1
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Kornev AP, Weng JH, Maillard RA, Taylor SS. Gauging Dynamics-driven Allostery Using a New Computational Tool: A CAP Case Study. J Mol Biol 2024; 436:168395. [PMID: 38097109 PMCID: PMC10851786 DOI: 10.1016/j.jmb.2023.168395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
In this study, we utilize Protein Residue Networks (PRNs), constructed using Local Spatial Pattern (LSP) alignment, to explore the dynamic behavior of Catabolite Activator Protein (CAP) upon the sequential binding of cAMP. We employed the Degree Centrality of these PRNs to investigate protein dynamics on a sub-nanosecond time scale, hypothesizing that it would reflect changes in CAP's entropy related to its thermal motions. We show that the binding of the first cAMP led to an increase in stability in the Cyclic-Nucleotide Binding Domain A (CNBD-A) and destabilization in CNBD-B, agreeing with previous reports explaining the negative cooperativity of cAMP binding in terms of an entropy-driven allostery. LSP-based PRNs also allow for the study of Betweenness Centrality, another graph-theoretical characteristic of PRNs, providing insights into global residue connectivity within CAP. Using this approach, we were able to correctly identify amino acids that were shown to be critical in mediating allosteric interactions in CAP. The agreement between our studies and previous experimental reports validates our method, particularly with respect to the reliability of Degree Centrality as a proxy for entropy related to protein thermal dynamics. Because LSP-based PRNs can be easily extended to include dynamics of small organic molecules, polynucleotides, or other allosteric proteins, the methods presented here mark a significant advancement in the field, positioning them as vital tools for a fast, cost-effective, and accurate analysis of entropy-driven allostery and identification of allosteric hotspots.
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Affiliation(s)
- Alexandr P Kornev
- Departmen of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Jui-Hung Weng
- Departmen of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rodrigo A Maillard
- Department of Chemistry, Georgetown University, Washington, DC 20007, USA
| | - Susan S Taylor
- Departmen of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
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2
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Rahimi M, Taghdir M, Abasi Joozdani F. Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease. Sci Rep 2023; 13:14179. [PMID: 37648682 PMCID: PMC10469195 DOI: 10.1038/s41598-023-40818-x] [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: 02/21/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure-function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.
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Affiliation(s)
- Mohammad Rahimi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran.
| | - Farzane Abasi Joozdani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
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3
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Rutz A, Das CK, Fasano A, Jaenecke J, Yadav S, Apfel UP, Engelbrecht V, Fourmond V, Léger C, Schäfer LV, Happe T. Increasing the O 2 Resistance of the [FeFe]-Hydrogenase CbA5H through Enhanced Protein Flexibility. ACS Catal 2022; 13:856-865. [PMID: 36733639 PMCID: PMC9886219 DOI: 10.1021/acscatal.2c04031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/08/2022] [Indexed: 12/29/2022]
Abstract
The high turnover rates of [FeFe]-hydrogenases under mild conditions and at low overpotentials provide a natural blueprint for the design of hydrogen catalysts. However, the unique active site (H-cluster) degrades upon contact with oxygen. The [FeFe]-hydrogenase fromClostridium beijerinckii (CbA5H) is characterized by the flexibility of its protein structure, which allows a conserved cysteine to coordinate to the active site under oxidative conditions. Thereby, intrinsic cofactor degradation induced by dioxygen is minimized. However, the protection from O2 is only partial, and the activity of the enzyme decreases upon each exposure to O2. By using site-directed mutagenesis in combination with electrochemistry, ATR-FTIR spectroscopy, and molecular dynamics simulations, we show that the kinetics of the conversion between the oxygen-protected inactive state (cysteine-bound) and the oxygen-sensitive active state can be accelerated by replacing a surface residue that is very distant from the active site. This sole exchange of methionine for a glutamate residue leads to an increased resistance of the hydrogenase to dioxygen. With our study, we aim to understand how local modifications of the protein structure can have a crucial impact on protein dynamics and how they can control the reactivity of inorganic active sites through outer sphere effects.
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Affiliation(s)
- Andreas Rutz
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical
Chemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Andrea Fasano
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Jan Jaenecke
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Shanika Yadav
- Inorganic
Chemistry Ι, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic
Chemistry Ι, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany,Fraunhofer
UMSICHT, 46047 Oberhausen, Germany
| | - Vera Engelbrecht
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vincent Fourmond
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Christophe Léger
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Lars V. Schäfer
- Theoretical
Chemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Thomas Happe
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany,
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4
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Pillai AS, Hochberg GK, Thornton JW. Simple mechanisms for the evolution of protein complexity. Protein Sci 2022; 31:e4449. [PMID: 36107026 PMCID: PMC9601886 DOI: 10.1002/pro.4449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/26/2023]
Abstract
Proteins are tiny models of biological complexity: specific interactions among their many amino acids cause proteins to fold into elaborate structures, assemble with other proteins into higher-order complexes, and change their functions and structures upon binding other molecules. These complex features are classically thought to evolve via long and gradual trajectories driven by persistent natural selection. But a growing body of evidence from biochemistry, protein engineering, and molecular evolution shows that naturally occurring proteins often exist at or near the genetic edge of multimerization, allostery, and even new folds, so just one or a few mutations can trigger acquisition of these properties. These sudden transitions can occur because many of the physical properties that underlie these features are present in simpler proteins as fortuitous by-products of their architecture. Moreover, complex features of proteins can be encoded by huge arrays of sequences, so they are accessible from many different starting points via many possible paths. Because the bridges to these features are both short and numerous, random chance can join selection as a key factor in explaining the evolution of molecular complexity.
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Affiliation(s)
- Arvind S. Pillai
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Institute for Protein DesignUniversity of WashingtonSeattleWAUSA
| | - Georg K.A. Hochberg
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Department of Chemistry, Center for Synthetic MicrobiologyPhilipps University MarburgMarburgGermany
| | - Joseph W. Thornton
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Departments of Human Genetics and Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
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5
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Krucinska J, Lombardo MN, Erlandsen H, Estrada A, Si D, Viswanathan K, Wright DL. Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens. Commun Biol 2022; 5:459. [PMID: 35562546 PMCID: PMC9106665 DOI: 10.1038/s42003-022-03384-y] [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: 09/11/2021] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors. Critical residue variations in two of the most clinically prevalent DHFR isoforms are identified as a common structural element in trimethoprim-resistant DHFR which impose changes on enzyme catalysis and ligand-cofactor cooperativity.
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Affiliation(s)
- Jolanta Krucinska
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Michael N Lombardo
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Heidi Erlandsen
- Center for Open Research Resources & Equipment (COR2E), University of Connecticut, 91N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Alexavier Estrada
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Debjani Si
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Kishore Viswanathan
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Dennis L Wright
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA.
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6
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Shanina E, Kuhaudomlarp S, Lal K, Seeberger PH, Imberty A, Rademacher C. Allosterische, Wirkstoff‐zugängliche Bindestellen in β‐Propeller‐Lektinen. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202109339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Elena Shanina
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Sakonwan Kuhaudomlarp
- University Grenoble Alpes CNRS CERMAV 38000 Grenoble Frankreich
- Department of Biochemistry Faculty of Science Mahidol University 10400 Bangkok Thailand
- Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University 10400 Bangkok Thailand
| | - Kanhaya Lal
- University Grenoble Alpes CNRS CERMAV 38000 Grenoble Frankreich
- Dipartimento di Chimica via Golgi 19 Università degli Studi di Milano 20133 Milano Italien
| | - Peter H. Seeberger
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Anne Imberty
- University Grenoble Alpes CNRS CERMAV 38000 Grenoble Frankreich
| | - Christoph Rademacher
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
- Department of Pharmaceutical Chemistry University of Vienna Althanstraße 14 1080 Wien Österreich
- Department of Microbiology, Immunobiology and Genetics Max F. Perutz Labs Campus Vienna Biocenter 5 1030 Wien Österreich
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7
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Shanina E, Kuhaudomlarp S, Lal K, Seeberger PH, Imberty A, Rademacher C. Druggable Allosteric Sites in β-Propeller Lectins. Angew Chem Int Ed Engl 2022; 61:e202109339. [PMID: 34713573 PMCID: PMC9298952 DOI: 10.1002/anie.202109339] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/05/2021] [Indexed: 12/24/2022]
Abstract
Carbohydrate‐binding proteins (lectins) are auspicious targets in drug discovery to combat antimicrobial resistance; however, their non‐carbohydrate drug‐like inhibitors are still unavailable. Here, we present a druggable pocket in a β‐propeller lectin BambL from Burkholderia ambifaria as a potential target for allosteric inhibitors. This site was identified employing 19F NMR fragment screening and a computational pocket prediction algorithm SiteMap. The structure–activity relationship study revealed the most promising fragment with a dissociation constant of 0.3±0.1 mM and a ligand efficiency of 0.3 kcal mol−1 HA−1 that affected the orthosteric site. This effect was substantiated by site‐directed mutagenesis in the orthosteric and secondary pockets. Future drug‐discovery campaigns that aim to develop small molecule inhibitors can benefit from allosteric sites in lectins as a new therapeutic approach against antibiotic‐resistant pathogens.
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Affiliation(s)
- Elena Shanina
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Sakonwan Kuhaudomlarp
- University Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.,Department of Biochemistry, Faculty of Science, Mahidol University, 10400, Bangkok, Thailand.,Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 10400, Bangkok, Thailand
| | - Kanhaya Lal
- University Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.,Dipartimento di Chimica via Golgi 19, Universita" degli Studi di Milano, 20133, Milano, Italy
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Anne Imberty
- University Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.,Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1080, Vienna, Austria.,Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Labs, Campus Vienna Biocenter 5, 1030, Vienna, Austria
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8
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Wawrzinek R, Wamhoff EC, Lefebre J, Rentzsch M, Bachem G, Domeniconi G, Schulze J, Fuchsberger FF, Zhang H, Modenutti C, Schnirch L, Marti MA, Schwardt O, Bräutigam M, Guberman M, Hauck D, Seeberger PH, Seitz O, Titz A, Ernst B, Rademacher C. A Remote Secondary Binding Pocket Promotes Heteromultivalent Targeting of DC-SIGN. J Am Chem Soc 2021; 143:18977-18988. [PMID: 34748320 PMCID: PMC8603350 DOI: 10.1021/jacs.1c07235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Dendritic cells (DC)
are antigen-presenting cells coordinating
the interplay of the innate and the adaptive immune response. The
endocytic C-type lectin receptors DC-SIGN and Langerin display expression
profiles restricted to distinct DC subtypes and have emerged as prime
targets for next-generation immunotherapies and anti-infectives. Using
heteromultivalent liposomes copresenting mannosides bearing aromatic
aglycones with natural glycan ligands, we serendipitously discovered
striking cooperativity effects for DC-SIGN+ but not for
Langerin+ cell lines. Mechanistic investigations combining
NMR spectroscopy with molecular docking and molecular dynamics simulations
led to the identification of a secondary binding pocket for the glycomimetics.
This pocket, located remotely of DC-SIGN’s carbohydrate bindings
site, can be leveraged by heteromultivalent avidity enhancement. We
further present preliminary evidence that the aglycone allosterically
activates glycan recognition and thereby contributes to DC-SIGN-specific
cell targeting. Our findings have important implications for both
translational and basic glycoscience, showcasing heteromultivalent
targeting of DCs to improve specificity and supporting potential allosteric
regulation of DC-SIGN and CLRs in general.
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Affiliation(s)
- Robert Wawrzinek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Eike-Christian Wamhoff
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Jonathan Lefebre
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Mareike Rentzsch
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Gunnar Bachem
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Gary Domeniconi
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Jessica Schulze
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Felix F Fuchsberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Hengxi Zhang
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Carlos Modenutti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Universidad de Buenos Aires, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Lennart Schnirch
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Marcelo A Marti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Universidad de Buenos Aires, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Oliver Schwardt
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Maria Bräutigam
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Mónica Guberman
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Dirk Hauck
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.,German Centre for Infection Research, Campus Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.,German Centre for Infection Research, Campus Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Beat Ernst
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany.,University of Vienna, Department of Pharmaceutical Sciences, Althanstrasse 14, 1090 Vienna, Austria.,University of Vienna, Department of Microbiology, Immunology and Genetics, Max F. Perutz Laboratories, Biocenter 5, 1030 Vienna, Austria
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9
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Huang CH, Chen YW, Huang TT, Kao YT. Effects of Distal Mutations on Ligand-Binding Affinity in E. coli Dihydrofolate Reductase. ACS OMEGA 2021; 6:26065-26076. [PMID: 34660967 PMCID: PMC8515367 DOI: 10.1021/acsomega.1c02995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Mutations far from the center of chemical activity in dihydrofolate reductase (DHFR) can affect several steps in the catalytic cycle. Mutations at highly conserved positions and the distal distance of the catalytic center (Met-42, Thr-113, and Gly-121) were designed, including single-point and double-point mutations. Upon ligand binding, the fluorescence of the intrinsic optical probe, tryptophan, decreases due to either fluorescence quenching or energy transfer. We demonstrated an optical approach in measuring the equilibrium dissociation constant for enzyme-cofactor, enzyme-substrate, and enzyme-product complexes in wildtype ecDHFR and each mutant. We propose that the effects of these distal mutations on ligand-binding affinity stem from the spatial steric hindrance, the disturbance on the hydrogen network, or the modification of the protein flexibility. The modified N-terminus tag in DHFR acts as a cap on the entrance of the substrate-binding cavity, squeezes the adenosine binding subdomain, and influences the binding of NADPH in some mutants. If the mutation positions are away from the N-terminus tag and the adenosine binding subdomain, the additive effects due to the N-terminus tag were not observed. In the double-mutant-cycle analysis, double mutations show nonadditive properties upon either cofactor or substrate binding. Also, in general, the first point mutation strongly affects the ligand binding compared to the second one.
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Affiliation(s)
- Chen-Hua Huang
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan, ROC
| | - Yun-Wen Chen
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan, ROC
| | - Tsun-Tsao Huang
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan, ROC
| | - Ya-Ting Kao
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan, ROC
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan, ROC
- Center
For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan, ROC
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10
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Singh A, Fenwick RB, Dyson HJ, Wright PE. Role of Active Site Loop Dynamics in Mediating Ligand Release from E. coli Dihydrofolate Reductase. Biochemistry 2021; 60:2663-2671. [PMID: 34428034 DOI: 10.1021/acs.biochem.1c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conformational fluctuations from ground-state to sparsely populated but functionally important excited states play a key role in enzyme catalysis. For Escherichia coli dihydrofolate reductase (DHFR), the release of the product tetrahydrofolate (THF) and oxidized cofactor NADP+ occurs through exchange between closed and occluded conformations of the Met20 loop. A "dynamic knockout" mutant of E. coli DHFR, where the E. coli sequence in the Met20 loop is replaced by the human sequence (N23PP/S148A), models human DHFR and is incapable of accessing the occluded conformation. 1H and 15N CPMG relaxation dispersion analysis for the ternary product complex of the mutant enzyme with NADP+ and the product analogue 5,10-dideazatetrahydrofolate (ddTHF) (E:ddTHF:NADP+) reveals the mechanism by which NADP+ is released when the Met20 loop cannot undergo the closed-to-occluded conformational transition. Two excited states were observed: one related to a faster, relatively high-amplitude conformational fluctuation in areas near the active site, associated with the shuttling of the nicotinamide ring of the cofactor out of the active site, and the other to a slower process where ddTHF undergoes small-amplitude motions within the binding site that are consistent with disorder observed in a room-temperature X-ray crystal structure of the N23PP/S148A mutant protein. These motions likely arise due to steric conflict of the pterin ring of ddTHF with the ribose-nicotinamide moiety of NADP+ in the closed active site. These studies demonstrate that site-specific kinetic information from relaxation dispersion experiments can provide intimate details of the changes in catalytic mechanism that result from small changes in local amino acid sequence.
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Affiliation(s)
- Amrinder Singh
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - R Bryn Fenwick
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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11
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Li M, Li M, Guo J. Molecular Mechanism of Ca 2+ in the Allosteric Regulation of Human Parathyroid Hormone Receptor-1. J Chem Inf Model 2021; 62:5110-5119. [PMID: 34464108 DOI: 10.1021/acs.jcim.1c00471] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Parathyroid hormone (PTH) is an endogenous ligand that activates the PTH type 1 receptor (PTH1R) signaling. Ca2+, a common second messenger, acts as an allosteric regulator for prolonging the activation of PTH1R. However, a clear picture of the underlying allosteric mechanism is still missing. Herein, extensive molecular dynamics (MD) simulations are performed for PTH1R-PTH complexes with and without Ca2+ ions, allowing us to delineate the molecular details of calcium-induced allostery. Our results indicate that acidic residues in the extracellular loop 1 (ECL1) (D251, E252, E254, and E258-E260) and PTH (E19 and E22) serve as key determinants for local Ca2+-coupling structures and rigidity of ECL1. Moreover, the binding of Ca2+ induces conformational changes of transmembrane domain 6/7 (TM6/7) that are related to PTH1R activation and strengthens the residue-residue communication within PTH and TMD allosterically. Moreover, our results demonstrate that the presence of Ca2+ ions potentiates the interaction between PTH and PTH1R via steered molecular dynamics (SMD) simulations, while the point mutation in the PTH (PTHR25C) weakens the binding of PTH and PTH1R. These results support that Ca2+ ions might further prolong the residence time of PTH on PTH1R and facilitate the positive allostery of PTH1R. Together, the present work provides new insights into the allosteric regulation mechanism of GPCRs induced by ions and related drug design targeting the PTH1R allosteric pathway.
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Affiliation(s)
- Mengrong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Miaomiao Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingjing Guo
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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12
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Singh P, Vandemeulebroucke A, Li J, Schulenburg C, Fortunato G, Kohen A, Hilvert D, Cheatum CM. Evolution of the Chemical Step in Enzyme Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | | | - Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Cindy Schulenburg
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Gabriel Fortunato
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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13
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Wang X, Zhang X, Peng C, Shi Y, Li H, Xu Z, Zhu W. D3DistalMutation: a Database to Explore the Effect of Distal Mutations on Enzyme Activity. J Chem Inf Model 2021; 61:2499-2508. [PMID: 33938221 DOI: 10.1021/acs.jcim.1c00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzyme activity is affected by amino acid mutations, particularly mutations near the active site. Increasing evidence has shown that distal mutations more than 10 Å away from the active site may significantly affect enzyme activity. However, it is difficult to study the enzyme regulation mechanism of distal mutations due to the lack of a systematic collection of three-dimensional (3D) structures, highlighting distal mutation site and the corresponding enzyme activity change. Therefore, we constructed a distal mutation database, namely, D3DistalMutation, which relates the distal mutation to enzyme activity. As a result, we observed that approximately 80% of distal mutations could affect enzyme activity and 72.7% of distal mutations would decrease or abolish enzyme activity in D3DistalMutation. Only 6.6% of distal mutations in D3DistalMutation could increase enzyme activity, which have great potential to the industrial field. Among these mutations, the Y to F, S to D, and T to D mutations are most likely to increase enzyme activity, which sheds some light on industrial catalysis. Distal mutations decreasing enzyme activity in the allosteric pocket play an indispensable role in allosteric drug design. In addition, the pockets in the enzyme structures are provided to explore the enzyme regulation mechanism of distal mutations. D3DistalMutation is accessible free of charge at https://www.d3pharma.com/D3DistalMutation/index.php.
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Affiliation(s)
- Xiaoyu Wang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Xinben Zhang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Peng
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yulong Shi
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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14
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Periwal N, Rathod SB, Pal R, Sharma P, Nebhnani L, Barnwal RP, Arora P, Srivastava KR, Sood V. In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. J Biomol Struct Dyn 2021; 40:8216-8231. [PMID: 33797336 PMCID: PMC8043164 DOI: 10.1080/07391102.2021.1908170] [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] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 has recently emerged as a pandemic that has caused more than 2.4 million deaths worldwide. Since the onset of infections, several full-length sequences of viral genome have been made available which have been used to gain insights into viral dynamics. We utilised a meta-data driven comparative analysis tool for sequences (Meta-CATS) algorithm to identify mutations in 829 SARS-CoV-2 genomes from around the world. The algorithm predicted sixty-one mutations among SARS-CoV-2 genomes. We observed that most of the mutations were concentrated around three protein coding genes viz nsp3 (non-structural protein 3), RdRp (RNA-directed RNA polymerase) and Nucleocapsid (N) proteins of SARS-CoV-2. We used various computational tools including normal mode analysis (NMA), C-α discrete molecular dynamics (DMD) and all-atom molecular dynamic simulations (MD) to study the effect of mutations on functionality, stability and flexibility of SARS-CoV-2 structural proteins including envelope (E), N and spike (S) proteins. PredictSNP predictor suggested that four mutations (L37H in E, R203K and P344S in N and D614G in S) out of seven were predicted to be neutral whilst the remaining ones (P13L, S197L and G204R in N) were predicted to be deleterious in nature thereby impacting protein functionality. NMA, C-α DMD and all-atom MD suggested some mutations to have stabilizing roles (P13L, S197L and R203K in N protein) where remaining ones were predicted to destabilize mutant protein. In summary, we identified significant mutations in SARS-CoV-2 genomes as well as used computational approaches to further characterize the possible effect of highly significant mutations on SARS-CoV-2 structural proteins. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Neha Periwal
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Shravan B Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, India
| | - Ranjan Pal
- Biocatalysis and Enzyme Engineering Lab, Regional Centre for Biotechnology, Faridabad, India
| | - Priya Sharma
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Lata Nebhnani
- Department of Chemistry, Gujarat University, Ahmedabad, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | - Kinshuk Raj Srivastava
- Biocatalysis and Enzyme Engineering Lab, Regional Centre for Biotechnology, Faridabad, India
| | - Vikas Sood
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
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15
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Bhattarai A, Emerson IA. Exploring the conformational dynamics and flexibility of intrinsically disordered HIV-1 Nef protein using molecular dynamic network approaches. 3 Biotech 2021; 11:156. [PMID: 33747706 DOI: 10.1007/s13205-021-02698-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/19/2021] [Indexed: 10/22/2022] Open
Abstract
Intrinsically disordered proteins represent a class of proteins that lack fixed and well-defined three-dimensional structures in solution. HIV-1 Nef is an intrinsically disordered peripheral membrane protein involved in the replication and pathogenesis of HIV-1 infection. Nef controls expression levels of cell surface CD4 molecules that are essential for adaptive immunity. Despite the lack of fixed and stable structures, Nef physically interacts with the host cellular proteins (AP-1/MHC-I) and modulates intracellular trafficking pathways. Therefore, it is essential to understand how this dynamic conformational flexibility affects Nef structures and function. In this study, we combined all-atom molecular dynamics (MD) simulations and dynamic network approaches to better understand the structure and dynamics of Nef in two different forms, the free unbound and the bound state. Using the MD simulation approach, we show that the intrinsically disordered Nef exhibit a large dynamic field with more atomic fluctuations and lesser thermodynamic stability in the unbound conditions. The conformations of Nef change over time, and this protein remains more compact, folded, and stable in the bound form. The dynamic network analysis revealed regions of the protein capable of modulating the conformational behavior of the disordered Nef. The average betweenness centrality (BC) unveiled residues that are critical for mediating protein-protein interactions. The average shortest path length (L) and the perturbation response scanning exposed residues that are likely to be important in steering protein conformational changes. Overall, the study demonstrates how all-atom MD simulations combined with the dynamic network approach can be used to gain further insights into the structure and dynamics-function relationship of intrinsically disordered HIV-1 Nef. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02698-8.
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16
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Goldstein M, Goodey NM. Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2253:185-219. [PMID: 33315225 DOI: 10.1007/978-1-0716-1154-8_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein motions play a fundamental role in enzyme catalysis and ligand binding. The relationship between protein motion and function has been extensively investigated in the model enzyme dihydrofolate reductase (DHFR). DHFR is an essential enzyme that catalyzes the reduction of dihydrofolate to tetrahydrofolate. Numerous experimental and computational methods have been used to probe the motions of DHFR through the catalytic cycle and to investigate the effect of distal mutations on DHFR motions and ligand binding. These experimental investigations have pushed forward the study of protein motions and their role in protein-ligand interactions. The introduction of mutations distal to the active site has been shown to have profound effects on ligand binding, hydride transfer rates and catalytic efficacy and these changes are captured by enzyme kinetics measurements. Distal mutations have been shown to exert their effects through a network of correlated amino acids and these effects have been investigated by NMR, protein dynamics, and analysis of coupled amino acids. The experimental methods and the findings that are reviewed here have broad implications for our understanding of enzyme mechanisms, ligand binding and for the future design and discovery of enzyme inhibitors.
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Affiliation(s)
- Melanie Goldstein
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA
| | - Nina M Goodey
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA.
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17
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Peña-Gomar I, Jiménez-Mariscal JL, Cerón M, Rosas-Trigueros J, Reyes-López CA. c.1898C>G/p.Ser633Trp Mutation in Alpha-L-Iduronidase: Clinical and Structural Implications. Protein J 2021; 40:68-77. [PMID: 33389473 DOI: 10.1007/s10930-020-09950-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 11/27/2022]
Abstract
Mucopolysaccharidosis type I is a rare autosomal recessive genetic disease caused by deficient activity of α-L-iduronidase. As a consequence of low or absent activity of this enzyme, glycosaminoglycans accumulate in the lysosomal compartments of multiple cell types throughout the body. Mucopolysaccharidosis type I has been classified into 3 clinical subtypes, ranging from a severe Hurler form to the more attenuated Hurler-Scheie and Scheie phenotypes. Over 200 gene variants causing the various forms of mucopolysaccharidosis type I have been reported. DNA isolated from dried blood spot was used to sequencing of all exons of the IDUA gene from a patient with a clinical phenotype of severe mucopolysaccharidosis type I syndrome. Enzyme activity of α-L-iduronidase was quantified by fluorimetric assay. Additionally, a molecular dynamics simulation approach was used to determine the effect of the Ser633Trp mutation on the structure and dynamics of the α-L-iduronidase. The DNA sequencing analysis and enzymatic activity shows a c.1898C>G mutation associated a patient with a homozygous state and α-L-iduronidase activity of 0.24 μmol/L/h, respectively. The molecular dynamics simulation analysis shows that the p.Ser633Trp mutation on the α-L-iduronidase affect significant the temporal and spatial properties of the different structural loops, the N-glycan attached to Asn372 and amino acid residues around the catalytic site of this enzyme. Low enzymatic activity observed for p.Ser633Trp variant of the α-L-iduronidase seems to lead to severe mucopolysaccharidosis type I phenotype, possibly associated with a perturbation of the structural dynamics in regions of the enzyme close to the active site.
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Affiliation(s)
- Iliana Peña-Gomar
- Hospital Pediátrico Tacubaya, Secretaría de Salud, Ciudad de México, Mexico
| | | | - Magdalena Cerón
- Clínica de Enfermedades Lisosomales, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Jorge Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, ESCOM, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Cesar A Reyes-López
- Laboratorio de Bioquímica Estructural, Sección de Estudios de Posgrado E Investigación, ENMyH, SEPI-ENMyH, Instituto Politécnico Nacional., Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticomán, C.P. 07320, Ciudad de México, Mexico.
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18
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Eck T, Patel S, Candela T, Leon H K, Little M, Reis NE, Liyanagunawardana U, Gubler U, Janson CA, Catalano J, Goodey NM. Mutational analysis confirms the presence of distal inhibitor-selectivity determining residues in B. stearothermophilus dihydrofolate reductase. Arch Biochem Biophys 2020; 692:108545. [PMID: 32810476 PMCID: PMC10727455 DOI: 10.1016/j.abb.2020.108545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022]
Abstract
Many antibacterial and antiparasitic drugs work by competitively inhibiting dihydrofolate reductase (DHFR), a vital enzyme in folate metabolism. The interactions between inhibitors and DHFR active site residues are known in many homologs but the contributions from distal residues are less understood. Identifying distal residues that aid in inhibitor binding can improve targeted drug development programs by accounting for distant influences that may be less conserved and subject to frequent resistance causing mutations. Previously, a novel, homology-based, computational approach that mines ligand inhibition data was used to predict residues involved in inhibitor selectivity in the DHFR family. Expectedly, some inhibitor selectivity determining residue positions were predicted to lie in the active site and coincide with experimentally known inhibitor selectivity determining positions. However, other residues that group spatially in clusters distal to the active site have not been previously investigated. In this study, the effect of introducing amino acid substitutions at one of these predicted clusters (His38-Ala39-Ile40) on the inhibitor selectivity profile in Bacillus stearothermophilus dihydrofolate reductase (Bs DHFR) was investigated. Mutations were introduced into these cluster positions to change sidechain chemistry and size. We determined kcat and KM values and measured KD values at equilibrium for two competitive DHFR inhibitors, trimethoprim (TMP) and pyrimethamine (PYR). Mutations in the His38-Ala39-Ile40 cluster significantly impacted inhibitor binding and TMP/PYR selectivity - seven out of nine mutations resulted in tighter binding to PYR when compared to TMP. These data suggest that the His38-Ala39-Ile40 cluster is a distal inhibitor selectivity determining region that favors PYR binding in Bs DHFR and, possibly, throughout the DHFR family.
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Affiliation(s)
- Tyler Eck
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Seema Patel
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Thomas Candela
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Katherine Leon H
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Michael Little
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Natalia E Reis
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | | | - Ueli Gubler
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Cheryl A Janson
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Jaclyn Catalano
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Nina M Goodey
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA.
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19
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Haran G, Mazal H. How fast are the motions of tertiary-structure elements in proteins? J Chem Phys 2020; 153:130902. [PMID: 33032421 DOI: 10.1063/5.0024972] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e., domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the functional cycles of protein machines and motors. Theoretical estimates suggest that domain motions should be very fast, occurring on the nanosecond or microsecond time scales. Indeed, free-energy barriers for domain motions are likely to involve salt bridges, which can break in microseconds. Experimental methods that can directly probe domain motions on fast time scales have appeared only in recent years. This Perspective discusses briefly some of these techniques, including nuclear magnetic resonance and single-molecule fluorescence spectroscopies. We introduce a few recent studies that demonstrate ultrafast domain motions and discuss their potential roles. Particularly surprising is the observation of tertiary-structure element dynamics that are much faster than the functional cycles in some protein machines. These swift motions can be rationalized on a case-by-case basis. For example, fast domain closure in multi-substrate enzymes may be utilized to optimize relative substrate orientation. Whether a large mismatch in time scales of conformational dynamics vs functional cycles is a general design principle in proteins remains to be determined.
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Affiliation(s)
- Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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20
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Site-Specific Tryptophan Labels Reveal Local Microsecond-Millisecond Motions of Dihydrofolate Reductase. Molecules 2020; 25:molecules25173819. [PMID: 32842574 PMCID: PMC7503464 DOI: 10.3390/molecules25173819] [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: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Many enzymes are known to change conformations during their catalytic cycle, but the role of these protein motions is not well understood. Escherichia coli dihydrofolate reductase (DHFR) is a small, flexible enzyme that is often used as a model system for understanding enzyme dynamics. Recently, native tryptophan fluorescence was used as a probe to study micro- to millisecond dynamics of DHFR. Yet, because DHFR has five native tryptophans, the origin of the observed conformational changes could not be assigned to a specific region within the enzyme. Here, we use DHFR mutants, each with a single tryptophan as a probe for temperature jump fluorescence spectroscopy, to further inform our understanding of DHFR dynamics. The equilibrium tryptophan fluorescence of the mutants shows that each tryptophan is in a different environment and that wild-type DHFR fluorescence is not a simple summation of all the individual tryptophan fluorescence signatures due to tryptophan–tryptophan interactions. Additionally, each mutant exhibits a two-phase relaxation profile corresponding to ligand association/dissociation convolved with associated conformational changes and a slow conformational change that is independent of ligand association and dissociation, similar to the wild-type enzyme. However, the relaxation rate of the slow phase depends on the location of the tryptophan within the enzyme, supporting the conclusion that the individual tryptophan fluorescence dynamics do not originate from a single collective motion, but instead report on local motions throughout the enzyme.
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21
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Mazal H, Haran G. Single-molecule FRET methods to study the dynamics of proteins at work. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019; 12:8-17. [PMID: 31989063 PMCID: PMC6984960 DOI: 10.1016/j.cobme.2019.08.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Feynman commented that "Everything that living things do can be understood in terms of the jiggling and wiggling of atoms". Proteins can jiggle and wiggle large structural elements such as domains and subunits as part of their functional cycles. Single-molecule fluorescence resonance energy transfer (smFRET) is an excellent tool to study conformational dynamics and decipher coordinated large-scale motions within proteins. smFRET methods introduced in recent years are geared toward understanding the time scales and amplitudes of function-related motions. This review discusses the methodology for obtaining and analyzing smFRET temporal trajectories that provide direct dynamic information on transitions between conformational states. It also introduces correlation methods that are useful for characterizing intramolecular motions. This arsenal of techniques has been used to study multiple molecular systems, from membrane proteins through molecular chaperones, and we examine some of these studies here. Recent exciting methodological novelties permit revealing very fast, submillisecond dynamics, whose relevance to protein function is yet to be fully grasped.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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22
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Kønig SM, Rissler V, Terkelsen T, Lambrughi M, Papaleo E. Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level. PLoS Comput Biol 2019; 15:e1007485. [PMID: 31825969 PMCID: PMC6927658 DOI: 10.1371/journal.pcbi.1007485] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/23/2019] [Accepted: 10/12/2019] [Indexed: 12/11/2022] Open
Abstract
Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell lymphoma-2 (Bcl-2) family regulate programmed cell death by the mitochondrial apoptosis pathway. In response to intracellular stress, the apoptotic balance is governed by interactions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions. Their dysfunction enables cancer cells to evade cell death. The critical role of Bcl-2 proteins in homeostasis and tumorigenesis, coupled with mounting insight in their structural properties, make them therapeutic targets of interest. A better understanding of gene expression, mutational profile, and molecular mechanisms of pro-survival Bcl-2 proteins in different cancer types, could help to clarify their role in cancer development and may guide advancement in drug discovery. Here, we shed light on the pro-survival Bcl-2 proteins in breast cancer using different bioinformatic approaches, linking -omics with structural data. We analyzed the changes in the expression of the Bcl-2 proteins and their BH3-containing interactors in breast cancer samples. We then studied, at the structural level, a selection of interactions, accounting for effects induced by mutations found in the breast cancer samples. We find two complexes between the up-regulated Bcl2A1 and two down-regulated BH3-only candidates (i.e., Hrk and Nr4a1) as targets associated with reduced apoptosis in breast cancer samples for future experimental validation. Furthermore, we predict L99R, M75R as damaging mutations altering protein stability, and Y120C as a possible allosteric mutation from an exposed surface to the BH3-binding site.
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Affiliation(s)
- Simon Mathis Kønig
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Vendela Rissler
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Thilde Terkelsen
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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23
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Li J, Fortunato G, Lin J, Agarwal PK, Kohen A, Singh P, Cheatum CM. Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase. Biochemistry 2019; 58:3861-3868. [PMID: 31423766 PMCID: PMC7296831 DOI: 10.1021/acs.biochem.9b00460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Understanding protein motions and their role in enzymatic reactions is an important and timely topic in enzymology. Protein motions that are involved in the chemical step of catalysis are particularly intriguing but difficult to identify. A global network of coupled residues in Escherichia coli dihydrofolate reductase (E. coli DHFR), which assists in catalyzing the chemical step, has previously been demonstrated through quantum mechanical/molecular mechanical and molecular dynamics simulations as well as bioinformatic analyses. A few specific residues (M42, G121, F125, and I14) were shown to function synergistically with measurements of single-turnover rates and the temperature dependence of intrinsic kinetic isotope effects (KIEsint) of site-directed mutants. This study hypothesizes that the global network of residues involved in the chemical step is evolutionarily conserved and probes homologous residues of the potential global network in human DHFR through measurements of the temperature dependence of KIEsint and computer simulations based on the empirical valence bond method. We study mutants M53W and S145V. Both of these remote residues are homologous to network residues in E. coli DHFR. Non-additive isotope effects on activation energy are observed between M53 and S145, indicating their synergistic effect on the chemical step in human DHFR, which suggests that both of these residues are part of a network affecting the chemical step in enzyme catalysis. This finding supports the hypothesis that human and E. coli DHFR share similar networks, consistent with evolutionary preservation of such networks.
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Affiliation(s)
- Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | | | - Jennifer Lin
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
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24
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Clancy B, Moree B, Salafsky J. Angular Mapping of Protein Structure Using Nonlinear Optical Measurements. Biophys J 2019; 117:500-508. [PMID: 31349993 PMCID: PMC6697465 DOI: 10.1016/j.bpj.2019.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/12/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022] Open
Abstract
Proteins are inherently dynamic, flexible molecules that execute precise conformational changes to perform their functions, but existing techniques to directly measure relevant structural changes in solution at room temperature remain limited. Here, we demonstrate a structural technique using second-harmonic generation and two-photon fluorescence under single-laser excitation to map both the mean angular orientation and the distribution width of a probe at various sites throughout the protein with high sensitivity. Our work resolves distinct dihydrofolate reductase (DHFR) ligand-protein conformations, allows interrogation of regions unresolvable by other techniques, and reveals structural differences between DHFR and a point mutant (DHFR-G121V). The technique, angular mapping of protein structure, enables direct and rapid determination of previously unseen aspects of protein structure in a benchtop optical system.
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25
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Tunable microsecond dynamics of an allosteric switch regulate the activity of a AAA+ disaggregation machine. Nat Commun 2019; 10:1438. [PMID: 30926805 PMCID: PMC6440998 DOI: 10.1038/s41467-019-09474-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/14/2019] [Indexed: 12/13/2022] Open
Abstract
Large protein machines are tightly regulated through allosteric communication channels. Here we demonstrate the involvement of ultrafast conformational dynamics in allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins. Each subunit of ClpB contains a unique coiled-coil structure, the middle domain (M domain), proposed as a control element that binds the co-chaperone DnaK. Using single-molecule FRET spectroscopy, we probe the M domain during the chaperone cycle and find it to jump on the microsecond time scale between two states, whose structures are determined. The M-domain jumps are much faster than the overall activity of ClpB, making it an effectively continuous, tunable switch. Indeed, a series of allosteric interactions are found to modulate the dynamics, including binding of nucleotides, DnaK and protein substrates. This mode of dynamic control enables fast cellular adaptation and may be a general mechanism for the regulation of cellular machineries. Large protein machines are tightly regulated through allosteric communication channels. Here authors use single-molecule FRET and demonstrate the involvement of ultrafast conformational dynamics in the allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins.
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26
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Niessen KA, Xu M, George DK, Chen MC, Ferré-D'Amaré AR, Snell EH, Cody V, Pace J, Schmidt M, Markelz AG. Protein and RNA dynamical fingerprinting. Nat Commun 2019; 10:1026. [PMID: 30833555 PMCID: PMC6399446 DOI: 10.1038/s41467-019-08926-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/04/2019] [Indexed: 01/30/2023] Open
Abstract
Protein structural vibrations impact biology by steering the structure to functional intermediate states; enhancing tunneling events; and optimizing energy transfer. Strong water absorption and a broad continuous vibrational density of states have prevented optical identification of these vibrations. Recently spectroscopic signatures that change with functional state were measured using anisotropic terahertz microscopy. The technique however has complex sample positioning requirements and long measurement times, limiting access for the biomolecular community. Here we demonstrate that a simplified system increases spectroscopic structure to dynamically fingerprint biomacromolecules with a factor of 6 reduction in data acquisition time. Using this technique, polarization varying anisotropy terahertz microscopy, we show sensitivity to inhibitor binding and unique vibrational spectra for several proteins and an RNA G-quadruplex. The technique’s sensitivity to anisotropic absorbance and birefringence provides rapid assessment of macromolecular dynamics that impact biology. The characterization of biomacromolecule structural vibrations has been impeded by a broad continuous vibrational density of states obscuring molecule specific vibrations. A terahertz microscopy system using polarization control produces signatures to dynamically fingerprint proteins and a RNA G-quadruplex.
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Affiliation(s)
| | - Mengyang Xu
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Deepu K George
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Michael C Chen
- National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | | | - Edward H Snell
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Vivian Cody
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - James Pace
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin, Milwaukee, WI, USA
| | - Andrea G Markelz
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA. .,Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA.
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27
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Gorman SD, D'Amico RN, Winston DS, Boehr DD. Engineering Allostery into Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:359-384. [PMID: 31707711 PMCID: PMC7508002 DOI: 10.1007/978-981-13-8719-7_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Our ability to engineer protein structure and function has grown dramatically over recent years. Perhaps the next level in protein design is to develop proteins whose function can be regulated in response to various stimuli, including ligand binding, pH changes, and light. Endeavors toward these goals have tested and expanded on our understanding of protein function and allosteric regulation. In this chapter, we provide examples from different methods for developing new allosterically regulated proteins. These methods range from whole insertion of regulatory domains into new host proteins, to covalent attachment of photoswitches to generate light-responsive proteins, and to targeted changes to specific amino acid residues, especially to residues identified to be important for relaying allosteric information across the protein framework. Many of the examples we discuss have already found practical use in medical and biotechnology applications.
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Affiliation(s)
- Scott D Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
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28
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Abstract
Even after a century of investigation, our understanding of how enzymes work remains far from complete. In particular, several factors that enable enzymes to achieve high catalytic efficiencies remain only poorly understood. A number of theories have been developed, which propose or reaffirm that enzymes work as structural scaffolds, serving to bring together and properly orient the participants so that the reaction can proceed; therefore, leading to enzymes being viewed as only passive participants in the catalyzed reaction. A growing body of evidence shows that enzymes are not rigid structures but are constantly undergoing a wide range of internal motions and conformational fluctuations. In this Perspective, on the basis of studies from our group, we discuss the emerging biophysical model of enzyme catalysis that provides a detailed understanding of the interconnection among internal protein motions, conformational substates, enzyme mechanisms, and the catalytic efficiency of enzymes. For a number of enzymes, networks of conserved residues that extend from the surface of the enzyme all the way to the active site have been discovered. These networks are hypothesized to serve as pathways of energy transfer that enables thermodynamical coupling of the surrounding solvent with enzyme catalysis and play a role in promoting enzyme function. Additionally, the role of enzyme structure and electrostatic effects has been well acknowledged for quite some time. Collectively, the recent knowledge gained about enzyme mechanisms suggests that the conventional paradigm of enzyme structure encoding function is incomplete and needs to be extended to structure encodes dynamics, and together these enzyme features encode function including catalytic rate acceleration.
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Affiliation(s)
- Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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29
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Iorgu AI, Baxter NJ, Cliff MJ, Levy C, Waltho JP, Hay S, Scrutton NS. Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes. ACS Catal 2018; 8:11589-11599. [PMID: 31119061 PMCID: PMC6516726 DOI: 10.1021/acscatal.8b02810] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/23/2018] [Indexed: 11/28/2022]
Abstract
![]()
Many enzymes that
catalyze hydride transfer reactions work via
a mechanism dominated by quantum mechanical tunneling. The involvement
of fast vibrational modes of the reactive complex is often inferred
in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol
tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer
mechanism in PETNR by designing conservative (L25I and I107L) and
side chain shortening (L25A and I107A) PETNR variants and using a
combination of experimental approaches (stopped-flow rapid kinetics,
X-ray crystallography, isotope/temperature dependence studies of H-transfer
and NMR spectroscopy). X-ray data show subtle changes in the local
environment of the targeted side chains but no major structural perturbation
caused by mutagenesis of these two second sphere active site residues.
However, temperature dependence studies of H-transfer revealed a coenzyme-specific
and complex thermodynamic equilibrium between different reactive configurations
in PETNR–coenzyme complexes. We find that mutagenesis of these
second sphere “noncatalytic” residues affects differently
the reactivity of PETNR with NADPH and NADH coenzymes. We attribute
this to subtle, dynamic structural changes in the PETNR active site,
the effects of which impact differently in the nonequivalent reactive
geometries of PETNR−NADH and PETNR−NADPH complexes.
This inference is confirmed through changes observed in the NMR chemical
shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P)
analogues. We show that H-transfer rates can (to some extent) be buffered
through entropy–enthalpy compensation, but that use of integrated
experimental tools reveals hidden complexities that implicate a role
for dynamics in this relatively simple H-transfer reaction. Similar
approaches are likely to be informative in other enzymes to understand
the relative importance of (distal) hydrophobic side chains and dynamics
in controlling the rates of enzymatic H-transfer.
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Affiliation(s)
- Andreea I. Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin Levy
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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30
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Mhashal AR, Pshetitsky Y, Eitan R, Cheatum CM, Kohen A, Major DT. Effect of Asp122 Mutation on the Hydride Transfer in E. coli DHFR Demonstrates the Goldilocks of Enzyme Flexibility. J Phys Chem B 2018; 122:8006-8017. [PMID: 30040418 DOI: 10.1021/acs.jpcb.8b05556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF) in the presence of NADPH. The key hydride transfer step in the reaction is facilitated by a combination of enzyme active site preorganization and correlated protein motions in the Michaelis-Menten (E:NADPH:DHF) complex. The present theoretical study employs mutagenesis to examine the relation between structural and functional properties of the enzyme. We mutate Asp122 in Escherichia coli DHFR, which is a conserved amino acid in the DHFR family. The consequent effect of the mutation on enzyme catalysis is examined from an energetic, structural and short-time dynamic perspective. Our investigations suggest that the structural and short-time dynamic perturbations caused by Asp122X mutations (X = Asn, Ser, Ala) are along the reaction coordinate and lower the rate of hydride transfer. Importantly, analysis of the correlated and principle component motions in the enzyme suggest that the mutation alters the coupled motions that are present in the wild-type enzyme. In the case of D122N and D122S, the mutations inhibit coupled motion, whereas in the case of D122A, the mutation enhances coupled motion, although all mutations result in similar rate reduction. These results emphasize a Goldilocks principle of enzyme flexibility, that is, enzymes should neither be too rigid nor too flexible.
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Affiliation(s)
- Anil R Mhashal
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Yaron Pshetitsky
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Reuven Eitan
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Christopher M Cheatum
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Amnon Kohen
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
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31
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Cui M, Du J, Yao X. The Binding Mechanism Between Inositol Phosphate (InsP) and the Jasmonate Receptor Complex: A Computational Study. FRONTIERS IN PLANT SCIENCE 2018; 9:963. [PMID: 30073006 PMCID: PMC6058352 DOI: 10.3389/fpls.2018.00963] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
Jasmonates are critical plant hormones, mediating stress response in plants and regulating plant growth and development. The jasmonate receptor is a multi-component complex, composed of Arabidopsis SKP-LIKE PROTEIN1 (ASK1), CORONATINE INSENSITIVE 1 (COI1), inositol phosphate (InsP), and jasmonate ZIM-domain protein (JAZ). COI1 acts as multi-component signaling hub that binds with each component. InsP is suggested to play important roles in the hormone perception. How InsP binds with COI1 and the structural changes in COI1 upon binding with InsP, JA-Ile, and JAZ are not well understood. In this study, we integrated multiple computational methods, such as molecular docking, molecular dynamics simulations, residue interaction network analysis and binding free energy calculation, to explore the effect of InsP on the dynamic behavior of COI1 and the recognition mechanism of each component of the jasmonate receptor complex. We found that upon binding with InsP, JA-Ile, and JAZ1, the structure of COI1 becomes more compact. The binding of InsP with COI1 stabilizes the conformation of COI1 and promotes the binding between JA-Ile or JAZ1 and COI1. Analysis of the network parameters led to the identification of some hub nodes in this network, including Met88, His118, Arg120, Arg121, Arg346, Tyr382, Arg409, Trp467, and Lys492. The structural and dynamic details will be helpful for understanding the recognition mechanism of each component and the discovery and design of novel jasmonate signaling pathway modulators.
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Affiliation(s)
- Mengqi Cui
- Shandong Province Key Laboratory of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Juan Du
- Shandong Province Key Laboratory of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - XiaoJun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
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32
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Ming D, Chen R, Huang H. Amino-Acid Network Clique Analysis of Protein Mutation Non-Additive Effects: A Case Study of Lysozme. Int J Mol Sci 2018; 19:ijms19051427. [PMID: 29747478 PMCID: PMC5983764 DOI: 10.3390/ijms19051427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/28/2018] [Accepted: 05/07/2018] [Indexed: 01/23/2023] Open
Abstract
Optimizing amino-acid mutations in enzyme design has been a very challenging task in modern bio-industrial applications. It is well known that many successful designs often hinge on extensive correlations among mutations at different sites within the enzyme, however, the underpinning mechanism for these correlations is far from clear. Here, we present a topology-based model to quantitively characterize non-additive effects between mutations. The method is based on the molecular dynamic simulations and the amino-acid network clique analysis. It examines if the two mutation sites of a double-site mutation fall into to a 3-clique structure, and associates such topological property of mutational site spatial distribution with mutation additivity features. We analyzed 13 dual mutations of T4 phage lysozyme and found that the clique-based model successfully distinguishes highly correlated or non-additive double-site mutations from those additive ones whose component mutations have less correlation. We also applied the model to protein Eglin c whose structural topology is significantly different from that of T4 phage lysozyme, and found that the model can, to some extension, still identify non-additive mutations from additive ones. Our calculations showed that mutation non-additive effects may heavily depend on a structural topology relationship between mutation sites, which can be quantitatively determined using amino-acid network k-cliques. We also showed that double-site mutation correlations can be significantly altered by exerting a third mutation, indicating that more detailed physicochemical interactions should be considered along with the network clique-based model for better understanding of this elusive mutation-correlation principle.
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Affiliation(s)
- Dengming Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Biotech Building Room B1-404, 30 South Puzhu Road, Nanjing 211816, Jiangsu, China.
| | - Rui Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Biotech Building Room B1-404, 30 South Puzhu Road, Nanjing 211816, Jiangsu, China.
| | - He Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Biotech Building Room B1-404, 30 South Puzhu Road, Nanjing 211816, Jiangsu, China.
- College of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, Jiangsu, China.
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33
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Fonseca R, Budday D, van den Bedem H. Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces. J Comput Chem 2018; 39:711-720. [PMID: 29315667 DOI: 10.1002/jcc.25138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 11/22/2017] [Accepted: 11/27/2017] [Indexed: 12/22/2022]
Abstract
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute joints and noncovalent interactions as holonomic constraints, can accurately characterize these native ensembles. However, sampling biomolecules remains challenging owing to their ultra-high dimensional configuration spaces, and the requirement to avoid (self-) collisions, which results in low acceptance rates. Here, we present two novel mechanisms to overcome these limitations. First, we introduce temporary constraints between near-colliding links. The resulting constraint varieties instantaneously redirect the search for collision-free conformations, and couple motions between distant parts of the linkage. Second, we adapt a randomized Poisson-disk motion planner, which prevents local oversampling and widens the search, to ultra-high dimensions. Tests on several model systems show that the sampling acceptance rate can increase from 16% to 70%, and that the conformational coverage in loop modeling measured as average closeness to existing loop conformations doubled. Correlated protein motions identified with our algorithm agree with those from MD simulations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Rasmus Fonseca
- Molecular and Cellular Physiology, Stanford University, Stanford, California.,Bioscience Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California
| | - Dominik Budday
- Chair of Applied Dynamics, University of Erlangen-Nuremberg, Erlangen, 91058, Germany
| | - Henry van den Bedem
- Bioscience Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California
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34
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Boehr DD, D'Amico RN, O'Rourke KF. Engineered control of enzyme structural dynamics and function. Protein Sci 2018; 27:825-838. [PMID: 29380452 DOI: 10.1002/pro.3379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 12/20/2022]
Abstract
Enzymes undergo a range of internal motions from local, active site fluctuations to large-scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions. Post-translational covalent modification can provide an additional level of enzyme control. These studies have not only provided insights into the functional role of protein motions, but they offer opportunities to create stimulus-responsive enzymes. These enzymes can be engineered to respond to a number of external stimuli, including light, pH, and the presence of novel allosteric modulators. Altogether, the ability to engineer and control enzyme structural dynamics can provide new tools for biotechnology and medicine.
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Affiliation(s)
- David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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35
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Shanmuganatham KK, Wallace RS, Ting-I Lee A, Plapp BV. Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Protein Sci 2018; 27:750-768. [PMID: 29271062 DOI: 10.1002/pro.3370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 01/06/2023]
Abstract
The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD+ and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.
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Affiliation(s)
- Karthik K Shanmuganatham
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Diagnostic Virology Laboratory, USDA, Ames, IA, 50010
| | - Rachel S Wallace
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Ann Ting-I Lee
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,No 92, Jing Mao 1st Rd., Taichung, Taiwan, 406, Republic of China
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109
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36
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Cossins BP, Lawson ADG, Shi J. Computational Exploration of Conformational Transitions in Protein Drug Targets. Methods Mol Biol 2018; 1762:339-365. [PMID: 29594780 DOI: 10.1007/978-1-4939-7756-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Protein drug targets vary from highly structured to completely disordered; either way dynamics governs function. Hence, understanding the dynamical aspects of how protein targets function can enable improved interventions with drug molecules. Computational approaches offer highly detailed structural models of protein dynamics which are becoming more predictive as model quality and sampling power improve. However, the most advanced and popular models still have errors owing to imperfect parameter sets and often cannot access longer timescales of many crucial biological processes. Experimental approaches offer more certainty but can struggle to detect and measure lightly populated conformations of target proteins and subtle allostery. An emerging solution is to integrate available experimental data into advanced molecular simulations. In the future, molecular simulation in combination with experimental data may be able to offer detailed models of important drug targets such that improved functional mechanisms or selectivity can be accessed.
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Affiliation(s)
- Benjamin P Cossins
- Computer-Aided Drug Design and Structural Biology, UCB Pharma, Slough, UK.
| | | | - Jiye Shi
- Computer-Aided Drug Design and Structural Biology, UCB Pharma, Slough, UK
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37
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Zhao J, Frauenkron-Machedjou VJ, Fulton A, Zhu L, Davari MD, Jaeger KE, Schwaneberg U, Bocola M. Unraveling the effects of amino acid substitutions enhancing lipase resistance to an ionic liquid: a molecular dynamics study. Phys Chem Chem Phys 2018; 20:9600-9609. [DOI: 10.1039/c7cp08470f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The key properties affecting lipase resistance towards an ionic liquid are uncovered through a molecular dynamics study.
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Affiliation(s)
- Jing Zhao
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- Tianjin Institute of Industrial Biotechnology
| | | | - Alexander Fulton
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52426 Jülich
- Germany
| | - Leilei Zhu
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- Tianjin Institute of Industrial Biotechnology
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52426 Jülich
- Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- DWI-Leibniz Institute for Interactive Materials
| | - Marco Bocola
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
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38
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Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G. Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase. Biochemistry 2017; 56:2477-2487. [DOI: 10.1021/acs.biochem.7b00098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Ouedraogo
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sheena Vasquez
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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39
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Frappier V, Chartier M, Najmanovich R. Applications of Normal Mode Analysis Methods in Computational Protein Design. Methods Mol Biol 2017; 1529:203-214. [PMID: 27914052 DOI: 10.1007/978-1-4939-6637-0_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design. Here, we present a detailed tutorial on how to perform such calculations using ENCoM.
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Affiliation(s)
- Vincent Frappier
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts avenue, Cambridge, MA, 02139, USA
- Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada
| | - Matthieu Chartier
- Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada
| | - Rafael Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montreal, Montreal, H3C 3J7, QC, Canada.
- Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada.
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40
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Luk LYP, Loveridge EJ, Allemann RK. Protein motions and dynamic effects in enzyme catalysis. Phys Chem Chem Phys 2016; 17:30817-27. [PMID: 25854702 DOI: 10.1039/c5cp00794a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The role of protein motions in promoting the chemical step of enzyme catalysed reactions remains a subject of considerable debate. Here, a unified view of the role of protein dynamics in dihydrofolate reductase catalysis is described. Recently the role of such motions has been investigated by characterising the biophysical properties of isotopically substituted enzymes through a combination of experimental and computational analyses. Together with previous work, these results suggest that dynamic coupling to the chemical coordinate is detrimental to catalysis and may have been selected against during DHFR evolution. The full catalytic power of Nature's catalysts appears to depend on finely tuning protein motions in each step of the catalytic cycle.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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41
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Hanske J, Aleksić S, Ballaschk M, Jurk M, Shanina E, Beerbaum M, Schmieder P, Keller BG, Rademacher C. Intradomain Allosteric Network Modulates Calcium Affinity of the C-Type Lectin Receptor Langerin. J Am Chem Soc 2016; 138:12176-86. [DOI: 10.1021/jacs.6b05458] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonas Hanske
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Stevan Aleksić
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Martin Ballaschk
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Marcel Jurk
- Department
of Bioinformatics, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Elena Shanina
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Monika Beerbaum
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Bettina G. Keller
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Christoph Rademacher
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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42
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Controlling Active Site Loop Dynamics in the (β/α)8 Barrel Enzyme Indole-3-Glycerol Phosphate Synthase. Catalysts 2016. [DOI: 10.3390/catal6090129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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43
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Abstract
Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions.
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Affiliation(s)
- P Singh
- University of Iowa, Iowa City, IA, United States
| | - Z Islam
- University of Iowa, Iowa City, IA, United States
| | - A Kohen
- University of Iowa, Iowa City, IA, United States.
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44
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Piovesan D, Minervini G, Tosatto SCE. The RING 2.0 web server for high quality residue interaction networks. Nucleic Acids Res 2016; 44:W367-74. [PMID: 27198219 PMCID: PMC4987896 DOI: 10.1093/nar/gkw315] [Citation(s) in RCA: 286] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/13/2016] [Indexed: 01/06/2023] Open
Abstract
Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico–chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain–domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π–π stacking and π–cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring.
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Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua 35121, Italy
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padua, Padua 35121, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, Padua 35121, Italy CNR Institute of Neuroscience, Padua 35121, Italy
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45
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Wong HE, Pack SP, Kwon I. Positional effects of hydrophobic non-natural amino acid mutagenesis into the surface region of murine dihydrofolate reductase on enzyme properties. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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46
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Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
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Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
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47
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016; 12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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Affiliation(s)
- Tatiana Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Ryan Moffatt
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
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48
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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49
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Wang Z, Antoniou D, Schwartz SD, Schramm VL. Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects, and Heavy Enzyme Studies. Biochemistry 2015; 55:157-66. [PMID: 26652185 DOI: 10.1021/acs.biochem.5b01241] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Escherichia coli dihydrofolate reductase (ecDHFR) is used to study fundamental principles of enzyme catalysis. It remains controversial whether fast protein motions are coupled to the hydride transfer catalyzed by ecDHFR. Previous studies with heavy ecDHFR proteins labeled with (13)C, (15)N, and nonexchangeable (2)H reported enzyme mass-dependent hydride transfer kinetics for ecDHFR. Here, we report refined experimental and computational studies to establish that hydride transfer is independent of protein mass. Instead, we found the rate constant for substrate dissociation to be faster for heavy DHFR. Previously reported kinetic differences between light and heavy DHFRs likely arise from kinetic steps other than the chemical step. This study confirms that fast (femtosecond to picosecond) protein motions in ecDHFR are not coupled to hydride transfer and provides an integrative computational and experimental approach to resolve fast dynamics coupled to chemical steps in enzyme catalysis.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Dimitri Antoniou
- Department of Chemistry and Biochemistry, University of Arizona , P.O. Box 210041, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona , P.O. Box 210041, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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50
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Ohmae E, Tanaka S, Miyashita Y, Katayanagi K, Matsuo K. Vacuum-Ultraviolet Circular Dichroism Spectra of Escherichia coli Dihydrofolate Reductase and Its Mutants: Contributions of Phenylalanine and Tyrosine Side Chains and Exciton Coupling of Two Tryptophan Side Chains. J Phys Chem B 2015; 119:13002-8. [PMID: 26407224 DOI: 10.1021/acs.jpcb.5b07480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vacuum-ultraviolet (VUV) circular dichroism (CD) spectroscopy has recently been used for secondary structure analysis of proteins; however, the contribution of aromatic side chains to protein VUV CD spectra is unresolved. In this report, VUV CD spectra of 10 Escherichia coli dihydrofolate reductase (DHFR) mutants, in which each phenylalanine or tyrosine residue was mutated to leucine, were measured down to 175 nm at 25 °C and pH 8.0 to elucidate the contributions of these aromatic side chains to the high-energy transitions of peptide bonds. The VUV CD spectra of these mutants were different from the spectrum of the wild-type protein, indicating that the contribution of the phenylalanine and tyrosine side chains of DHFR extends to the VUV region. Furthermore, the VUV CD spectrum and the folate- or NADP(+)-induced spectral change of F103L mutant DHFR indicated a modification and regeneration of exciton coupling between the Trp47 and Trp74 side chains, respectively, suggesting that exciton coupling may also contribute to the CD spectrum of DHFR in the VUV region. These results should be useful for theoretically characterizing the contribution of aromatic side chains to protein CD spectra, leading to the improvement of protein secondary-structure analysis by VUV CD spectroscopy.
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Affiliation(s)
- Eiji Ohmae
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University , Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Suguru Tanaka
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University , Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Yurina Miyashita
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University , Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Katsuo Katayanagi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University , Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University , 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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