1
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Abstract
Metal cofactors are critical centers for different biochemical processes of metalloproteins, and often, this metal coordination renders additional structural stability. In this study, we explore the additional stability conferred by the copper ion on azurin by analyzing both the apo and holo forms using temperature replica exchange molecular dynamics (REMD) data. We find a 14 K decrease in denaturation temperature for apo (406 K) azurin relative to that of holo (420 K), indicating a copper ion-induced additional thermal stability for holo azurin. The unfolding of apo azurin begins with the melting of α-helix and β-sheet V, similar to that of holo form. β-Sheets IV, VII, and VIII are comparatively more stable than other β-strands and melt at higher temperatures. Similar to holo azurin, the strong hydrophobic interactions among the apolar residues in the protein core is the key factor that renders high stability to apo protein as well. We construct free energy surfaces at different temperatures to capture the major conformations along the unfolding basins of the protein. Using contact maps from different basins we show the changes in the interaction between different residues along the unfolding pathway. Furthermore, we compare the Cα root-mean-square fluctuations (Cα-RMSF) and B-factor of all residues of apo and holo forms to understand the flexibility of different regions. The concerted displacement of α-helix and β-sheets V and VI from the protein core is another distinction we observe for apo compared to the holo form, where β-sheet VI was relatively stable.
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Affiliation(s)
- Albin Joy
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Rajib Biswas
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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2
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Joy A, Biswas R. Molecular Insight into the High Thermal Stability of Metalloprotein Azurin. J Phys Chem B 2022; 126:2496-2506. [PMID: 35324174 DOI: 10.1021/acs.jpcb.2c00622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the events characterizing the steps of the unfolding pathway of blue copper metalloprotein azurin using replica exchange molecular dynamics (REMD). Our studies show that the unfolding of azurin begins with the melting of α-helix and β-sheets II and V. This is followed by the melting of other β-sheets and the exposure of hydrophobic protein core to the solvent, resulting in disruptions of its tertiary structure. Free energy surfaces constructed at different temperatures portray different basins that signify the stability of different melted structures in the unfolding process. The contact maps at different temperatures reveal that the strong hydrophobic interaction within the core of the protein is the vital force that renders high stability to this protein. Analysis of the individual β-sheets by looking into their amino acid sequence shows that β-sheets with charged side chains on the surface melt fast compared to others. The β-barrel of azurin is able to dynamically rearrange, and it helps the protein to preserve its hydrophobic core, holding back the native topology from melting fast. B-factor analysis shows that residues of β-sheets III, IV, and VII deviate less from their initial structure at the transition temperature.
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Affiliation(s)
- Albin Joy
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Rajib Biswas
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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3
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Maffucci I, Laage D, Stirnemann G, Sterpone F. Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes. Phys Chem Chem Phys 2020; 22:18361-18373. [DOI: 10.1039/d0cp02738c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The thermal resistance of two homolog enzymes is investigated, with an emphasis on their local stability and flexibility, and on the possible implications regarding their reactivity.
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Affiliation(s)
- Irene Maffucci
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Damien Laage
- PASTEUR
- Département de chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
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4
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Abdizadeh H, Tamer YT, Acar O, Toprak E, Atilgan AR, Atilgan C. Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance. Phys Chem Chem Phys 2018; 19:11416-11428. [PMID: 28422217 DOI: 10.1039/c7cp01458a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dihydrofolate reductase (DHFR) is a ubiquitous enzyme with an essential role in cell metabolism. DHFR catalyzes the reduction of dihydrofolate to tetrahydrofolate, which is a precursor for purine and thymidylate synthesis. Several DHFR targeting antifolate drugs including trimethoprim, a competitive antibacterial inhibitor, have therefore been developed and are clinically used. Evolution of resistance against antifolates is a common public health problem rendering these drugs ineffective. To combat the resistance problem, it is important to understand resistance-conferring changes in the DHFR structure and accordingly develop alternative strategies. Here, we structurally and dynamically characterize Escherichia coli DHFR in its wild type (WT) and trimethoprim resistant L28R mutant forms in the presence of the substrate and its inhibitor trimethoprim. We use molecular dynamics simulations to determine the conformational space, loop dynamics and hydrogen bond distributions at the active site of DHFR for the WT and the L28R mutant. We also report their experimental kcat, Km, and Ki values, accompanied by isothermal titration calorimetry measurements of DHFR that distinguish enthalpic and entropic contributions to trimethoprim binding. Although mutations that confer resistance to competitive inhibitors typically make enzymes more promiscuous and decrease affinity to both the substrate and the inhibitor, strikingly, we find that the L28R mutant has a unique resistance mechanism. While the binding affinity differences between the WT and the mutant for the inhibitor and the substrate are small, the newly formed extra hydrogen bonds with the aminobenzoyl glutamate tail of DHF in the L28R mutant leads to increased barriers for the dissociation of the substrate and the product. Therefore, the L28R mutant indirectly gains resistance by enjoying prolonged binding times in the enzyme-substrate complex. While this also leads to slower product release and decreases the catalytic rate of the L28R mutant, the overall effect is the maintenance of a sufficient product formation rate. Finally, the experimental and computational analyses together reveal the changes that occur in the energetic landscape of DHFR upon the resistance-conferring L28R mutation. We show that the negative entropy associated with the binding of trimethoprim in WT DHFR is due to water organization at the binding interface. Our study lays the framework to study structural changes in other trimethoprim resistant DHFR mutants.
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Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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5
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Goedegebuur F, Dankmeyer L, Gualfetti P, Karkehabadi S, Hansson H, Jana S, Huynh V, Kelemen BR, Kruithof P, Larenas EA, Teunissen PJM, Ståhlberg J, Payne CM, Mitchinson C, Sandgren M. Improving the thermal stability of cellobiohydrolase Cel7A from Hypocrea jecorina by directed evolution. J Biol Chem 2017; 292:17418-17430. [PMID: 28860192 DOI: 10.1074/jbc.m117.803270] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/24/2017] [Indexed: 11/06/2022] Open
Abstract
Secreted mixtures of Hypocrea jecorina cellulases are able to efficiently degrade cellulosic biomass to fermentable sugars at large, commercially relevant scales. H. jecorina Cel7A, cellobiohydrolase I, from glycoside hydrolase family 7, is the workhorse enzyme of the process. However, the thermal stability of Cel7A limits its use to processes where temperatures are no higher than 50 °C. Enhanced thermal stability is desirable to enable the use of higher processing temperatures and to improve the economic feasibility of industrial biomass conversion. Here, we enhanced the thermal stability of Cel7A through directed evolution. Sites with increased thermal stability properties were combined, and a Cel7A variant (FCA398) was obtained, which exhibited a 10.4 °C increase in Tm and a 44-fold greater half-life compared with the wild-type enzyme. This Cel7A variant contains 18 mutated sites and is active under application conditions up to at least 75 °C. The X-ray crystal structure of the catalytic domain was determined at 2.1 Å resolution and showed that the effects of the mutations are local and do not introduce major backbone conformational changes. Molecular dynamics simulations revealed that the catalytic domain of wild-type Cel7A and the FCA398 variant exhibit similar behavior at 300 K, whereas at elevated temperature (475 and 525 K), the FCA398 variant fluctuates less and maintains more native contacts over time. Combining the structural and dynamic investigations, rationales were developed for the stabilizing effect at many of the mutated sites.
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Affiliation(s)
- Frits Goedegebuur
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands,
| | - Lydia Dankmeyer
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands
| | | | - Saeid Karkehabadi
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Henrik Hansson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Suvamay Jana
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Vicky Huynh
- DuPont Industrial Biosciences, Palo Alto, California 94304
| | | | - Paulien Kruithof
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands
| | | | | | - Jerry Ståhlberg
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Christina M Payne
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | | | - Mats Sandgren
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
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6
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Geronimo I, Denning CA, Rogers WE, Othman T, Huxford T, Heidary DK, Glazer EC, Payne CM. Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450BM3 Variants. Biochemistry 2016; 55:3594-606. [PMID: 27267136 PMCID: PMC7422958 DOI: 10.1021/acs.biochem.6b00183] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450BM3 is a heme-containing enzyme from Bacillus megaterium that exhibits high monooxygenase activity and has a self-sufficient electron transfer system in the full-length enzyme. Its potential synthetic applications drive protein engineering efforts to produce variants capable of oxidizing nonnative substrates such as pharmaceuticals and aromatic pollutants. However, promiscuous P450BM3 mutants often exhibit lower stability, thereby hindering their industrial application. This study demonstrated that the heme domain R47L/F87V/L188Q/E267V/F81I pentuple mutant (PM) is destabilized because of the disruption of hydrophobic contacts and salt bridge interactions. This was directly observed from crystal structures of PM in the presence and absence of ligands (palmitic acid and metyrapone). The instability of the tertiary structure and heme environment of substrate-free PM was confirmed by pulse proteolysis and circular dichroism, respectively. Binding of the inhibitor, metyrapone, significantly stabilized PM, but the presence of the native substrate, palmitic acid, had no effect. On the basis of high-temperature molecular dynamics simulations, the lid domain, β-sheet 1, and Cys ligand loop (a β-bulge segment connected to the heme) are the most labile regions and, thus, potential sites for stabilizing mutations. Possible approaches to stabilization include improvement of hydrophobic packing interactions in the lid domain and introduction of new salt bridges into β-sheet 1 and the heme region. An understanding of the molecular factors behind the loss of stability of P450BM3 variants therefore expedites site-directed mutagenesis studies aimed at developing thermostability.
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Affiliation(s)
- Inacrist Geronimo
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, United States
| | - Catherine A. Denning
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - W. Eric Rogers
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - Thaer Othman
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - David K. Heidary
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Edith C. Glazer
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, United States
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7
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Ruiz-Pernía JJ, Behiry E, Luk LYP, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Minimization of dynamic effects in the evolution of dihydrofolate reductase. Chem Sci 2016; 7:3248-3255. [PMID: 29997817 PMCID: PMC6006479 DOI: 10.1039/c5sc04209g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/02/2016] [Indexed: 11/22/2022] Open
Abstract
Protein isotope labeling is a powerful technique to probe functionally important motions in enzyme catalysis and can be applied to investigate the conformational dynamics of proteins. Previous investigations have indicated that dynamic coupling is detrimental to catalysis by dihydrofolate reductase (DHFR) from the mesophile Escherichia coli (EcDHFR). Comparison of DHFRs from organisms adapted to survive at a wide range of temperatures suggests that dynamic coupling in DHFR catalysis has been minimized during evolution; it arises from reorganizational motions needed to facilitate charge transfer events. Contrary to the behaviour observed for the DHFR from the moderate thermophile Geobacillus stearothermophilus (BsDHFR), the chemical transformation catalyzed by the cold-adapted bacterium Moritella profunda (MpDHFR) is only weakly affected by protein isotope substitutions at low temperatures, but the isotopically substituted enzyme is a substantially inferior catalyst at higher, non-physiological temperatures. QM/MM studies revealed that this behaviour is caused by the enzyme's structural sensitivity to temperature changes, which enhances unfavorable dynamic coupling at higher temperatures by promoting additional recrossing trajectories on the transition state dividing surface. We postulate that these motions are minimized by fine-tuning DHFR flexibility through optimization of the free energy surface of the reaction, such that a nearly static reaction-ready configuration with optimal electrostatic properties is maintained under physiological conditions.
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Affiliation(s)
- J Javier Ruiz-Pernía
- Departament de Química Física i Analítica , Universitat Jaume I , 12071 Castelló , Spain .
| | - Enas Behiry
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - Louis Y P Luk
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - E Joel Loveridge
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - Iñaki Tuñón
- Departament de Química Física , Universitat de València , 46100 Burjassot , Spain .
| | - Vicent Moliner
- Departament de Química Física i Analítica , Universitat Jaume I , 12071 Castelló , Spain .
| | - Rudolf K Allemann
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
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8
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Wiley AP, Swain MT, Phillips SC, Essex JW, Edge CM. Parametrization of Reversible Digitally Filtered Molecular Dynamics Simulations. J Chem Theory Comput 2015; 1:24-35. [PMID: 26641112 DOI: 10.1021/ct049970t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reversible Digitally Filtered Molecular Dynamics (RDFMD) is a method of amplifying or suppressing motions in a molecular dynamics simulation, through the application of a digital filter to the simulation velocities. RDFMD and its derivatives have been previously used to promote conformational motions in liquid-phase butane, the Syrian hamster prion protein, alanine dipeptide, and the pentapeptide, YPGDV. The RDFMD method has associated with it a number of parameters that require specification to optimize the desired response. In this paper methods for the systematic analysis of these parameters are presented and applied to YPGDV with the specific emphasis of ensuring a gentle and progressive method that produces maximum conformation change from the energy put into the system. The portability of the new parameter set is then shown with an application to the M20 loop of E-coli dihydrofolate reductase. A conformational change is induced from a closed to an open structure similar to that seen in the DHFR-NADP(+) complex.
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Affiliation(s)
- Adrian P Wiley
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.,GlaxoSmithKline, New Frontiers Science Park (North), Coldharbour Road, Harlow CM19 5AD, U.K
| | - Martin T Swain
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.,GlaxoSmithKline, New Frontiers Science Park (North), Coldharbour Road, Harlow CM19 5AD, U.K
| | - Stephen C Phillips
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.,GlaxoSmithKline, New Frontiers Science Park (North), Coldharbour Road, Harlow CM19 5AD, U.K
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.,GlaxoSmithKline, New Frontiers Science Park (North), Coldharbour Road, Harlow CM19 5AD, U.K
| | - Colin M Edge
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.,GlaxoSmithKline, New Frontiers Science Park (North), Coldharbour Road, Harlow CM19 5AD, U.K
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9
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Zhang PP, Zhao L, Long SY, Tian P. The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study. J Mol Model 2015; 21:72. [PMID: 25750022 DOI: 10.1007/s00894-015-2625-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 02/15/2015] [Indexed: 11/24/2022]
Abstract
Human cytosolic sulfotransferases (hSULTs) are important phase II metabolic enzymes. They catalyze transfer of the sulfuryl-group (-SO3) from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to the hydroxyl or primary amine moieties of a large number of endogenous and xenobiotic substrates. Broad selectivity and specificity of binding and activity within the sulfortransferases family could be detected by thermal denaturation assays, which have been made more and more suitable for high throughput screening based on recent technical advances. Here molecular dynamics simulations were used to explore the effect of the cofactor (PAPS) and substrate (LCA) on the thermal stability of the enzyme. It was found that the apo-enzyme unfolded fastest upon heating. The holo-enzyme with bound substrate LCA unfolded slowest. This thermo-denaturation order is consistent with that observed in experiments. Further it was found that the cofactor and substrate will pronouncedly increase the thermal stability of the active pocket regions that interact directly with the ligands. In addition, cofactor and substrate show noticeable synergy effect on the thermal stability of the enzyme.
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Affiliation(s)
- Pu-pu Zhang
- School of Life Sciences, Jilin University, Changchun, China
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10
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Kasper JR, Liu PF, Park C. Structure of a partially unfolded form of Escherichia coli dihydrofolate reductase provides insight into its folding pathway. Protein Sci 2014; 23:1728-37. [PMID: 25252157 DOI: 10.1002/pro.2555] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/07/2022]
Abstract
Proteins frequently fold via folding intermediates that correspond to local minima on the conformational energy landscape. Probing the structure of the partially unfolded forms in equilibrium under native conditions can provide insight into the properties of folding intermediates. To elucidate the structures of folding intermediates of Escherichia coli dihydrofolate reductase (DHFR), we investigated transient partial unfolding of DHFR under native conditions. We probed the structure of a high-energy conformation susceptible to proteolysis (cleavable form) using native-state proteolysis. The free energy for unfolding to the cleavable form is clearly less than that for global unfolding. The dependence of the free energy on urea concentration (m-value) also confirmed that the cleavable form is a partially unfolded form. By assessing the effect of mutations on the stability of the partially unfolded form, we found that native contacts in a hydrophobic cluster formed by the F-G and Met-20 loops on one face of the central β-sheet are mostly lost in the partially unfolded form. Also, the folded region of the partially unfolded form is likely to have some degree of structural heterogeneity. The structure of the partially unfolded form is fully consistent with spectroscopic properties of the near-native kinetic intermediate observed in previous folding studies of DHFR. The findings suggest that the last step of the folding of DHFR involves organization in the structure of two large loops, the F-G and Met-20 loops, which is coupled with compaction of the rest of the protein.
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Affiliation(s)
- Joseph R Kasper
- Department of Medicinal Chemistry and Molecular Pharmacology, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, 47907
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11
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Wang Z, Singh P, Czekster CM, Kohen A, Schramm VL. Protein mass-modulated effects in the catalytic mechanism of dihydrofolate reductase: beyond promoting vibrations. J Am Chem Soc 2014; 136:8333-41. [PMID: 24820793 PMCID: PMC4063187 DOI: 10.1021/ja501936d] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The role of fast protein dynamics
in enzyme catalysis has been
of great interest in the past decade. Recent “heavy enzyme”
studies demonstrate that protein mass-modulated vibrations are linked
to the energy barrier for the chemical step of catalyzed reactions.
However, the role of fast dynamics in the overall catalytic mechanism
of an enzyme has not been addressed. Protein mass-modulated effects
in the catalytic mechanism of Escherichia coli dihydrofolate
reductase (ecDHFR) are explored by isotopic substitution (13C, 15N, and non-exchangeable 2H) of the wild-type
ecDHFR (l-DHFR) to generate a vibrationally perturbed
“heavy ecDHFR” (h-DHFR). Steady-state,
pre-steady-state, and ligand binding kinetics, intrinsic kinetic isotope
effects (KIEint) on the chemical step, and thermal unfolding
experiments of both l- and h-DHFR
show that the altered protein mass affects the conformational ensembles
and protein–ligand interactions, but does not affect the hydride
transfer at physiological temperatures (25–45 °C). Below
25 °C, h-DHFR shows altered transition state
(TS) structure and increased barrier-crossing probability of the chemical
step compared with l-DHFR, indicating temperature-dependent
protein vibrational coupling to the chemical step. Protein mass-modulated
vibrations in ecDHFR are involved in TS interactions at cold temperatures
and are linked to dynamic motions involved in ligand binding at physiological
temperatures. Thus, mass effects can affect enzymatic catalysis beyond
alterations in promoting vibrations linked to chemistry.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
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12
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Guo J, Loveridge EJ, Luk LYP, Allemann RK. Effect of Dimerization on Dihydrofolate Reductase Catalysis. Biochemistry 2013; 52:3881-7. [DOI: 10.1021/bi4005073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jiannan Guo
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - E. Joel Loveridge
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - Louis Y. P. Luk
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
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13
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Rorick M. Quantifying protein modularity and evolvability: a comparison of different techniques. Biosystems 2012; 110:22-33. [PMID: 22796584 DOI: 10.1016/j.biosystems.2012.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 06/20/2012] [Accepted: 06/27/2012] [Indexed: 10/28/2022]
Abstract
Modularity increases evolvability by reducing constraints on adaptation and by allowing preexisting parts to function in new contexts for novel uses. Protein evolution provides an excellent context to study the causes and consequences of biological modularity. In order to address such questions, however, an index for protein modularity is necessary. This paper proposes a simple index for protein modularity-"module density"-which is the number of evolutionarily independent modules that compose a protein divided by the number of amino acids in the protein. The decomposition of proteins into constituent modules can be accomplished by either of two classes of methods. The first class of methods relies on "suppositional" criteria to assign amino acids to modules, whereas the second class of methods relies on "coevolutionary" criteria for this task. One simple and practical method from the first class consists of approximating the number of modules in a protein as the number of regular secondary structure elements (i.e., helices and sheets). Methods based on coevolutionary criteria require more elaborate data, but they have the advantage of being able to specify modules without prior assumptions about why they exist. Given the increasing availability of datasets sampling protein mutational spectra (e.g., from comparative genomics, experimental evolution, and computational prediction), methods based on coevolutionary criteria will likely become more promising in the near future. The ability to meaningfully quantify protein modularity via simple indices has the potential to aid future efforts to understand protein evolutionary rate determinants, improve molecular evolution models and engineer novel proteins.
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Affiliation(s)
- Mary Rorick
- University of Michigan, Department of Ecology and Evolutionary Biology, Ann Arbor, MI 48109-1048, United States.
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14
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Loveridge EJ, Tey LH, Behiry EM, Dawson WM, Evans RM, Whittaker SBM, Günther UL, Williams C, Crump MP, Allemann RK. The role of large-scale motions in catalysis by dihydrofolate reductase. J Am Chem Soc 2011; 133:20561-70. [PMID: 22060818 PMCID: PMC3590880 DOI: 10.1021/ja208844j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Dihydrofolate reductase has long been used as a model system to study the coupling of protein motions to enzymatic hydride transfer. By studying environmental effects on hydride transfer in dihydrofolate reductase (DHFR) from the cold-adapted bacterium Moritella profunda (MpDHFR) and comparing the flexibility of this enzyme to that of DHFR from Escherichia coli (EcDHFR), we demonstrate that factors that affect large-scale (i.e., long-range, but not necessarily large amplitude) protein motions have no effect on the kinetic isotope effect on hydride transfer or its temperature dependence, although the rates of the catalyzed reaction are affected. Hydrogen/deuterium exchange studies by NMR-spectroscopy show that MpDHFR is a more flexible enzyme than EcDHFR. NMR experiments with EcDHFR in the presence of cosolvents suggest differences in the conformational ensemble of the enzyme. The fact that enzymes from different environmental niches and with different flexibilities display the same behavior of the kinetic isotope effect on hydride transfer strongly suggests that, while protein motions are important to generate the reaction ready conformation, an optimal conformation with the correct electrostatics and geometry for the reaction to occur, they do not influence the nature of the chemical step itself; large-scale motions do not couple directly to hydride transfer proper in DHFR.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
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15
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Radestock S, Gohlke H. Protein rigidity and thermophilic adaptation. Proteins 2011; 79:1089-108. [DOI: 10.1002/prot.22946] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/28/2010] [Accepted: 11/07/2010] [Indexed: 11/05/2022]
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16
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Tey LH, Loveridge EJ, Swanwick RS, Flitsch SL, Allemann RK. Highly site-selective stability increases by glycosylation of dihydrofolate reductase. FEBS J 2010; 277:2171-9. [DOI: 10.1111/j.1742-4658.2010.07634.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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17
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Liu C, Yang Z. Reversible folding/unfolding of small a-helix in explicit solvent investigated by ABEEMσπ/MM. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0257-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Hu X, Lu Q, Kaplan DL, Cebe P. Microphase Separation Controlled β-Sheet Crystallization Kinetics in Fibrous Proteins. Macromolecules 2009. [DOI: 10.1021/ma802481p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiao Hu
- Department of Physics and Astronomy, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155
| | - Qiang Lu
- Department of Physics and Astronomy, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155
| | - David L. Kaplan
- Department of Physics and Astronomy, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155
| | - Peggy Cebe
- Department of Physics and Astronomy, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155
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19
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Spina M, Cuccioloni M, Mozzicafreddo M, Montecchia F, Pucciarelli S, Eleuteri AM, Fioretti E, Angeletti M. Mechanism of inhibition of wt-dihydrofolate reductase from E. coli by tea epigallocatechin-gallate. Proteins 2008; 72:240-51. [PMID: 18214969 DOI: 10.1002/prot.21914] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Dihydrofolate reductase (DHFR) is a ubiquitous enzyme involved in major biological process, including DNA synthesis and cancer inhibition, and its modulation is the object of extensive structural, kinetic, and pharmacological studies. In particular, earlier studies showed that green tea catechins are powerful inhibitors of bovine liver and chicken liver DHFR. In this article, we report the results of inhibition kinetics for the enzyme from another source (DHFR from E. coli) exerted by (-)-epigallocatechingallate (EGCG). Using different analytical techniques, we reported that EGCG acts as a bisubstrate inhibitor on the bacterial DHFR. Moreover, the combined approach of biosensor, kinetic, and molecular modelling analysis disclosed the ability of EGCG to bind to the enzyme both on substrate (DHF) and cofactor (NADPH) site. Collectively, our data have confirmed the selectivity of antifolate compounds with respect to the different source of enzyme (bacterial or mammalian DHFR) and the possible role of tea catechins as chemopreventive agents.
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Affiliation(s)
- Michele Spina
- Department of Molecular, Cellular and Animal Biology, University of Camerino, Via Gentile III da Varano, 62032, Camerino (MC), Italy.
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20
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Wang J, Zhao L, Dou X, Zhang Z. Study of Multiple Unfolding Trajectories and Unfolded States of the Protein GB1 Under the Physical Property Space. J Biomol Struct Dyn 2008; 25:609-19. [DOI: 10.1080/07391102.2008.10507207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Chng CP, Kitao A. Thermal unfolding simulations of bacterial flagellin: insight into its refolding before assembly. Biophys J 2008; 94:3858-71. [PMID: 18263660 PMCID: PMC2367190 DOI: 10.1529/biophysj.107.123927] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 01/10/2008] [Indexed: 11/18/2022] Open
Abstract
Flagellin is the subunit of the bacterial filament, the micrometer-long propeller of a bacterial flagellum. The protein is believed to undergo unfolding for transport through the channel of the filament and to refold in a chamber at the end of the channel before being assembled into the growing filament. We report a thermal unfolding simulation study of S. typhimurium flagellin in aqueous solution as an attempt to gain atomic-level insight into the refolding process. Each molecule comprises two filament-core domains {D0, D1} and two hypervariable-region domains {D2, D3}. D2 can be separated into subdomains D2a and D2b. We observed a similar unfolding order of the domains as reported in experimental thermal denaturation. D2a and D3 exhibited high thermal stability and contained persistent three-stranded beta-sheets in the denatured state which could serve as folding cores to guide refolding. A recent mutagenesis study on flagellin stability seems to suggest the importance of the folding cores. Using crude size estimates, our data suggests that the chamber might be large enough for either denatured hypervariable-region domains or filament-core domains, but not whole flagellin; this implicates a two-staged refolding process.
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Affiliation(s)
- Choon-Peng Chng
- Department of Computational Biology, Graduate School of Frontier Sciences, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
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22
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Pang J, Allemann RK. Molecular dynamics simulation of thermal unfolding of Thermatoga maritima DHFR. Phys Chem Chem Phys 2007; 9:711-8. [PMID: 17268682 DOI: 10.1039/b611210b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular dynamics simulations of the temperature-induced unfolding reaction of native dimeric dihydrofolate reductase from the hyperthermophile Thermatoga maritima (TmDHFR) and the experimentally inaccessible TmDHFR monomer were carried out at 400 K, 450 K and 500 K. The results revealed that the unfolding of TmDHFR subunits followed a similar path to that of the monomeric DHFR from the mesophile E. coli (EcDHFR). An initial collapse of the adenosine-binding domain (ABD) was followed by the loss of the N-terminal and loop domains (NDLD). Interestingly, the elements of the secondary structure of the isolated TmDHFR monomer were maintained for significantly longer periods of time for the hyperthermophilic enzyme, suggesting that subunit stability contributes to the enhanced resistance of TmDHFR to temperature-induced unfolding. The interactions between the subunits of the TmDHFR dimer led to a stabilisation of the NDLD. The hydrogen bonds between residues 140-143 in betaG of one subunit and residues 125-127 in betaF of the other subunit were retained for significant parts of the simulations at all temperatures. These intermolecular hydrogen bonds were lost after the unfolding of the individual subunits. The high stability of the dimer mediated by strong intersubunit contacts together with an intrinsically enhanced stability of the subunits compared to EcDHFR provides a molecular rational for the higher stability of the thermophilic enzyme. The computed unfolding pathways suggest that the partly folded dimer may be a genuine folding intermediate.
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Affiliation(s)
- Jiayun Pang
- School of Chemistry, Cardiff University, Main Building Park Place, Cardiff, UK
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23
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Lei H, Duan Y. The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein. J Chem Phys 2006; 121:12104-11. [PMID: 15634176 DOI: 10.1063/1.1822916] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, the thermal stability of a designed alpha/beta protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7-9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (alpha helix and beta hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix.
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Affiliation(s)
- Hongxing Lei
- Bioinformatics Program and Department of Applied Science, University of California, Davis, California 95616, USA
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24
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Reich L, Weikl TR. Substructural cooperativity and parallel versus sequential events during protein unfolding. Proteins 2006; 63:1052-8. [PMID: 16544293 DOI: 10.1002/prot.20966] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
According to the "old view," proteins fold along well-defined sequential pathways, whereas the "new view" sees protein folding as a highly parallel stochastic process on funnel-shaped energy landscapes. We have analyzed parallel and sequential processes on a large number of molecular dynamics unfolding trajectories of the protein CI2 at high temperatures. Using rigorous statistical measures, we quantify the degree of sequentiality on two structural levels. The unfolding process is highly parallel on the microstructural level of individual contacts. On a coarser, macrostructural level of contact clusters, characteristic parallel and sequential events emerge. These characteristic events can be understood from loop-closure dependencies between the contact clusters. A correlation analysis of the unfolding times of the contacts reveals a high degree of substructural cooperativity within the contact clusters.
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Affiliation(s)
- Lothar Reich
- Theory Department, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
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25
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Akanuma S, Miyagawa H, Kitamura K, Yamagishi A. A detailed unfolding pathway of a (beta/alpha)8-barrel protein as studied by molecular dynamics simulations. Proteins 2006; 58:538-46. [PMID: 15614829 DOI: 10.1002/prot.20349] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The (beta/alpha)(8)-barrel is the most common protein fold. Similar structural properties for folding intermediates of (beta/alpha)(8)-barrel proteins involved in tryptophan biosynthesis have been reported in a number of experimental studies; these intermediates have the last two beta-strands and three alpha-helices partially unfolded, with other regions of the polypeptide chain native-like in conformation. To investigate the detailed folding/unfolding pathways of these (beta/alpha)(8)-barrel proteins, temperature-induced unfolding simulations of N-(5'-phosphoribosyl)anthranilate isomerase from Escherichia coli were carried out using a special-purpose parallel computer system. Unfolding simulations at five different temperatures showed a sequential unfolding pathway comprised of several events. Early events in unfolding involved disruption of the last two strands and three helices, producing an intermediate ensemble similar to those detected in experimental studies. Then, denaturation of the first two betaalpha units and separation of the sixth strand from the fifth took place independently. The remaining central betaalphabetaalphabeta module persisted the longest during all simulations, suggesting an important role for this module as the incipient folding scaffold. Our simulations also predicted the presence of a nucleation site, onto which several hydrophobic residues condensed forming the foundation for the central betaalphabetaalphabeta module.
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Affiliation(s)
- Satoshi Akanuma
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Tokyo, Japan
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26
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Svensson AKE, Zitzewitz JA, Matthews C, Smith VF. The relationship between chain connectivity and domain stability in the equilibrium and kinetic folding mechanisms of dihydrofolate reductase from E.coli. Protein Eng Des Sel 2006; 19:175-85. [PMID: 16452118 PMCID: PMC5441858 DOI: 10.1093/protein/gzj017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Accepted: 01/06/2006] [Indexed: 11/14/2022] Open
Abstract
The role of domains in defining the equilibrium and kinetic folding properties of dihydrofolate reductase (DHFR) from Escherichia coli was probed by examining the thermodynamic and kinetic properties of a set of variants in which the chain connectivity in the discontinuous loop domain (DLD) and the adenosine-binding domain (ABD) was altered by permutation. To test the concept that chain cleavage can selectively destabilize the domain in which the N- and C-termini are resident, permutations were introduced at one position within the ABD, one within the DLD and one at a boundary between the domains. The results demonstrated that a continuous ABD is required for a stable thermal intermediate and a continuous DLD is required for a stable urea intermediate. The permutation at the domain interface had both a thermal and urea intermediate. Strikingly, the observable kinetic folding responses of all three permuted proteins were very similar to the wild-type protein. These results demonstrate a crucial role for stable domains in defining the energy surface for the equilibrium folding reaction of DHFR. If domain connectivity affects the kinetic mechanism, the effects must occur in the sub-millisecond time range.
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27
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Swanwick RS, Daines AM, Tey LH, Flitsch SL, Allemann RK. Increased Thermal Stability of Site-Selectively Glycosylated Dihydrofolate Reductase. Chembiochem 2005; 6:1338-40. [PMID: 16003807 DOI: 10.1002/cbic.200500103] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Richard S Swanwick
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
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28
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Abstract
We developed a method CHOP dissecting proteins into domain-like fragments. The basic idea was to cut proteins beginning from very reliable experimental information (PDB), proceeding to expert annotations of domain-like regions (Pfam-A), and completing through cuts based on termini of known proteins. In this way, CHOP dissected more than two thirds of all proteins from 62 proteomes. Analysis of our structural domain-like fragments revealed four surprising results. First, >70% of all dissected proteins contained more than one fragment. Second, most domains spanned on average over approximately 100 residues. This average was similar for eukaryotic and prokaryotic proteins, and it is also valid-although previously not described-for all proteins in the PDB. Third, single-domain proteins were significant longer than most domains in multidomain proteins. Fourth, three fourths of all domains appeared shorter than 210 residues. We believe that our CHOP fragments constituted an important resource for functional and structural genomics. Nevertheless, our main motivation to develop CHOP was that the single-linkage clustering method failed to adequately group full-length proteins. In contrast, CLUP-the simple clustering scheme CLUP introduced here-succeeded largely to group the CHOP fragments from 62 proteomes such that all members of one cluster shared a basic structural core. CLUP found >63,000 multi- and >118,000 single-member clusters. Although most fragments were restricted to a particular cluster, approximately 24% of the fragments were duplicated in at least two clusters. Our thresholds for grouping two fragments into the same cluster were rather conservative. Nevertheless, our results suggested that structural genomics initiatives have to target >30,000 fragments to at least cover the multimember clusters in 62 proteomes.
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Affiliation(s)
- Jinfeng Liu
- CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
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29
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Gunasekaran K, Ma B, Nussinov R. Triggering loops and enzyme function: identification of loops that trigger and modulate movements. J Mol Biol 2003; 332:143-59. [PMID: 12946353 DOI: 10.1016/s0022-2836(03)00893-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme function often involves a conformational change. There is a general agreement that loops play a vital role in correctly positioning the catalytically important residues. Nevertheless, predicting the functional loops and most importantly their role in enzyme function remains a difficult task. A major reason for this difficulty is that loops that undergo conformational change are frequently not well conserved in their primary sequence. beta1,4-Galactosyltransferase is one such enzyme. There, the amino acid sequence of a long loop that undergoes a large conformational change upon substrate binding is not well conserved. Our molecular dynamics simulations show that the large conformational change in the long loop is brought about by a second, interacting loop. Interestingly, while the structural change of the second loop is much smaller than that of the long loop, its sequence (particularly glycine residues) is highly conserved. We further examine the generality of the proposition that there are loops that trigger movements but nevertheless show little or no structural changes in crystals. We focus on two other enzymes, enolase and lipase. We chose these enzymes, since they too undergo conformational change upon ligand binding, however, they have different folds and different functions. Through multiple sets of simulations we show that the conformational change of the functional loop(s) is brought about through communication of flexibility by triggering loops that have several glycine residues. We further propose that similar to the conservation of common favorable fold types and structural motifs, evolution has also conserved common "skillful" mechanisms. Mechanisms may be conserved across different folds, sequences and functions, with adaptation to specific enzymatic roles.
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Affiliation(s)
- K Gunasekaran
- Basic Research Program, SAIC-Frederick Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, Bldg. 469 Rm. 151, Frederick, MD 21702, USA
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30
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Abstract
We develop a simple model for computing the rates and routes of folding of two-state proteins from the contact maps of their native structures. The model is based on the graph-theoretical concept of effective contact order (ECO). The model predicts that proteins fold by "zipping up" in a sequence of small-loop-closure events, depending on the native chain fold. Using a simple equation, with a few physical rate parameters, we obtain a good correlation with the folding rates of 24 two-state folding proteins. The model rationalizes data from Phi-value analysis that have been interpreted in terms of delocalized or polarized transition states. This model indicates how much of protein folding may take place in parallel, not along a single reaction coordinate or with a single transition state.
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Affiliation(s)
- Thomas R Weikl
- Department of Pharmaceutical Chemistry, University of California, Box 2240, San Francisco, CA 94143-2240, USA.
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