zheng
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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4
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Chaturvedi SS, Bím D, Christov CZ, Alexandrova AN. From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics. Chem Sci 2023; 14:10997-11011. [PMID: 37860658 PMCID: PMC10583697 DOI: 10.1039/d3sc02982d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme function. Furthermore, we present several case studies illustrating successful enzyme-design efforts incorporating enzyme strategies mentioned above to achieve improved catalytic properties. Finally, we envision the future of enzyme design research, spotlighting the challenges yet to be overcome and the synergy of intrinsic electric fields, second coordination sphere interactions, and conformational dynamics to push the state-of-the-art boundaries.
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Affiliation(s)
- Shobhit S Chaturvedi
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
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5
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Shen X, Zhang S, Long J, Chen C, Wang M, Cui Z, Chen B, Tan T. A Highly Sensitive Model Based on Graph Neural Networks for Enzyme Key Catalytic Residue Prediction. J Chem Inf Model 2023; 63:4277-4290. [PMID: 37399293 DOI: 10.1021/acs.jcim.3c00273] [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: 07/05/2023]
Abstract
Determining the catalytic site of enzymes is a great help for understanding the relationship between protein sequence, structure, and function, which provides the basis and targets for designing, modifying, and enhancing enzyme activity. The unique local spatial configuration bound to the substrate at the active center of the enzyme determines the catalytic ability of enzymes and plays an important role in the catalytic site prediction. As a suitable tool, the graph neural network can better understand and identify the residue sites with unique local spatial configurations due to its remarkable ability to characterize the three-dimensional structural features of proteins. Consequently, a novel model for predicting enzyme catalytic sites has been developed, which incorporates a uniquely designed adaptive edge-gated graph attention neural network (AEGAN). This model is capable of effectively handling sequential and structural characteristics of proteins at various levels, and the extracted features enable an accurate description of the local spatial configuration of the enzyme active site by sampling the local space around candidate residues and special design of amino acid physical and chemical properties. To evaluate its performance, the model was compared with existing catalytic site prediction models using different benchmark datasets and achieved the best results on each benchmark dataset. The model exhibited a sensitivity of 0.9659, accuracy of 0.9226, and area under the precision-recall curve (AUPRC) of 0.9241 on the independent test set constructed for evaluation. Furthermore, the F1-score of this model is nearly four times higher than that of the best-performing similar model in previous studies. This research can serve as a valuable tool to help researchers understand protein sequence-structure-function relationships while facilitating the characterization of novel enzymes of unknown function.
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Affiliation(s)
- Xiaowei Shen
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Shiding Zhang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Jianyu Long
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Changjing Chen
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Meng Wang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Ziheng Cui
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Biqiang Chen
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, 100029, Beijing, China
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6
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Bearne SL. Capturing the free energy of transition state stabilization: insights from the inhibition of mandelate racemase. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220041. [PMID: 36633273 PMCID: PMC9835602 DOI: 10.1098/rstb.2022.0041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mandelate racemase (MR) catalyses the Mg2+-dependent interconversion of (R)- and (S)-mandelate. To effect catalysis, MR stabilizes the altered substrate in the transition state (TS) by approximately 26 kcal mol-1 (-ΔGtx), such that the upper limit of the virtual dissociation constant of the enzyme-TS complex is 2 × 10-19 M. Designing TS analogue inhibitors that capture a significant amount of ΔGtx for binding presents a challenge since there are a limited number of protein binding determinants that interact with the substrate and the structural simplicity of mandelate constrains the number of possible isostructural variations. Indeed, current intermediate/TS analogue inhibitors of MR capture less than or equal to 30% of ΔGtx because they fail to fully capitalize on electrostatic interactions with the metal ion, and the strength and number of all available electrostatic and H-bond interactions with binding determinants present at the TS. Surprisingly, phenylboronic acid (PBA), 2-formyl-PBA, and para-chloro-PBA capture 31-38% of ΔGtx. The boronic acid group interacts with the Mg2+ ion and multiple binding determinants that effect TS stabilization. Inhibitors capable of forming multiple interactions can exploit the cooperative interactions that contribute to optimum binding of the TS. Hence, maximizing interactions with multiple binding determinants is integral to effective TS analogue inhibitor design. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
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7
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Cardiac Contractility Modulation Therapy in Patients with Amyloid Cardiomyopathy and Heart Failure, Case Report, Review of the Biophysics of CCM Function, and AMY-CCM Registry Presentation. J Clin Med 2023; 12:jcm12031184. [PMID: 36769832 PMCID: PMC9917884 DOI: 10.3390/jcm12031184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Cardiac amyloidosis may result in an aggressive form of heart failure (HF). Cardiac contractility modulation (CCM) has been shown to be a concrete therapeutic option in patients with symptomatic HF, but there is no evidence of its application in patients with cardiac amyloidosis. We present the case of TTR amyloidosis, where CCM therapy proved to be effective. The patient had a history of multiple HF hospitalizations due to an established diagnosis of wild type TTR-Amyloidosis with significant cardiac involvement. Since he was highly symptomatic, except during continuous dobutamine and diuretic infusion, it was opted to pursue CCM therapy device implantation. At follow up, a significant improvement in clinical status was reported with an increase of EF, functional status (6 min walk test improved from zero meters at baseline, to 270 m at 1 month and to 460 m at 12 months), and a reduction in pulmonary pressures. One year after device implantation, no other HF hospital admission was needed. CCM therapy may be effective in this difficult clinical setting. The AMY-CCM Registry, which has just begun, will evaluate the efficacy of CCM in patients with HF and diagnosed TTR amyloidosis to bring new evidence on its potential impact as a therapeutic option.
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8
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Babić M, Janković P, Marchesan S, Mauša G, Kalafatovic D. Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs. J Chem Inf Model 2022; 62:6398-6410. [PMID: 36223497 DOI: 10.1021/acs.jcim.2c00977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ester hydrolysis is of wide biomedical interest, spanning from the green synthesis of pharmaceuticals to biomaterials' development. Existing peptide-based catalysts exhibit low catalytic efficiency compared to natural enzymes, due to the conformational heterogeneity of peptides. Moreover, there is lack of understanding of the correlation between the primary sequence and catalytic function. For this purpose, we statistically analyzed 22 EC 3.1 hydrolases with known catalytic triads, characterized by unique and well-defined mechanisms. The aim was to identify patterns at the sequence level that will better inform the creation of short peptides containing important information for catalysis, based on the catalytic triad, oxyanion holes and the triad residues microenvironments. Moreover, fragmentation schemes of the primary sequence of selected enzymes alongside the study of their amino acid frequencies, composition, and physicochemical properties are proposed. The results showed highly conserved catalytic sites with distinct positional patterns and chemical microenvironments that favor catalysis and revealed variations in catalytic site composition that could be useful for the design of minimalistic catalysts.
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Affiliation(s)
- Marko Babić
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia
| | - Patrizia Janković
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127Trieste, Italy
| | - Goran Mauša
- Faculty of Engineering, University of Rijeka, 51000Rijeka, Croatia
| | - Daniela Kalafatovic
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia.,Center for Advanced Computing and Modeling, University of Rijeka, 51000Rijeka, Croatia
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9
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Magalhães ÁF, Powner MW. Prebiotic triose glycolysis promoted by co-catalytic proline and phosphate in neutral water. Chem Commun (Camb) 2022; 58:13519-13522. [PMID: 36398592 DOI: 10.1039/d2cc05466c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Proline and phosphate promote a near-quantitative aldol reaction between glycolaldehyde phosphate and formaldehyde at neutral pH in water. Our results demonstrate the important role of general acid-base catalysis in water and underscore the essential role that amino acid catalysis may have played in early evolution of life's core metabolic pathways.
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Affiliation(s)
- Álvaro F Magalhães
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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10
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Arifuzzaman MD, Bose I, Bahrami F, Zhao Y. Imprinted Polymeric Nanoparticles as Artificial Enzymes for Ester Hydrolysis at Room Temperature and pH 7. CHEM CATALYSIS 2022; 2:2049-2065. [PMID: 38098612 PMCID: PMC10720975 DOI: 10.1016/j.checat.2022.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Natural esterases hydrolyze esters under physiological pHs but chemists often have to use strongly acidic or basic conditions for the same hydrolysis. We report synthetic nanoparticle catalysts that hydrolyze nonactivated alkyl esters at room temperature and neutral pH, with enzyme-like catalytic mechanisms and exquisite substrate selectivity. Unlike natural enzymes that denature easily at elevated temperatures, the synthetic catalysts become more active at higher temperatures.
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Affiliation(s)
| | | | - Foroogh Bahrami
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, U.S.A
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, U.S.A
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11
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Gao S, Zhang W, Barrow SL, Iavarone AT, Klinman JP. Temperature-dependent hydrogen deuterium exchange shows impact of analog binding on adenosine deaminase flexibility but not embedded thermal networks. J Biol Chem 2022; 298:102350. [PMID: 35933011 PMCID: PMC9483566 DOI: 10.1016/j.jbc.2022.102350] [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: 04/04/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
The analysis of hydrogen deuterium exchange by mass spectrometry as a function of temperature and mutation (TDHDX-MS) has emerged as a generic and efficient tool for the spatial resolution of protein networks that are proposed to function in the thermal activation of catalysis. In this work, we extend TDHDX from apo-enzyme structures to protein-ligand complexes. Using adenosine deaminase as a prototype, we compared the impacts of a substrate analog (1-deaza-adenosine or DAA) and a very tight-binding inhibitor/transition state analog (pentostatin) at single and multiple temperatures. At a single temperature, we observed different HDX-MS properties for the two ligands, as expected from their 106-fold differences in strength of binding. By contrast, analogous patterns for TDHDX-MS emerge in the presence of both DAA and pentostatin, indicating similar impacts of either ligand on the enthalpic barriers for local protein unfolding. We extended TDHDX to a function-altering mutant of adenosine deaminase in the presence of pentostatin and revealed a protein thermal network that is highly similar to that previously reported for the apo-enzyme (Gao et al., 2020, JACS 142, 19936-19949). Finally, we discuss the differential impacts of pentostatin binding on overall protein flexibility vs. site-specific thermal transfer pathways in the context of models for substrate-induced changes to a distributed protein conformational landscape that act in synergy with embedded protein thermal networks to achieve efficient catalysis.
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Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Samuel L Barrow
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, United States.
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12
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Targeting the alternative oxidase (AOX) for human health and food security, a pharmaceutical and agrochemical target or a rescue mechanism? Biochem J 2022; 479:1337-1359. [PMID: 35748702 PMCID: PMC9246349 DOI: 10.1042/bcj20180192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022]
Abstract
Some of the most threatening human diseases are due to a blockage of the mitochondrial electron transport chain (ETC). In a variety of plants, fungi, and prokaryotes, there is a naturally evolved mechanism for such threats to viability, namely a bypassing of the blocked portion of the ETC by alternative enzymes of the respiratory chain. One such enzyme is the alternative oxidase (AOX). When AOX is expressed, it enables its host to survive life-threatening conditions or, as in parasites, to evade host defenses. In vertebrates, this mechanism has been lost during evolution. However, we and others have shown that transfer of AOX into the genome of the fruit fly and mouse results in a catalytically engaged AOX. This implies that not only is the AOX a promising target for combating human or agricultural pathogens but also a novel approach to elucidate disease mechanisms or, in several cases, potentially a therapeutic cure for human diseases. In this review, we highlight the varying functions of AOX in their natural hosts and upon xenotopic expression, and discuss the resulting need to develop species-specific AOX inhibitors.
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13
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Chen K, Zhao Y. Dynamic Tuning in Synthetic Glycosidase for Selective Hydrolysis of Alkyl and Aryl Glycosides. J Org Chem 2022; 87:4195-4203. [PMID: 35254827 PMCID: PMC9089355 DOI: 10.1021/acs.joc.1c03029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymes use sophisticated conformational control to optimize the dynamics of their protein framework for efficient catalysis. Although it is difficult to employ a similar strategy to improve catalysis in a synthetic enzyme, we here report that modulation of the dynamics of the substrate in the active site is readily achievable in a complex between a molecularly imprinted nanoparticle and its acid cofactor, through tuning of the size and shape of the imprinted site. As the alkyl glucoside substrate is bound with increasing strength and held in a more tightly fitted pocket, the acid-catalyzed glycan hydrolysis becomes more difficult. A larger, wider active site, although less able to bind the substrate, affords a higher catalytic activity, likely due to easier alignment of the substrate and the acid cofactor for a general acid catalysis. The substrate selectivity is controlled by both the tightness of the aglycon-binding site and the orientation of the glycan-binding boroxole group.
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Affiliation(s)
- Kaiqian Chen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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14
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Wang J, Konigsberg WH. Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion. Front Mol Biosci 2022; 9:824794. [PMID: 35300112 PMCID: PMC8921852 DOI: 10.3389/fmolb.2022.824794] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/14/2022] [Indexed: 11/15/2022] Open
Abstract
Almost all DNA polymerases (pols) exhibit bell-shaped activity curves as a function of both pH and Mg2+ concentration. The pol activity is reduced when the pH deviates from the optimal value. When the pH is too low the concentration of a deprotonated general base (namely, the attacking 3′-hydroxyl of the 3′ terminal residue of the primer strand) is reduced exponentially. When the pH is too high the concentration of a protonated general acid (i.e., the leaving pyrophosphate group) is reduced. Similarly, the pol activity also decreases when the concentration of the divalent metal ions deviates from its optimal value: when it is too low, the binding of the two catalytic divalent metal ions required for the full activity is incomplete, and when it is too high a third divalent metal ion binds to pyrophosphate, keeping it in the replication complex longer and serving as a substrate for pyrophosphorylysis within the complex. Currently, there is a controversy about the role of the third metal ion which we will address in this review.
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15
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Parveen A, Devika R. Fibrinolytic Enzyme - An Overview. Curr Pharm Biotechnol 2022; 23:1336-1345. [PMID: 34983344 DOI: 10.2174/1389201023666220104143113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/21/2021] [Accepted: 10/13/2021] [Indexed: 11/22/2022]
Abstract
Cardiovascular diseases, like coronary heart disease or artery disorders (arteriosclerosis, including artery solidification), heart failure (myocardial infarction), arrhythmias, congestive heart condition, stroke, elevated vital signs (hypertension), rheumatic heart disorder, and other circulatory system dysfunctions are the most common causes of death worldwide. Cardiovascular disorders are treated with stenting, coronary bypass surgery grafting, anticoagulants, antiplatelet agents, and other pharmacological and surgical procedures; however, these have limitations due to their adverse effects. Fibrinolytic agents degrade fibrin through enzymatic and biochemical processes. There are various enzymes that are currently used as a treatment for CVDs, like Streptokinase, Nattokinase, Staphylokinase, Urokinase, etc. These enzymes are derived from various sources like bacteria, fungi, algae, marine organisms, plants, snakes, and other organisms. This review deals with the fibrinolytic enzymes, their mechanisms, sources, and their therapeutic potential.
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Affiliation(s)
- Parveen A
- Department of Biotechnology, Biotechnology, Aarupadai Institute of Technology, Vinayaka Missions University, Chennai, India
| | - Devika R
- Department of Biotechnology, Biotechnology, Aarupadai Institute of Technology, Vinayaka Missions University, Chennai, India
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16
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Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Front Mol Biosci 2022; 9:1072733. [PMID: 36699705 PMCID: PMC9868570 DOI: 10.3389/fmolb.2022.1072733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide RNA (gRNA) that serves as a binding scaffold to guide it to the target DNA duplex via a RecA-like strand-displacement mechanism but without ATP binding or hydrolysis. The target search begins with the protospacer adjacent motif or PAM-interacting domain, recognizing it at the major groove of the duplex and melting its downstream duplex where an RNA-DNA heteroduplex is formed at nanomolar affinity. The rate-limiting step is the formation of an R-loop structure where the HNH domain inserts between the target heteroduplex and the displaced non-target DNA strand. Once the R-loop structure is formed, the non-target strand is rapidly cleaved by RuvC and ejected from the active site. This event is immediately followed by cleavage of the target DNA strand by the HNH domain and product release. Within CRISPR-associated protein 9, the HNH domain is inserted into the RuvC domain near the RuvC active site via two linker loops that provide allosteric communication between the two active sites. Due to the high flexibility of these loops and active sites, biophysical techniques have been instrumental in characterizing the dynamics and mechanism of the CRISPR-associated protein 9 nucleases, aiding structural studies in the visualization of the complete active sites and relevant linker structures. Here, we review biochemical, structural, and biophysical studies on the underlying mechanism with emphasis on how CRISPR-associated protein 9 selects the target DNA duplex and rejects non-target sequences.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Mohd Ahsan
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Souvik Sinha
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Erin Skeens
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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Pérez de la Lastra JM, Baca-González V, González-Acosta S, Asensio-Calavia P, Otazo-Pérez A, Morales-delaNuez A. Antibodies targeting enzyme inhibition as potential tools for research and drug development. Biomol Concepts 2021; 12:215-232. [PMID: 35104929 DOI: 10.1515/bmc-2021-0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/31/2021] [Indexed: 12/29/2022] Open
Abstract
Antibodies have transformed biomedical research and are now being used for different experimental applications. Generally, the interaction of enzymes with their specific antibodies can lead to a reduction in their enzymatic activity. The effect of the antibody is dependent on its narrow i.e. the regions of the enzyme to which it is directed. The mechanism of this inhibition is rarely a direct combination of the antibodies with the catalytic site, but is rather due to steric hindrance, barring the substrate access to the active site. In several systems, however, the interaction with the antibody induces conformational changes on the enzyme that can either inhibit or enhance its catalytic activity. The extent of enzyme inhibition or enhancement is, therefore, a reflection of the nature and distribution of the various antigenic determinants on the enzyme molecule. Currently, the mode of action of many enzymes has been elucidated at the molecular level. We here review the molecular mechanisms and recent trends by which antibodies inhibit the catalytic activity of enzymes and provide examples of how specific antibodies can be useful for the neutralization of biologically active molecules.
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Affiliation(s)
- José Manuel Pérez de la Lastra
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
| | - Victoria Baca-González
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Sergio González-Acosta
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
| | - Patricia Asensio-Calavia
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Andrea Otazo-Pérez
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Antonio Morales-delaNuez
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
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18
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Zanella BTT, Magiore IC, Duran BOS, Pereira GG, Vicente IST, Carvalho PLPF, Salomão RAS, Mareco EA, Carvalho RF, de Paula TG, Barros MM, Dal-Pai-Silva M. Ascorbic Acid Supplementation Improves Skeletal Muscle Growth in Pacu ( Piaractus mesopotamicus) Juveniles: In Vivo and In Vitro Studies. Int J Mol Sci 2021; 22:2995. [PMID: 33804272 PMCID: PMC7998472 DOI: 10.3390/ijms22062995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
In fish, fasting leads to loss of muscle mass. This condition triggers oxidative stress, and therefore, antioxidants can be an alternative to muscle recovery. We investigated the effects of antioxidant ascorbic acid (AA) on the morphology, antioxidant enzyme activity, and gene expression in the skeletal muscle of pacu (Piaractus mesopotamicus) following fasting, using in vitro and in vivo strategies. Isolated muscle cells of the pacu were subjected to 72 h of nutrient restriction, followed by 24 h of incubation with nutrients or nutrients and AA (200 µM). Fish were fasted for 15 days, followed by 6 h and 15 and 30 days of refeeding with 100, 200, and 400 mg/kg of AA supplementation. AA addition increased cell diameter and the expression of anabolic and cell proliferation genes in vitro. In vivo, 400 mg/kg of AA increased anabolic and proliferative genes expression at 6 h of refeeding, the fiber diameter and the expression of genes related to cell proliferation at 15 days, and the expression of catabolic and oxidative metabolism genes at 30 days. Catalase activity remained low in the higher supplementation group. In conclusion, AA directly affected the isolated muscle cells, and the higher AA supplementation positively influenced muscle growth after fasting.
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Affiliation(s)
- Bruna Tereza Thomazini Zanella
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, UNESP, Botucatu 18618-689, São Paulo, Brazil; (B.T.T.Z.); (I.C.M.); (G.G.P.); (R.F.C.); (T.G.d.P.)
| | - Isabele Cristina Magiore
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, UNESP, Botucatu 18618-689, São Paulo, Brazil; (B.T.T.Z.); (I.C.M.); (G.G.P.); (R.F.C.); (T.G.d.P.)
| | - Bruno Oliveira Silva Duran
- Department of Histology, Embryology and Cell Biology, Institute of Biological Sciences, Federal University of Goiás (UFG), Goiânia 74690-900, Goiás, Brazil;
| | - Guilherme Gutierrez Pereira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, UNESP, Botucatu 18618-689, São Paulo, Brazil; (B.T.T.Z.); (I.C.M.); (G.G.P.); (R.F.C.); (T.G.d.P.)
| | - Igor Simões Tiagua Vicente
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University, UNESP, Botucatu 18618-681, São Paulo, Brazil; (I.S.T.V.); (P.L.P.F.C.); (M.M.B.)
| | - Pedro Luiz Pucci Figueiredo Carvalho
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University, UNESP, Botucatu 18618-681, São Paulo, Brazil; (I.S.T.V.); (P.L.P.F.C.); (M.M.B.)
| | - Rondinelle Artur Simões Salomão
- Environment and Regional Development Graduate Program, University of Western São Paulo, Presidente Prudente 19050-680, São Paulo, Brazil; (R.A.S.S.); (E.A.M.)
| | - Edson Assunção Mareco
- Environment and Regional Development Graduate Program, University of Western São Paulo, Presidente Prudente 19050-680, São Paulo, Brazil; (R.A.S.S.); (E.A.M.)
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, UNESP, Botucatu 18618-689, São Paulo, Brazil; (B.T.T.Z.); (I.C.M.); (G.G.P.); (R.F.C.); (T.G.d.P.)
| | - Tassiana Gutierrez de Paula
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, UNESP, Botucatu 18618-689, São Paulo, Brazil; (B.T.T.Z.); (I.C.M.); (G.G.P.); (R.F.C.); (T.G.d.P.)
| | - Margarida Maria Barros
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University, UNESP, Botucatu 18618-681, São Paulo, Brazil; (I.S.T.V.); (P.L.P.F.C.); (M.M.B.)
| | - Maeli Dal-Pai-Silva
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, UNESP, Botucatu 18618-689, São Paulo, Brazil; (B.T.T.Z.); (I.C.M.); (G.G.P.); (R.F.C.); (T.G.d.P.)
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19
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Nguyen MT, Moiani D, Ahmed Z, Arvai AS, Namjoshi S, Shin DS, Fedorov Y, Selvik EJ, Jones DE, Pink J, Yan Y, Laverty DJ, Nagel ZD, Tainer JA, Gerson SL. An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:143-159. [PMID: 33675849 PMCID: PMC8722130 DOI: 10.1016/j.pbiomolbio.2021.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/13/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Human uracil DNA-glycosylase (UDG) is the prototypic and first identified DNA glycosylase with a vital role in removing deaminated cytosine and incorporated uracil and 5-fluorouracil (5-FU) from DNA. UDG depletion sensitizes cells to high APOBEC3B deaminase and to pemetrexed (PEM) and floxuridine (5-FdU), which are toxic to tumor cells through incorporation of uracil and 5-FU into DNA. To identify small-molecule UDG inhibitors for pre-clinical evaluation, we optimized biochemical screening of a selected diversity collection of >3,000 small-molecules. We found aurintricarboxylic acid (ATA) as an inhibitor of purified UDG at an initial calculated IC50 < 100 nM. Subsequent enzymatic assays confirmed effective ATA inhibition but with an IC50 of 700 nM and showed direct binding to the human UDG with a KD of <700 nM. ATA displays preferential, dose-dependent binding to purified human UDG compared to human 8-oxoguanine DNA glycosylase. ATA did not bind uracil-containing DNA at these concentrations. Yet, combined crystal structure and in silico docking results unveil ATA interactions with the DNA binding channel and uracil-binding pocket in an open, destabilized UDG conformation. Biologically relevant ATA inhibition of UDG was measured in cell lysates from human DLD1 colon cancer cells and in MCF-7 breast cancer cells using a host cell reactivation assay. Collective findings provide proof-of-principle for development of an ATA-based chemotype and “door stopper” strategy targeting inhibitor binding to a destabilized, open pre-catalytic glycosylase conformation that prevents active site closing for functional DNA binding and nucleotide flipping needed to excise altered bases in DNA.
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Affiliation(s)
- My T Nguyen
- Case Western Reserve University, Department of Biochemistry, Cleveland, OH, 44106, USA
| | - Davide Moiani
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Andrew S Arvai
- Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sarita Namjoshi
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Dave S Shin
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuriy Fedorov
- Case Small-Molecule Screening Core, School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Edward J Selvik
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - John Pink
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yan Yan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daniel J Laverty
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Stanton L Gerson
- Case Western Reserve University, Department of Biochemistry, Cleveland, OH, 44106, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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20
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Maurer D, Breit B. Urea-Substituted Tetramethylcyclopentadienyl Ligands for Supramolecularly Accelerated Rh III -Catalyzed ortho-C-H Olefination of Benzoic Acid Derivatives. Chemistry 2021; 27:2643-2648. [PMID: 33294985 PMCID: PMC7898290 DOI: 10.1002/chem.202005130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 11/17/2022]
Abstract
The design and synthesis of air‐stable and conveniently crystallizable RhIII‐cyclopentadienyl catalysts substituted with a urea moiety, which are able to accelerate the C−H olefination of benzoic acid derivatives, is reported. Through kinetic studies and NMR titration experiments, the catalysts’ substrate recognition ability mediated by hydrogen bonding was identified to be the reason for this effect. Introduction of pyridone‐phosphine ligands capable of forming additional H‐bond interactions increased the catalytic performance even further. By unveiling a proportionality between reaction rate and relative complex formation enthalpy the hypothesis of a supramolecular catalyst preformation was supported. Its application to a variety of substrates proved the catalyst system's advantages, generally increasing the yields when compared to the results obtained with widely used [RhCp*Cl2]2.
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Affiliation(s)
- David Maurer
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Bernhard Breit
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
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21
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Paterson AL, Liu DJ, Kanbur U, Sadow AD, Perras FA. Observing the three-dimensional dynamics of supported metal complexes. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01241f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of heterogeneous catalysts are linked to their activity and selectivity but are poorly understood. NMR enables for the determination of high-resolution dynamic structures for such sites and the mapping of accessible conformations.
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22
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Roda S, Santiago G, Guallar V. Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:1-31. [PMID: 32951809 DOI: 10.1016/bs.apcsb.2020.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
With the increase of the need to use more sustainable processes for the industry in our society, the modeling of enzymes has become crucial to fully comprehend their mechanism of action and use this knowledge to enhance and design their properties. A lot of methods to study enzymes computationally exist and they have been classified on sequence-based, structure-based, and the more new artificial intelligence-based ones. Albeit the abundance of methods to help predict the function of an enzyme, molecular modeling is crucial when trying to understand the enzyme mechanism, as they aim to correlate atomistic information with experimental data. Among them, methods that simulate the system dynamics at a molecular mechanics level of theory (classical force fields) have shown to offer a comprehensive study. In this book chapter, we will analyze these techniques, emphasizing the importance of precise modeling of enzyme-substrate interactions. In the end, a brief explanation of the transference of the information from research studies to the industry is given accompanied with two examples of family enzymes where their modeling has helped their exploitation.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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23
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Rivoire O. Geometry and Flexibility of Optimal Catalysts in a Minimal Elastic Model. J Phys Chem B 2020; 124:807-813. [PMID: 31990545 DOI: 10.1021/acs.jpcb.0c00244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have general knowledge of the principles by which catalysts accelerate the rate of chemical reactions but no precise understanding of the geometrical and physical constraints to which their design is subject. To analyze these constraints, we introduce a minimal model of catalysis based on elastic networks where the implications of the geometry and flexibility of a catalyst can be studied systematically. The model demonstrates the relevance and limitations of the principle of transition-state stabilization: optimal catalysts are found to have a geometry complementary to the transition state but a degree of flexibility that nontrivially depends on the parameters of the reaction as well as on external parameters such as the concentrations of reactants and products. The results illustrate how simple physical models can provide valuable insights into the design of catalysts.
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Affiliation(s)
- Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM , PSL Research University , 75005 Paris , France
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24
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Rajabi M, Farhadian S, Shareghi B, Asgharzadeh S, Momeni L. Noncovalent interactions of bovine trypsin with curcumin and effect on stability, structure, and function. Colloids Surf B Biointerfaces 2019; 183:110287. [DOI: 10.1016/j.colsurfb.2019.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 01/20/2023]
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25
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Kohen A. Kinetic Isotope Effects as Probes for Hydrogen Tunneling, Coupled Motion and Dynamics Contributions to Enzyme Catalysis. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967403103165486] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Since the early days of enzymology attempts have been made to deconvolute the various contributions of physical phenomena to enzyme catalysis. Here we present experimental and theoretical studies that examine the possible role of hydrogen tunneling, coupled motion, and enzyme dynamics in catalysis. In this review, we first introduce basic concepts of enzyme catalysis from a physical chemistry point of view. Then, we present several recent developments in the application of experimental tools that can probe tunneling, coupled motion, dynamic effects and other possible physical phenomena that may contribute to catalysis. These tools include kinetic isotope effects (KIEs), their temperature dependency and H/D/T mutual relations (the Swain–Schaad relationship). Several theories and models that assist in understanding those phenomena are also described. The possibility that these models invoke a direct role for the enzyme's dynamics (environmental fluctuations and rearrangements) is discussed. Finally, the need to compare the enzymatic reaction to the uncatalyzed one while investigating contributions to catalysis is emphasised.
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Affiliation(s)
- Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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26
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Wang J, Smithline ZB. Crystallographic evidence for two-metal-ion catalysis in human pol η. Protein Sci 2018; 28:439-447. [PMID: 30368948 DOI: 10.1002/pro.3541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 02/06/2023]
Abstract
Extensive evidence exists that DNA polymerases use two metal ions to catalyze the phosphoryl transfer reaction. Recently, competing evidence emerged, suggesting that a third metal ion, known as MnC, may be involved in catalysis. The binding of MnC was observed in crystal structures of the replication complexes of human polymerase (pol) η, pol β, and pol μ. Its occupancy (qMnC ) in the pol η replication complexes exhibited a strong correlation with the occupancy of the formed product pyrophosphate (qPPi ), i.e., qMnC ∝ qPPi . However, a key piece of information was missing that is needed to distinguish between two possible sequences of events: (i) the chemical reaction occurs first with only two meal ions, followed by the binding of MnC in a "catch-the-product" mode; and (ii) MnC binds first, followed by the chemical reaction with all three metal ions in a "push-the-reaction-forward" mode. Both mechanisms can lead to a strong correlation between qMnC and qPPi . However, qMnC ≤ qPPi in the first scenario, whereas qMnC ≥ qPPi in the second. In this study, an analysis of crystallographic data published recently for pol η complexes shows that the formation of the product pyrophosphate definitely precedes the binding of MnC. Therefore, just like all other DNA polymerases, human pol η employs a two-metal-ion catalytic mechanism. Rather than help to catalyze the reaction, MnC stabilizes the formed product, which remains trapped inside the crystals, before it slowly diffuses out.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
| | - Zachary B Smithline
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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27
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Abstract
Catalysis and mobility of reactants in fluid are normally thought to be decoupled. Violating this classical paradigm, this paper presents the catalyst laws of motion. Comparing experimental data to the theory presented here, we conclude that part of the free energy released by chemical reaction is channeled into driving catalysts to execute wormlike trajectories by piconewton forces performing work of a few kBT against fluid viscosity, where the rotational diffusion rate dictates the trajectory persistence length. This active motion agitates the fluid medium and produces antichemotaxis, the migration of catalyst down the gradient of the reactant concentration. Alternative explanations of enhanced catalyst mobility are examined critically. Using a microscopic theory to analyze experiments, we demonstrate that enzymes are active matter. Superresolution fluorescence measurements—performed across four orders of magnitude of substrate concentration, with emphasis on the biologically relevant regime around or below the Michaelis–Menten constant—show that catalysis boosts the motion of enzymes to be superdiffusive for a few microseconds, enhancing their effective diffusivity over longer timescales. Occurring at the catalytic turnover rate, these fast ballistic leaps maintain direction over a duration limited by rotational diffusion, driving enzymes to execute wormlike trajectories by piconewton forces performing work of a few kBT against viscosity. The boosts are more frequent at high substrate concentrations, biasing the trajectories toward substrate-poor regions, thus exhibiting antichemotaxis, demonstrated here experimentally over a wide range of aqueous concentrations. Alternative noncatalytic, passive mechanisms that predict chemotaxis, cross-diffusion, and phoresis, are critically analyzed. We examine the physical interpretation of our findings, speculate on the underlying mechanism, and discuss the avenues they open with biological and technological implications. These findings violate the classical paradigm that chemical reaction and motility are distinct processes, and suggest reaction–motion coupling as a general principle of catalysis.
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28
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Bruschini M, Ercolani G, Gallina S, Mencarelli P. Record Rate Enhancements for Tetrathiafulvalene Guests in the Formation of Bipyridinium- and Diazapyrenium-Based [2]Pseudorotaxanes. J Org Chem 2018; 83:11446-11449. [PMID: 30067031 DOI: 10.1021/acs.joc.8b01786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The catalytic effects of guests 5-7 on the cyclization of 1 and 3 have been measured at 62 °C in MeCN. A record rate acceleration of more than 2000 times has been observed in the cyclization of the tricationic host 3 featuring large diazapyrenium π-surfaces by tetrathiafulvalene guests 6 and 7. The results emphasize the role played by extended π-surfaces in the host and the goodness of a tetrathiafulvalene core in the guest, enhanced by polyethereal side arms.
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Affiliation(s)
- Michele Bruschini
- Dipartimento di Chimica e CNR-IMC , Università di Roma La Sapienza , P. le Aldo Moro, 2 , 00185 Roma , Italy
| | - Gianfranco Ercolani
- Dipartimento di Scienze e Tecnologie Chimiche , Università di Roma Tor Vergata , Via della Ricerca Scientifica , 00133 Roma , Italy
| | - Stefano Gallina
- Dipartimento di Chimica e CNR-IMC , Università di Roma La Sapienza , P. le Aldo Moro, 2 , 00185 Roma , Italy
| | - Paolo Mencarelli
- Dipartimento di Chimica e CNR-IMC , Università di Roma La Sapienza , P. le Aldo Moro, 2 , 00185 Roma , Italy
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29
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Abstract
What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.
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Affiliation(s)
- Stephen D Fried
- Proteins and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305;
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Yao Z, Zhang L, Gao B, Cui D, Wang F, He X, Zhang JZH, Wei D. A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B. J Chem Inf Model 2016; 56:1979-1994. [DOI: 10.1021/acs.jcim.5b00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhiqiang Yao
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Lujia Zhang
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Bei Gao
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Dongbing Cui
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Fengqing Wang
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xiao He
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z. H. Zhang
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Dongzhi Wei
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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Goshen-Lago T, Goldberg-Carp A, Melamed D, Darlyuk-Saadon I, Bai C, Ahn NG, Admon A, Engelberg D. Variants of the yeast MAPK Mpk1 are fully functional independently of activation loop phosphorylation. Mol Biol Cell 2016; 27:2771-83. [PMID: 27413009 PMCID: PMC5007096 DOI: 10.1091/mbc.e16-03-0167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
MAPKs are catalytically and biologically active only when dually phosphorylated on a TEY motif. Mutations in the yeast MAPK Mpk1 are described that render it fully functional when mutated in its TEY motif and even when it carries a kinase-dead mutation. MAP kinases of the ERK family are conserved from yeast to humans. Their catalytic activity is dependent on dual phosphorylation of their activation loop’s TEY motif, catalyzed by MAPK kinases (MEKs). Here we studied variants of Mpk1, a yeast orthologue of Erk, which is essential for cell wall integrity. Cells lacking MPK1, or the genes encoding the relevant MEKs, MKK1 and MKK2, do not proliferate under cell wall stress, imposed, for example, by caffeine. Mutants of Mpk1, Mpk1(Y268C) and Mpk1(Y268A), function independently of Mkk1 and Mkk2. We show that these variants are phosphorylated at their activation loop in mkk1∆mkk2∆ and mkk1∆mkk2∆pbs2∆ste7∆ cells, suggesting that they autophosphorylate. However, strikingly, when Y268C/A mutations were combined with the kinase-dead mutation, K54R, or mutations at the TEY motif, T190A+Y192F, the resulting proteins still allowed mkk1∆mkk2∆ cells to proliferate under caffeine stress. Mutating the equivalent residue, Tyr-280/Tyr-261, in Erk1/Erk2 significantly impaired Erk1/2’s catalytic activity. This study describes the first case in which a MAPK, Erk/Mpk1, imposes a phenotype via a mechanism that is independent of TEY phosphorylation and an unusual case in which an equivalent mutation in a highly conserved domain of yeast and mammalian Erks causes an opposite effect.
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Affiliation(s)
- Tal Goshen-Lago
- Department of Biological Chemistry, Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Anat Goldberg-Carp
- Department of Biological Chemistry, Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dganit Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ilona Darlyuk-Saadon
- CREATE-NUS-HUJ, Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore, Singapore 138602 Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
| | - Chen Bai
- CREATE-NUS-HUJ, Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore, Singapore 138602 Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
| | - Natalie G Ahn
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - David Engelberg
- Department of Biological Chemistry, Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel CREATE-NUS-HUJ, Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore, Singapore 138602 Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
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32
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Matyushov DV. Protein electron transfer: is biology (thermo)dynamic? JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:473001. [PMID: 26558324 DOI: 10.1088/0953-8984/27/47/473001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life's ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein's elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic activated kinetics, which extends the transition-state theory to dynamically dispersive media. Releasing the grip of thermodynamics in kinetic calculations through nonergodicity provides the mechanism for an efficient optimization between reaction rates and the spectrum of relaxation times of the protein-water thermal bath. Bath dynamics, it appears, play as important role as the free energy in optimizing biology's performance.
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Affiliation(s)
- Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
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Colomb W, Sarkar SK. Extracting physics of life at the molecular level: A review of single-molecule data analyses. Phys Life Rev 2015; 13:107-37. [PMID: 25660417 DOI: 10.1016/j.plrev.2015.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
Abstract
Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.
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Affiliation(s)
- Warren Colomb
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States.
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34
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Rajabi K. Microsecond pulsed hydrogen/deuterium exchange of electrosprayed ubiquitin ions stored in a linear ion trap. Phys Chem Chem Phys 2015; 17:3607-16. [DOI: 10.1039/c4cp04716h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The pulsed HDX MS method is sampling a population of ubiquitin ions with a similar backbone fold as solution.
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Affiliation(s)
- Khadijeh Rajabi
- Department of Chemistry
- University of British Columbia (UBC)
- Vancouver
- Canada
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35
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Warszawski S, Netzer R, Tawfik DS, Fleishman SJ. A "fuzzy"-logic language for encoding multiple physical traits in biomolecules. J Mol Biol 2014; 426:4125-4138. [PMID: 25311857 PMCID: PMC4270444 DOI: 10.1016/j.jmb.2014.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/21/2014] [Accepted: 10/02/2014] [Indexed: 12/16/2022]
Abstract
To carry out their activities, biological macromolecules balance different physical traits, such as stability, interaction affinity, and selectivity. How such often opposing traits are encoded in a macromolecular system is critical to our understanding of evolutionary processes and ability to design new molecules with desired functions. We present a framework for constraining design simulations to balance different physical characteristics. Each trait is represented by the equilibrium fractional occupancy of the desired state relative to its alternatives, ranging from none to full occupancy, and the different traits are combined using Boolean operators to effect a "fuzzy"-logic language for encoding any combination of traits. In another paper, we presented a new combinatorial backbone design algorithm AbDesign where the fuzzy-logic framework was used to optimize protein backbones and sequences for both stability and binding affinity in antibody-design simulation. We now extend this framework and find that fuzzy-logic design simulations reproduce sequence and structure design principles seen in nature to underlie exquisite specificity on the one hand and multispecificity on the other hand. The fuzzy-logic language is broadly applicable and could help define the space of tolerated and beneficial mutations in natural biomolecular systems and design artificial molecules that encode complex characteristics.
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Affiliation(s)
- Shira Warszawski
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ravit Netzer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sarel J Fleishman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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36
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An Z, He J, Dai Y, Yu C, Li B, He J. Enhanced heterogeneous asymmetric catalysis via the acid–base cooperation between achiral silanols of mesoporous supports and immobilized chiral amines. J Catal 2014. [DOI: 10.1016/j.jcat.2014.06.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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37
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Tiwari MK, Kalia VC, Kang YC, Lee JK. Role of a remote leucine residue in the catalytic function of polyol dehydrogenase. ACTA ACUST UNITED AC 2014; 10:3255-63. [DOI: 10.1039/c4mb00459k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study examined the role of remote residues on the structure and function of zinc-dependent polyol dehydrogenases.
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Affiliation(s)
| | - Vipin C. Kalia
- Microbial Biotechnology and Genomics
- CSIR-Institute of Genomics and Integrative Biology
- Delhi-110007, India
| | - Yun Chan Kang
- Department of Materials Science and Engineering
- Korea University
- Seoul 136-713, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering
- Seoul 143–701, Republic of Korea
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38
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Reymond JL, Chen Y. Antibody-Catalyzed Uni- and Multi-Substrate Reactions Compared Using Transition-State Binding (KTS). Isr J Chem 2013. [DOI: 10.1002/ijch.199600027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles. Proc Natl Acad Sci U S A 2013; 110:12271-6. [PMID: 23840058 DOI: 10.1073/pnas.1310964110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pauling's suggestion that enzymes are complementary in structure to the activated complexes of the reactions they catalyze has provided the conceptual basis to explain how enzymes obtain their fantastic catalytic prowess, and has served as a guiding principle in drug design for over 50 y. However, this model by itself fails to predict the magnitude of enzymes' rate accelerations. We construct a thermodynamic framework that begins with the classic concept of differential binding but invokes additional terms that are needed to account for subtle effects in the catalytic cycle's proton inventory. Although the model presented can be applied generally, this analysis focuses on ketosteroid isomerase (KSI) as an example, where recent experiments along with a large body of kinetic and thermodynamic data have provided strong support for the noncanonical thermodynamic contribution described. The resulting analysis precisely predicts the free energy barrier of KSI's reaction as determined from transition-state theory using only empirical thermodynamic data. This agreement is suggestive that a complete free energy inventory of the KSI catalytic cycle has been identified.
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40
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Muller F. The nature and mechanism of superoxide production by the electron transport chain: Its relevance to aging. J Am Aging Assoc 2013; 23:227-53. [PMID: 23604868 DOI: 10.1007/s11357-000-0022-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Most biogerontologists agree that oxygen (and nitrogen) free radicals play a major role in the process of aging. The evidence strongly suggests that the electron transport chain, located in the inner mitochondrial membrane, is the major source of reactive oxygen species in animal cells. It has been reported that there exists an inverse correlation between the rate of superoxide/hydrogen peroxide production by mitochondria and the maximum longevity of mammalian species. However, no correlation or most frequently an inverse correlation exists between the amount of antioxidant enzymes and maximum longevity. Although overexpression of the antioxidant enzymes SOD1 and CAT (as well as SOD1 alone) have been successful at extending maximum lifespan in Drosophila, this has not been the case in mice. Several labs have overexpressed SOD1 and failed to see a positive effect on longevity. An explanation for this failure is that there is some level of superoxide damage that is not preventable by SOD, such as that initiated by the hydroperoxyl radical inside the lipid bilayer, and that accumulation of this damage is responsible for aging. I therefore suggest an alternative approach to testing the free radical theory of aging in mammals. Instead of trying to increase the amount of antioxidant enzymes, I suggest using molecular biology/transgenics to decrease the rate of superoxide production, which in the context of the free radical theory of aging would be expected to increase longevity. This paper aims to summarize what is known about the nature and mechanisms of superoxide production and what genes are involved in controlling the rate of superoxide production.
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Affiliation(s)
- F Muller
- Laboratory of David M. Kramer, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
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41
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Chakraborty S. A quantitative measure of electrostatic perturbation in holo and apo enzymes induced by structural changes. PLoS One 2013; 8:e59352. [PMID: 23516628 PMCID: PMC3597595 DOI: 10.1371/journal.pone.0059352] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/13/2013] [Indexed: 11/19/2022] Open
Abstract
Biological pathways are subject to subtle manipulations that achieve a wide range of functional variation in differing physiological niches. In many instances, changes in the structure of an enzyme on ligand binding germinate electrostatic perturbations that form the basis of its changed catalytic or transcriptional efficiency. Computational methods that seek to gain insights into the electrostatic changes in enzymes require expertise to setup and computing prowess. In the current work, we present a fast, easy and reliable methodology to compute electrostatic perturbations induced by ligand binding (MEPP). The theoretical foundation of MEPP is the conserved electrostatic potential difference (EPD) in cognate pairs of active site residues in proteins with the same functionality. Previously, this invariance has been used to unravel promiscuous serine protease and metallo-β-lactamase scaffolds in alkaline phosphatases. Given that a similarity in EPD is significant, we expect differences in the EPD to be significant too. MEPP identifies residues or domains that undergo significant electrostatic perturbations, and also enumerates residue pairs that undergo significant polarity change. The gain in a certain polarity of a residue with respect to neighboring residues, or the reversal of polarity between two residues might indicate a change in the preferred ligand. The methodology of MEPP has been demonstrated on several enzymes that employ varying mechanisms to perform their roles. For example, we have attributed the change in polarity in residue pairs to be responsible for the loss of metal ion binding in fructose 1,6-bisphosphatases, and corroborated the pre-organized state of the active site of the enzyme with respect to functionally relevant changes in electric fields in ketosteroid isomerases.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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42
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Intrinsic evolutionary constraints on protease structure, enzyme acylation, and the identity of the catalytic triad. Proc Natl Acad Sci U S A 2013; 110:E653-61. [PMID: 23382230 DOI: 10.1073/pnas.1221050110] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The study of proteolysis lies at the heart of our understanding of biocatalysis, enzyme evolution, and drug development. To understand the degree of natural variation in protease active sites, we systematically evaluated simple active site features from all serine, cysteine and threonine proteases of independent lineage. This convergent evolutionary analysis revealed several interrelated and previously unrecognized relationships. The reactive rotamer of the nucleophile determines which neighboring amide can be used in the local oxyanion hole. Each rotamer-oxyanion hole combination limits the location of the moiety facilitating proton transfer and, combined together, fixes the stereochemistry of catalysis. All proteases that use an acyl-enzyme mechanism naturally divide into two classes according to which face of the peptide substrate is attacked during catalysis. We show that each class is subject to unique structural constraints that have governed the convergent evolution of enzyme structure. Using this framework, we show that the γ-methyl of Thr causes an intrinsic steric clash that precludes its use as the nucleophile in the traditional catalytic triad. This constraint is released upon autoproteolysis and we propose a molecular basis for the increased enzymatic efficiency introduced by the γ-methyl of Thr. Finally, we identify several classes of natural products whose mode of action is sensitive to the division according to the face of attack identified here. This analysis of protease structure and function unifies 50 y of biocatalysis research, providing a framework for the continued study of enzyme evolution and the development of inhibitors with increased selectivity.
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43
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Jiang L, Zheng H, Lu H. Use of Linear and Weibull Functions to Model Ascorbic Acid Degradation in Chinese Winter Jujube during Postharvest Storage in Light and Dark Conditions. J FOOD PROCESS PRES 2012. [DOI: 10.1111/jfpp.12040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Lingling Jiang
- College of Chemistry and Life Science; Zhejiang Normal University; Jinhua 321004 China
| | - Hong Zheng
- College of Chemistry and Life Science; Zhejiang Normal University; Jinhua 321004 China
| | - Hongfei Lu
- College of Chemistry and Life Science; Zhejiang Normal University; Jinhua 321004 China
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44
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Kumar A, Venkatesu P. Overview of the stability of α-chymotrypsin in different solvent media. Chem Rev 2012; 112:4283-307. [PMID: 22506806 DOI: 10.1021/cr2003773] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Simón L, Goodman JM. Hydrogen-bond stabilization in oxyanion holes: grand jeté to three dimensions. Org Biomol Chem 2012; 10:1905-13. [PMID: 22273994 DOI: 10.1039/c2ob06717j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We recently reported crystallographic evidence that the hydrogen bonds which can stabilize oxygen-centered negative charge within enzyme oxyanion holes are rarely found in the place they should be expected on the basis of the analysis of small-molecule crystal structures. We investigated this phenomenon using calculations on simplified active site models. A recent paper suggested that several aspects of the analysis required further exploration. In this paper we: (i) review the results of our crystallographic study; (ii) report molecular dynamics studies which investigate the effect of protein movement; (iii) report ONIOM calculations which trace the reaction coordinate for an oxyanion hole reaction in the presence of a complete enzyme active site. These results show that the limitations of gas phase calculations on simplified models do not invalidate our comparison of competing active site geometries. These new results reaffirm the conclusion that oxyanion holes are not usually stabilized by planar arrangements of H-bonds, and that this sub-optimal transition state stabilization leads to better overall catalysis.
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Affiliation(s)
- Luis Simón
- Facultad de Ciencias Químicas, Universidad de Salamanca, Plaza de los Caídos 1-5, Salamanca, E37004, Spain.
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46
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Iyer P, Bajorath J. Mechanism-based bipartite matching molecular series graphs to identify structural modifications of receptor ligands that lead to mechanism hopping. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00281g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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47
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Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis. PLoS Biol 2011; 9:e1001193. [PMID: 22087074 PMCID: PMC3210774 DOI: 10.1371/journal.pbio.1001193] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/27/2011] [Indexed: 11/19/2022] Open
Abstract
Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme–substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme–substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design.
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48
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Jiang W, He X, Wang Y, Xu B, Li J, Liu F. Reactivity of Schiff Base Manganese(III) Complexes with Different Pendants toward the Hydrolysis of p-Nitrophenyl Picolinate. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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49
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Maddux NR, Joshi SB, Volkin DB, Ralston JP, Middaugh CR. Multidimensional methods for the formulation of biopharmaceuticals and vaccines. J Pharm Sci 2011; 100:4171-97. [PMID: 21647886 PMCID: PMC3949199 DOI: 10.1002/jps.22618] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 04/13/2011] [Accepted: 04/21/2011] [Indexed: 01/14/2023]
Abstract
Determining and preserving the higher order structural integrity and conformational stability of proteins, plasmid DNA, and macromolecular complexes such as viruses, virus-like particles, and adjuvanted antigens are often a significant barrier to the successful stabilization and formulation of biopharmaceutical drugs and vaccines. These properties typically must be investigated with multiple lower resolution experimental methods because each technique monitors only a narrow aspect of the overall conformational state of a macromolecular system. This review describes the use of empirical phase diagrams (EPDs) to combine large amounts of data from multiple high-throughput instruments and construct a map of a target macromolecule's physical state as a function of temperature, solvent conditions, and other stress variables. We present a tutorial on the mathematical methodology, an overview of some of the experimental methods typically used, and examples of some of the previous major formulation applications. We also explore novel applications of EPDs including potential new mathematical approaches as well as possible new biopharmaceutical applications such as analytical comparability, chemical stability, and protein dynamics.
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Affiliation(s)
- Nathaniel R. Maddux
- Department of Physics and Astronomy, University of Kansas, 1082 Malott, 1251 Wescoe Hall Drive, Lawrence, KS 66045
| | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, University of Kansas, 2010 Becker Drive, Lawrence, KS 66047
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, University of Kansas, 2010 Becker Drive, Lawrence, KS 66047
| | - John P. Ralston
- Department of Physics and Astronomy, University of Kansas, 1082 Malott, 1251 Wescoe Hall Drive, Lawrence, KS 66045
| | - C. Russell Middaugh
- Department of Pharmaceutical Chemistry, University of Kansas, 2010 Becker Drive, Lawrence, KS 66047
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Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase. Proc Natl Acad Sci U S A 2011; 108:16612-7. [PMID: 21949360 DOI: 10.1073/pnas.1113874108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding how electric fields and their fluctuations in the active site of enzymes affect efficient catalysis represents a critical objective of biochemical research. We have directly measured the dynamics of the electric field in the active site of a highly proficient enzyme, Δ(5)-3-ketosteroid isomerase (KSI), in response to a sudden electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields.
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