1
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Juretić D, Bonačić Lošić Ž. Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation. ENTROPY (BASEL, SWITZERLAND) 2024; 26:151. [PMID: 38392406 PMCID: PMC10888251 DOI: 10.3390/e26020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.
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Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, Šetalište Ivana Meštrovića 45, 21000 Split, Croatia
- Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
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2
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Tran TT, Fanucci GE. Natural Polymorphisms D60E and I62V Stabilize a Closed Conformation in HIV-1 Protease in the Absence of an Inhibitor or Substrate. Viruses 2024; 16:236. [PMID: 38400012 PMCID: PMC10892587 DOI: 10.3390/v16020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
HIV infection remains a global health issue plagued by drug resistance and virological failure. Natural polymorphisms (NPs) contained within several African and Brazilian protease (PR) variants have been shown to induce a conformational landscape of more closed conformations compared to the sequence of subtype B prevalent in North America and Western Europe. Here we demonstrate through experimental pulsed EPR distance measurements and molecular dynamic (MD) simulations that the two common NPs D60E and I62V found within subtypes F and H can induce a closed conformation when introduced into HIV-1PR subtype B. Specifically, D60E alters the conformation in subtype B through the formation of a salt bridge with residue K43 contained within the nexus between the flap and hinge region of the HIV-1 PR fold. On the other hand, I62V modulates the packing of the hydrophobic cluster of the cantilever and fulcrum, also resulting in a more closed conformation.
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Affiliation(s)
| | - Gail E. Fanucci
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
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3
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Kędzierski P, Zaczkowska M, Sokalski WA. Extreme Catalytic Power of Ketosteroid Isomerase Related to the Reversal of Proton Dislocations in Hydrogen-Bond Network. J Phys Chem B 2020; 124:3661-3666. [PMID: 32293890 PMCID: PMC7467711 DOI: 10.1021/acs.jpcb.0c01489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Dynamic
electrostatic catalytic field (DECF) vectors derived from
transition state and reactant wavefunctions for the two-step reaction
occurring within ketosteroid isomerase (KSI) have been calculated
using MP2/aug-cc-pVTZ and lower theory levels to determine the magnitude
of the catalytic effect and the optimal directions of proton transfers
in the KSI hydrogen-bond network. The most surprising and meaningful
finding is that the KSI catalytic activity is enhanced by proton dislocations
proceeding in opposite directions for each of the two consecutive
reaction steps in the same hydrogen network. Such a mechanism allows
an ultrafast switching of the catalytic proton wire environment, possibly
related to the exceptionally high KSI catalytic power.
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Affiliation(s)
- Paweł Kędzierski
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Maria Zaczkowska
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - W Andrzej Sokalski
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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4
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Kasprzycki P, Kopycki P, Listkowski A, Gorski A, Radzewicz C, Birch DJS, Waluk J, Fita P. Influence of local microenvironment on the double hydrogen transfer in porphycene. Phys Chem Chem Phys 2020; 22:17117-17128. [PMID: 32687131 DOI: 10.1039/d0cp02687e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We performed time-resolved transient absorption and fluorescence anisotropy measurements in order to study tautomerization of porphycene in rigid polymer matrices at cryogenic temperatures. Studies were carried out in poly(methyl methacrylate) (PMMA), poly(vinyl butyral) (PVB), and poly(vinyl alcohol) (PVA). The results prove that in all studied media hydrogen tunnelling plays a significant role in the double hydrogen transfer which becomes very sensitive to properties of the environment below approx. 150 K. We also demonstrate that there exist two populations of porphycene molecules in rigid media: "hydrogen-transferring" molecules, in which tautomerization occurs on time scales below 1 ns and "frozen" molecules in which double hydrogen transfer is too slow to be monitored with nanosecond techniques. The number of "frozen" molecules increases when the sample is cooled. We explain this effect by interactions of guest molecules with a rigid host matrix which disturbs symmetry of porphycene and hinders tunnelling. Temperature dependence of the number of hydrogen-transferring molecules suggests that the factor which restores the symmetry of the double-minimum potential well in porphycene are intermolecular vibrations localized in separated regions of the amorphous polymer.
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Affiliation(s)
- Piotr Kasprzycki
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland. and Institute of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka, Warsaw 01-224, Poland.
| | - Przemysław Kopycki
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Arkadiusz Listkowski
- Institute of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka, Warsaw 01-224, Poland. and Faculty of Mathematics and Science, Cardinal Stefan Wyszyński University, Dewajtis 5, 01-815 Warsaw, Poland
| | - Aleksander Gorski
- Institute of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka, Warsaw 01-224, Poland.
| | - Czesław Radzewicz
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - David J S Birch
- Photophysics Group, Centre for Molecular Nanometrology, Department of Physics, Scottish Universities Physics Alliance, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Jacek Waluk
- Institute of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka, Warsaw 01-224, Poland. and Faculty of Mathematics and Science, Cardinal Stefan Wyszyński University, Dewajtis 5, 01-815 Warsaw, Poland
| | - Piotr Fita
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
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5
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Wang L, Fried SD, Markland TE. Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site. J Phys Chem B 2017; 121:9807-9815. [DOI: 10.1021/acs.jpcb.7b06985] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lu Wang
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Stephen D. Fried
- Medical Research
Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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6
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Characterization of Cercospora nicotianae Hypothetical Proteins in Cercosporin Resistance. PLoS One 2015; 10:e0140676. [PMID: 26474162 DOI: 10.1371/journal.pone.0140676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/29/2015] [Indexed: 11/19/2022] Open
Abstract
The photoactivated toxin, cercosporin, produced by Cercospora species, plays an important role in pathogenesis of this fungus to host plants. Cercosporin has almost universal toxicity to cells due to its production of reactive oxygen species including singlet oxygen. For that reason, Cercospora species, which are highly resistant to their own toxin, are good candidates to identify genes for resistance to cercosporin and to the reactive oxygen species it produces. In previous research, the zinc cluster transcription factor CRG1 (cercosporin resistance gene 1) was found to be crucial for Cercospora species' resistance against cercosporin, and subtractive hybridization analysis identified 185 genes differentially expressed between Cercospora nicotianae wild type (wt) and a crg1 mutant. The focus of this work was to identify and characterize the hypothetical proteins that were identified in the Cercospora nicotianae subtractive library as potential resistance factors. Quantitative RT-PCR analysis of the 20 genes encoding hypothetical proteins showed that two, 24cF and 71cR, were induced under conditions of cercosporin toxicity, suggesting a role in resistance. Transformation and expression of 24cF and 71cR in the cercosporin-sensitive fungus, Neurospora crassa, showed that 71cR provided increased resistance to cercosporin toxicity, whereas no significant increase was observed in 24cF transformants. Gene disruption was used to generate C. nicotianae 71cR mutants; these mutants did not differ from wt C. nicotianae in cercosporin resistance or production. Quantitative RT-PCR analysis showed induction of other resistance genes in the 71cR mutant that may compensate for the loss of 71cR. Analysis of 71cR conserved domains and secondary and tertiary structure identify the protein as having an NTF2-like superfamily DUF1348 domain with unknown function, to be intracellular and localized in the cytosol, and to have similarities to proteins in the steroid delta-isomerase family.
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7
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Liang H, Chai B, Chen G, Chen W, Chen S, Xiao H, Lin S. Electric field-driven acid-base transformation: proton transfer from acid(HBr/HF) to base(NH3/H2O). Chem Res Chin Univ 2015. [DOI: 10.1007/s40242-015-4464-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site. Proc Natl Acad Sci U S A 2014; 111:18454-9. [PMID: 25503367 DOI: 10.1073/pnas.1417923111] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.
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9
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Ito M, Brinck T. Novel Approach for Identifying Key Residues in Enzymatic Reactions: Proton Abstraction in Ketosteroid Isomerase. J Phys Chem B 2014; 118:13050-8. [DOI: 10.1021/jp508423s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mika Ito
- Applied
Physical Chemistry, KTH Royal Institute of Technology, Teknikringen
30, 100 44 Stockholm, Sweden
| | - Tore Brinck
- Applied
Physical Chemistry, KTH Royal Institute of Technology, Teknikringen
30, 100 44 Stockholm, Sweden
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10
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Carvalho ATP, Barrozo A, Doron D, Kilshtain AV, Major DT, Kamerlin SCL. Challenges in computational studies of enzyme structure, function and dynamics. J Mol Graph Model 2014; 54:62-79. [PMID: 25306098 DOI: 10.1016/j.jmgm.2014.09.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/13/2014] [Accepted: 09/16/2014] [Indexed: 01/23/2023]
Abstract
In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.
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Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Alexandra Vardi Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel.
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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11
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Chakravorty DK, Merz KM. Studying allosteric regulation in metal sensor proteins using computational methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:181-218. [PMID: 25443958 DOI: 10.1016/bs.apcsb.2014.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this chapter, we describe advances made in understanding the mechanism of allosteric regulation of DNA operator binding in the ArsR/SmtB family of metal-sensing proteins using computational methods. The paradigm, zinc-sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Here, we discuss studies that helped to characterize a metal ion-mediated hydrogen-bonding pathway (HBP) that plays a dominant role in the allosteric mechanism of DNA operator binding in these proteins. The chapter discusses computational methods used to provide a molecular basis for the large conformational motions and allosteric coupling free energy (~6kcal/mol) associated with Zn(II) binding in CzrA. We present an accurate and convenient means by which to include metal ions in the nuclear magnetic resonance (NMR) structure determination process using molecular dynamics (MD) constrained by NMR-derived data. The method provides a realistic and physically viable description of the metal-binding site(s) and has potentially broad applicability in the structure determination of metal ion-bound proteins, protein folding, and metal template protein-design studies. Finally, our simulations provide strong support for a proposed HBP that physically connects the metal-binding residue, His97, to the DNA-binding interface through the αR helix that is present only in the Zn(II)-bound state. We find the interprotomer hydrogen bond interaction to be significantly stronger (~8kcal/mol) at functional allosteric metal-binding sites compared to the apo proteins. This interaction works to overcome the considerable disorder at these hydrogen-bonding sites in apo protein and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. This interaction is found to be considerably weaker in nonresponsive metal-binding sites. These findings suggest a conserved functional role of metal-mediated second-shell coordination hydrogen bonds at allosterically responsive sites in zinc-sensing transcription regulators.
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Affiliation(s)
- Dhruva K Chakravorty
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA.
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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12
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Carter JD, Mathias JD, Gomez EF, Ran Y, Xu F, Galiano L, Tran NQ, D'Amore PW, Wright CS, Chakravorty DK, Fanucci GE. Characterizing solution surface loop conformational flexibility of the GM2 activator protein. J Phys Chem B 2014; 118:10607-17. [PMID: 25127419 PMCID: PMC4161144 DOI: 10.1021/jp505938t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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GM2AP
has a β-cup topology with numerous X-ray structures
showing multiple conformations for some of the surface loops, revealing
conformational flexibility that may be related to function, where
function is defined as either membrane binding associated with ligand
binding and extraction or interaction with other proteins. Here, site-directed
spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy
and molecular dynamic (MD) simulations are used to characterize the
mobility and conformational flexibility of various structural regions
of GM2AP. A series of 10 single cysteine amino acid substitutions
were generated, and the constructs were chemically modified with the
methanethiosulfonate spin label. Continuous wave (CW) EPR line shapes
were obtained and subsequently simulated using the microscopic order
macroscopic disorder (MOMD) program. Line shapes for sites that have
multiple conformations in the X-ray structures required two spectral
components, whereas spectra of the remaining sites were adequately
fit with single-component parameters. For spin labeled sites L126C
and I66C, spectra were acquired as a function of temperature, and
simulations provided for the determination of thermodynamic parameters
associated with conformational change. Binding to GM2 ligand did not
alter the conformational flexibility of the loops, as evaluated by
EPR and NMR spectroscopies. These results confirm that the conformational
flexibility observed in the surface loops of GM2AP crystals is present
in solution and that the exchange is slow on the EPR time scale (>ns).
Furthermore, MD simulation results are presented and agree well with
the conformational heterogeneity revealed by SDSL.
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Affiliation(s)
- Jeffery D Carter
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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13
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Molecular dynamics simulations of mutated Mycobacterium tuberculosis l-alanine dehydrogenase to illuminate the role of key residues. J Mol Graph Model 2014; 50:61-70. [DOI: 10.1016/j.jmgm.2014.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/23/2014] [Accepted: 03/25/2014] [Indexed: 11/23/2022]
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14
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Schwans JP, Hanoian P, Lengerich BJ, Sunden F, Gonzalez A, Tsai Y, Hammes-Schiffer S, Herschlag D. Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. Biochemistry 2014; 53:2541-55. [PMID: 24597914 PMCID: PMC4004248 DOI: 10.1021/bi401671t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The
positioning of catalytic groups within proteins plays an important
role in enzyme catalysis, and here we investigate the positioning
of the general base in the enzyme ketosteroid isomerase (KSI). The
oxygen atoms of Asp38, the general base in KSI, were previously shown
to be involved in anion–aromatic interactions with two neighboring
Phe residues. Here we ask whether those interactions are sufficient,
within the overall protein architecture, to position Asp38 for catalysis
or whether the side chains that pack against Asp38 and/or the residues
of the structured loop that is capped by Asp38 are necessary to achieve
optimal positioning for catalysis. To test positioning, we mutated
each of the aforementioned residues, alone and in combinations, in
a background with the native Asp general base and in a D38E mutant
background, as Glu at position 38 was previously shown to be mispositioned
for general base catalysis. These double-mutant cycles reveal positioning
effects as large as 103-fold, indicating that structural
features in addition to the overall protein architecture and the Phe
residues neighboring the carboxylate oxygen atoms play roles in positioning.
X-ray crystallography and molecular dynamics simulations suggest that
the functional effects arise from both restricting dynamic fluctuations
and disfavoring potential mispositioned states. Whereas it may have
been anticipated that multiple interactions would be necessary for
optimal general base positioning, the energetic contributions from
positioning and the nonadditive nature of these interactions are not
revealed by structural inspection and require functional dissection.
Recognizing the extent, type, and energetic interconnectivity of interactions
that contribute to positioning catalytic groups has implications for
enzyme evolution and may help reveal the nature and extent of interactions
required to design enzymes that rival those found in biology.
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Affiliation(s)
- Jason P Schwans
- Department of Biochemistry, Stanford University , B400 Beckman Center, 279 Campus Drive, Stanford, California 94305, United States
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15
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Chakravorty DK, Wang B, Lee CW, Guerra AJ, Giedroc DP, Merz KM. Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. JOURNAL OF BIOMOLECULAR NMR 2013; 56:125-137. [PMID: 23609042 PMCID: PMC3773525 DOI: 10.1007/s10858-013-9729-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/10/2013] [Indexed: 06/02/2023]
Abstract
Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.
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Affiliation(s)
- Dhruva K. Chakravorty
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
| | - Bing Wang
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
| | - Chul Won Lee
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Alfredo J. Guerra
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Kenneth M. Merz
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
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16
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Layfield JP, Hammes-Schiffer S. Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding. J Am Chem Soc 2012; 135:717-25. [PMID: 23210919 DOI: 10.1021/ja3084384] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.
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Affiliation(s)
- Joshua P Layfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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17
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Abstract
This brief review analyzes the underlying physical principles of enzyme catalysis, with an emphasis on the role of equilibrium enzyme motions and conformational sampling. The concepts are developed in the context of three representative systems, namely, dihydrofolate reductase, ketosteroid isomerase, and soybean lipoxygenase. All of these reactions involve hydrogen transfer, but many of the concepts discussed are more generally applicable. The factors that are analyzed in this review include hydrogen tunneling, proton donor-acceptor motion, hydrogen bonding, pKa shifting, electrostatics, preorganization, reorganization, and conformational motions. The rate constant for the chemical step is determined primarily by the free energy barrier, which is related to the probability of sampling configurations conducive to the chemical reaction. According to this perspective, stochastic thermal motions lead to equilibrium conformational changes in the enzyme and ligands that result in configurations favorable for the breaking and forming of chemical bonds. For proton, hydride, and proton-coupled electron transfer reactions, typically the donor and acceptor become closer to facilitate the transfer. The impact of mutations on the catalytic rate constants can be explained in terms of the factors enumerated above. In particular, distal mutations can alter the conformational motions of the enzyme and therefore the probability of sampling configurations conducive to the chemical reaction. Methods such as vibrational Stark spectroscopy, in which environmentally sensitive probes are introduced site-specifically into the enzyme, provide further insight into these aspects of enzyme catalysis through a combination of experiments and theoretical calculations.
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Affiliation(s)
- Sharon Hammes-Schiffer
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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18
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Singla N, Chowdhury P. Role of hydrogen bonding in excited state intramolecular proton transfer of Indole-7-Carboxaldehyde: A theoretical and experimental study. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.08.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Guan Y, Yang B. Kinetic modeling for hydrogen-abstraction reaction of methylcyclohexane with the CH3 radical. Chem Eng Sci 2012. [DOI: 10.1016/j.ces.2012.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase. Proc Natl Acad Sci U S A 2012; 109:E299-308. [PMID: 22308339 DOI: 10.1073/pnas.1111566109] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK(a) prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK(a) near 7 was included. UV-absorbance and (13)C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis.
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21
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Chakravorty DK, Wang B, Ucisik MN, Merz KM. Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF. J Am Chem Soc 2011; 133:19330-3. [PMID: 22029374 DOI: 10.1021/ja208662z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The periplasmic Cu(+)/Ag(+) chaperone CusF features a novel cation-π interaction between a Cu(+)/Ag(+) ion and Trp44 at the metal binding site. The nature and strength of the Cu(+)/Ag(+)-Trp44 interactions were investigated using computational methodologies. Quantum-mechanical (QM) calculations showed that the Cu(+) and Ag(+) interactions with Trp44 are of similar strength (~14 kcal/mol) and bond order. Quantum-mechanical/molecular-mechanical (QM/MM) calculations showed that Cu(+) binds in a distorted tetrahedral coordination environment in the Trp44Met mutant, which lacks the cation-π interaction. Molecular dynamics (MD) simulations of CusF in the apo and Cu(+)-bound states emphasized the importance of the Cu(+)-Trp44 interaction in protecting Cu(+) from water oxidation. The protein structure does not change over the time scale of hundreds of nanoseconds in the metal-bound state. The metal recognition site exhibits small motions in the apo state but remains largely preorganized toward metal binding. Trp44 remains oriented to form the cation-π interaction in the apo state and faces an energetic penalty to move away from the metal ion. Cu(+) binding quenches the protein's internal motions in regions linked to binding CusB, suggesting that protein motions play an essential role in Cu(+) transfer to CusB.
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Affiliation(s)
- Dhruva K Chakravorty
- Department of Chemistry and Quantum Theory Project, University of Florida, 2238 New Physics Building, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
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22
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Reengineering rate-limiting, millisecond enzyme motions by introduction of an unnatural amino acid. Biophys J 2011; 101:411-20. [PMID: 21767494 DOI: 10.1016/j.bpj.2011.05.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/18/2011] [Accepted: 05/19/2011] [Indexed: 01/20/2023] Open
Abstract
Rate-limiting millisecond motions in wild-type (WT) Ribonuclease A (RNase A) are modulated by histidine 48. Here, we incorporate an unnatural amino acid, thia-methylimidazole, at this site (H48C-4MI) to investigate the effects of a single residue on protein motions over multiple timescales and on enzyme catalytic turnover. Molecular dynamics simulations reveal that H48C-4MI retains some crucial WT-like hydrogen bonding interactions but the extent of protein-wide correlated motions in the nanosecond regime is decreased relative to WT. NMR Carr-Purcell-Meiboom-Gill relaxation dispersion experiments demonstrate that millisecond conformational motions in H48C-4MI are present over a similar pH range compared to WT. Furthermore, incorporation of this nonnatural amino acid allows retention of WT-like catalytic activity over the full pH range. These studies demonstrate that the complexity of the protein energy landscape during the catalytic cycle can be maintained using unnatural amino acids, which may prove useful in enzyme design efforts.
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23
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Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase. Proc Natl Acad Sci U S A 2011; 108:16612-7. [PMID: 21949360 DOI: 10.1073/pnas.1113874108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding how electric fields and their fluctuations in the active site of enzymes affect efficient catalysis represents a critical objective of biochemical research. We have directly measured the dynamics of the electric field in the active site of a highly proficient enzyme, Δ(5)-3-ketosteroid isomerase (KSI), in response to a sudden electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields.
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24
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Borden WT. Current Applications of Computational Chemistry in JACS—Molecules, Mechanisms, and Materials. J Am Chem Soc 2011; 133:14841-3. [DOI: 10.1021/ja206656w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Hanoian P, Hammes-Schiffer S. Water in the active site of ketosteroid isomerase. Biochemistry 2011; 50:6689-700. [PMID: 21710970 DOI: 10.1021/bi200703y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two in the Y16S mutant and one in the Y16F and FFF mutants, with intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of (1)H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less probable in WT KSI.
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Affiliation(s)
- Philip Hanoian
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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26
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Zhou ZJ, Li XP, Liu ZB, Li ZR, Huang XR, Sun CC. Electric Field-Driven Acid−Base Chemistry: Proton Transfer from Acid (HCl) to Base (NH3/H2O). J Phys Chem A 2011; 115:1418-22. [DOI: 10.1021/jp110408y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhong-Jun Zhou
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Xiao-Ping Li
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Zhen-Bo Liu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Zhi-Ru Li
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Xu-Ri Huang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Chia-Chung Sun
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
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27
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The empirical valence bond model: theory and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.10] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Hanoian P, Sigala PA, Herschlag D, Hammes-Schiffer S. Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling. Biochemistry 2010; 49:10339-48. [PMID: 21049962 DOI: 10.1021/bi101428e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational studies are performed to analyze the physical properties of hydrogen bonds donated by Tyr16 and Asp103 to a series of substituted phenolate inhibitors bound in the active site of ketosteroid isomerase (KSI). As the solution pK(a) of the phenolate increases, these hydrogen bond distances decrease, the associated nuclear magnetic resonance (NMR) chemical shifts increase, and the fraction of protonated inhibitor increases, in agreement with prior experiments. The quantum mechanical/molecular mechanical calculations provide insight into the electronic inductive effects along the hydrogen bonding network that includes Tyr16, Tyr57, and Tyr32, as well as insight into hydrogen bond coupling in the active site. The calculations predict that the most-downfield NMR chemical shift observed experimentally corresponds to the Tyr16-phenolate hydrogen bond and that Tyr16 is the proton donor when a bound naphtholate inhibitor is observed to be protonated in electronic absorption experiments. According to these calculations, the electronic inductive effects along the hydrogen bonding network of tyrosines cause the Tyr16 hydroxyl to be more acidic than the Asp103 carboxylic acid moiety, which is immersed in a relatively nonpolar environment. When one of the distal tyrosine residues in the network is mutated to phenylalanine, thereby diminishing this inductive effect, the Tyr16-phenolate hydrogen bond becomes longer and the Asp103-phenolate hydrogen bond shorter, as observed in NMR experiments. Furthermore, the calculations suggest that the differences in the experimental NMR data and electronic absorption spectra for pKSI and tKSI, two homologous bacterial forms of the enzyme, are due predominantly to the third tyrosine that is present in the hydrogen bonding network of pKSI but not tKSI. These studies also provide experimentally testable predictions about the impact of mutating the distal tyrosine residues in this hydrogen bonding network on the NMR chemical shifts and electronic absorption spectra.
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Affiliation(s)
- Philip Hanoian
- Department of Chemistry,Pennsylvania State University, University Park, PA 16802, USA
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