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Sarkar S, Shah Tuglak Khan F, Guchhait T, Rath SP. Binuclear complexes with single M-F-M bridge (M: Fe, Mn, and Cu): A critical analysis of the impact of fluoride for isoelectronic hydroxide substitution. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.215003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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2
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Beal NJ, Corry TA, O'Malley PJ. Comparison of Experimental and Broken Symmetry Density Functional Theory Calculated Electron Paramagnetic Resonance Parameters for the Manganese Catalase Active Site in the Superoxidized Mn III/Mn IV State. J Phys Chem B 2018; 122:2881-2890. [PMID: 29470911 DOI: 10.1021/acs.jpcb.7b11649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Broken symmetry density functional theory has been used to calculate g-tensor, 55Mn, 14N, and 17O hyperfine couplings for active site models of superoxidized MnIII/MnIV manganese catalase both in its native and azide-inhibited form. While a good agreement is found between the calculated and experimental g-tensor and 55Mn hyperfine couplings for all models, the active site geometry and Mn ion oxidation state can only be readily distinguished based on a comparison of the calculated and experimental 14N azide and 17O HFCs. This comparison shows that only models containing a Jahn-Teller distorted 5-coordinate (MnIII)2 site and a 6-coordinate (MnIV)1 site can satisfactorily reproduce the experimental 14N and 17O hyperfine couplings.
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Affiliation(s)
- Nathan J Beal
- School of Chemistry , The University of Manchester , Manchester M13 9PL , U.K
| | - Thomas A Corry
- School of Chemistry , The University of Manchester , Manchester M13 9PL , U.K
| | - Patrick J O'Malley
- School of Chemistry , The University of Manchester , Manchester M13 9PL , U.K
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3
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Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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4
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Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters. Proc Natl Acad Sci U S A 2016; 113:10310-5. [PMID: 27573840 DOI: 10.1073/pnas.1607734113] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Natural resistance-associated macrophage protein (Nramp) family transporters catalyze uptake of essential divalent transition metals like iron and manganese. To discriminate against abundant competitors, the Nramp metal-binding site should favor softer transition metals, which interact either covalently or ionically with coordinating molecules, over hard calcium and magnesium, which interact mainly ionically. The metal-binding site contains an unusual, but conserved, methionine, and its sulfur coordinates transition metal substrates, suggesting a vital role in their transport. Using a bacterial Nramp model system, we show that, surprisingly, this conserved methionine is dispensable for transport of the physiological manganese substrate and similar divalents iron and cobalt, with several small amino acid replacements still enabling robust uptake. Moreover, the methionine sulfur's presence makes the toxic metal cadmium a preferred substrate. However, a methionine-to-alanine substitution enables transport of calcium and magnesium. Thus, the putative evolutionary pressure to maintain the Nramp metal-binding methionine likely exists because it-more effectively than any other amino acid-increases selectivity for low-abundance transition metal transport in the presence of high-abundance divalents like calcium and magnesium.
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5
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Beal NJ, O'Malley PJ. Manganese Oxidation State Assignment for Manganese Catalase. J Am Chem Soc 2016; 138:4358-61. [PMID: 27007277 DOI: 10.1021/jacs.6b02600] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation state assignment of the manganese ions present in the superoxidized manganese (III/IV) catalase active site is determined by comparing experimental and broken symmetry density functional theory calculated (14)N, (17)O, and (1)H hyperfine couplings. Experimental results have been interpreted to indicate that the substrate water is coordinated to the Mn(III) ion. However, by calculating hyperfine couplings for both scenarios we show that water is coordinated to the Mn(IV) ion and that the assigned oxidation states of the two manganese ions present in the site are the opposite of that previously proposed based on experimental measurements alone.
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Affiliation(s)
- Nathan J Beal
- School of Chemistry, The University of Manchester , Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Patrick J O'Malley
- School of Chemistry, The University of Manchester , Oxford Road, Manchester, M13 9PL, United Kingdom
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6
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Xiao S, Klein ML, LeBard DN, Levine BG, Liang H, MacDermaid CM, Alfonso-Prieto M. Magnesium-Dependent RNA Binding to the PA Endonuclease Domain of the Avian Influenza Polymerase. J Phys Chem B 2014; 118:873-89. [DOI: 10.1021/jp408383g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Michael L. Klein
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - David N. LeBard
- Department of Chemistry, Yeshiva University, New York, New York 10033, United States
| | - Benjamin G. Levine
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Christopher M. MacDermaid
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Mercedes Alfonso-Prieto
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
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7
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Whittaker JW. Non-heme manganese catalase--the 'other' catalase. Arch Biochem Biophys 2011; 525:111-20. [PMID: 22198285 DOI: 10.1016/j.abb.2011.12.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 12/09/2011] [Accepted: 12/10/2011] [Indexed: 12/24/2022]
Abstract
Non-heme manganese catalases are widely distributed over microbial life and represent an environmentally important alternative to heme-containing catalases in antioxidant defense. Manganese catalases contain a binuclear manganese complex as their catalytic active site rather than a heme, and cycle between Mn(2)(II,II) and Mn(2)(III,III) states during turnover. X-ray crystallography has revealed the key structural elements of the binuclear manganese active site complex that can serve as the starting point for computational studies on the protein. Four manganese catalase enzymes have been isolated and characterized, and the enzyme appears to have a broad phylogenetic distribution including both bacteria and archae. More than 100 manganese catalase genes have been annotated in genomic databases, although the assignment of many of these putative manganese catalases needs to be experimentally verified. Iron limitation, exposure to low levels of peroxide stress, thermostability and cyanide resistance may provide the biological and environmental context for the occurrence of manganese catalases.
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Affiliation(s)
- James W Whittaker
- Institute for Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006-8921, USA.
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8
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Li YL, Mei Y, Zhang DW, Xie DQ, Zhang JZH. Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization. J Phys Chem B 2011; 115:10154-62. [PMID: 21766867 DOI: 10.1021/jp203505v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures and dynamics of a recently designed dizinc metalloprotein (DFsc) (J. Mol. Biol. 2003, 334, 1101) are studied by molecular dynamics simulation using a dynamically adapted polarized force field derived from fragment quantum calculation for protein in solvent. To properly describe the effect of charge transfer and polarization in the present approach, quantum chemistry calculation of the zinc-binding group is periodically performed (on-the-fly) to update the atomic charges of the zinc-binding group during the MD simulation. Comparison of the present result with those obtained from simulations under standard AMBER force field reveals that charge transfer and polarization are critical to maintaining the correct asymmetric metal coordination in the DFsc. Detailed analysis of the result also shows that dynamic fluctuation of the zinc-binding group facilitates solvent interaction with the zinc ions. In particular, the dynamic fluctuation of the zinc-zinc distance is shown to be an important feature of the catalytic function of the di-ion zinc-binding group. Our study demonstrates that the dynamically adapted polarization approach is computationally practical and can be used to study other metalloprotein systems.
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Affiliation(s)
- Yong L Li
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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Lu SY, Jiang YJ, Zou JW, Wu TX. Dissection of the difference between the group I metal ions in inhibiting GSK3β: a computational study. Phys Chem Chem Phys 2011; 13:7014-23. [PMID: 21409189 DOI: 10.1039/c0cp02498h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Glycogen synthase kinase 3β (GSK3β) is a serine/threonine kinase that requires two cofactor Mg(2+) ions for catalysis in regulating many important cellular signals. Experimentally, Li(+) is a competitive inhibitor of GSK3β relative to Mg(2+), while this mechanism is not experienced with other group I metal ions. Herein, we use native Mg(2)(2+)-Mg(1)(2+) GSK3β and its Mg(2)(2+)-M(1)(+) (M = Li, Na, K, and Rb) derivatives to investigate the effect of metal ion substitution on the mechanism of inhibition through two-layer ONIOM-based quantum mechanics/molecular mechanics (QM/MM) calculations and molecular dynamics (MD) simulations. The results of ONIOM calculations elucidate that the interaction of Na(+), K(+), and Rb(+) with ATP is weaker compared to that of Mg(2+) and Li(+) with ATP, and the critical triphosphate moiety of ATP undergoes a large conformational change in the Na(+), K(+), and Rb(+) substituted systems. As a result, the three metal ions (Na(+), K(+), and Rb(+)) are not stable and depart from the active site, while Mg(2+) and Li(+) can stabilize in the active site, evident in MD simulations. Comparisons of Mg(2)(2+)-Mg(1)(2+) and Mg(2)(2+)-Li(1)(+) systems reveal that the inline phosphor-transfer of ATP and the two conserved hydrogen bonds between Lys85 and ATP, together with the electrostatic potential at the Li(1)(+) site, are disrupted in the Mg(2)(2+)-Li(1)(+) system. These computational results highlight the possible mechanism why Li(+) inhibits GSK3β.
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Affiliation(s)
- Shao-Yong Lu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
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10
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Morin A, Meiler J, Mizoue LS. Computational design of protein-ligand interfaces: potential in therapeutic development. Trends Biotechnol 2011; 29:159-66. [PMID: 21295366 DOI: 10.1016/j.tibtech.2011.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Revised: 12/22/2010] [Accepted: 01/05/2011] [Indexed: 01/16/2023]
Abstract
Computational design of protein-ligand interfaces finds optimal amino acid sequences within a small-molecule binding site of a protein for tight binding of a specific small molecule. It requires a search algorithm that can rapidly sample the vast sequence and conformational space, and a scoring function that can identify low energy designs. This review focuses on recent advances in computational design methods and their application to protein-small molecule binding sites. Strategies for increasing affinity, altering specificity, creating broad-spectrum binding, and building novel enzymes from scratch are described. Future prospects for applications in drug development are discussed, including limitations that will need to be overcome to achieve computational design of protein therapeutics with novel modes of action.
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Affiliation(s)
- Andrew Morin
- Departments of Chemistry, Pharmacology, and Biomedical Informatics, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
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11
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Iranzo O, Chakraborty S, Hemmingsen L, Pecoraro VL. Controlling and fine tuning the physical properties of two identical metal coordination sites in de novo designed three stranded coiled coil peptides. J Am Chem Soc 2011; 133:239-51. [PMID: 21162521 PMCID: PMC3149768 DOI: 10.1021/ja104433n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein we report how de novo designed peptides can be used to investigate whether the position of a metal site along a linear sequence that folds into a three-stranded α-helical coiled coil defines the physical properties of Cd(II) ions in either CdS(3) or CdS(3)O (O-being an exogenous water molecule) coordination environments. Peptides are presented that bind Cd(II) into two identical coordination sites that are located at different topological positions at the interior of these constructs. The peptide GRANDL16PenL19IL23PenL26I binds two Cd(II) as trigonal planar 3-coordinate CdS(3) structures whereas GRANDL12AL16CL26AL30C sequesters two Cd(II) as pseudotetrahedral 4-coordinate CdS(3)O structures. We demonstrate how for the first peptide, having a more rigid structure, the location of the identical binding sites along the linear sequence does not affect the physical properties of the two bound Cd(II). However, the sites are not completely independent as Cd(II) bound to one of the sites ((113)Cd NMR chemical shift of 681 ppm) is perturbed by the metalation state (apo or [Cd(pep)(Hpep)(2)](+) or [Cd(pep)(3)](-)) of the second center ((113)Cd NMR chemical shift of 686 ppm). GRANDL12AL16CL26AL30C shows a completely different behavior. The physical properties of the two bound Cd(II) ions indeed depend on the position of the metal center, having pK(a2) values for the equilibrium [Cd(pep)(Hpep)(2)](+) → [Cd(pep)(3)](-) + 2H(+) (corresponding to deprotonation and coordination of cysteine thiols) that range from 9.9 to 13.9. In addition, the L26AL30C site shows dynamic behavior, which is not observed for the L12AL16C site. These results indicate that for these systems one cannot simply assign a "4-coordinate structure" and assume certain physical properties for that site since important factors such as packing of the adjacent Leu, size of the intended cavity (endo vs exo) and location of the metal site play crucial roles in determining the final properties of the bound Cd(II).
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Affiliation(s)
- Olga Iranzo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Fax: (+1) 734-936-7628,
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida República, EAN, 2785-572 Oeiras, Portugal
| | - Saumen Chakraborty
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Fax: (+1) 734-936-7628,
| | - Lars Hemmingsen
- Department of Basic Sciences and Environment, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Fax: (+1) 734-936-7628,
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12
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Suárez M, Jaramillo A. Challenges in the computational design of proteins. J R Soc Interface 2009; 6 Suppl 4:S477-91. [PMID: 19324680 PMCID: PMC2843960 DOI: 10.1098/rsif.2008.0508.focus] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Accepted: 02/04/2009] [Indexed: 11/12/2022] Open
Abstract
Protein design has many applications not only in biotechnology but also in basic science. It uses our current knowledge in structural biology to predict, by computer simulations, an amino acid sequence that would produce a protein with targeted properties. As in other examples of synthetic biology, this approach allows the testing of many hypotheses in biology. The recent development of automated computational methods to design proteins has enabled proteins to be designed that are very different from any known ones. Moreover, some of those methods mostly rely on a physical description of atomic interactions, which allows the designed sequences not to be biased towards known proteins. In this paper, we will describe the use of energy functions in computational protein design, the use of atomic models to evaluate the free energy in the unfolded and folded states, the exploration and optimization of amino acid sequences, the problem of negative design and the design of biomolecular function. We will also consider its use together with the experimental techniques such as directed evolution. We will end by discussing the challenges ahead in computational protein design and some of their future applications.
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Affiliation(s)
- María Suárez
- Laboratoire de Biochimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
- Epigenomics Project, Genopole, Université d'Evry Val d'Essonne-Genopole-CNRS, Tour Evry2, Etage 10, Terrasses de l'Agora, 91034 Evry Cedex, France
| | - Alfonso Jaramillo
- Laboratoire de Biochimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
- Epigenomics Project, Genopole, Université d'Evry Val d'Essonne-Genopole-CNRS, Tour Evry2, Etage 10, Terrasses de l'Agora, 91034 Evry Cedex, France
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13
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O’Connell JP, Gani R, Mathias PM, Maurer G, Olson JD, Crafts PA. Thermodynamic Property Modeling for Chemical Process and Product Engineering: Some Perspectives. Ind Eng Chem Res 2009. [DOI: 10.1021/ie801535a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John P. O’Connell
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904-4741, CAPEC, Technical University of Denmark, DK-2800, Lyngby, Denmark, Fluor Corporation, 3 Polaris Way, Aliso Viejo, California 92698, Applied Thermodynamics, University of Kaiserslautern, D-67653, Kaiserslautern, Germany, Dow Chemical Company, South Charleston, West Virginia 25303, AstraZeneca Pharmaceutical Ltd., Macclesfield, Cheshire, SK10 2NA, U. K
| | - Rafiqul Gani
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904-4741, CAPEC, Technical University of Denmark, DK-2800, Lyngby, Denmark, Fluor Corporation, 3 Polaris Way, Aliso Viejo, California 92698, Applied Thermodynamics, University of Kaiserslautern, D-67653, Kaiserslautern, Germany, Dow Chemical Company, South Charleston, West Virginia 25303, AstraZeneca Pharmaceutical Ltd., Macclesfield, Cheshire, SK10 2NA, U. K
| | - Paul M. Mathias
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904-4741, CAPEC, Technical University of Denmark, DK-2800, Lyngby, Denmark, Fluor Corporation, 3 Polaris Way, Aliso Viejo, California 92698, Applied Thermodynamics, University of Kaiserslautern, D-67653, Kaiserslautern, Germany, Dow Chemical Company, South Charleston, West Virginia 25303, AstraZeneca Pharmaceutical Ltd., Macclesfield, Cheshire, SK10 2NA, U. K
| | - Gerd Maurer
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904-4741, CAPEC, Technical University of Denmark, DK-2800, Lyngby, Denmark, Fluor Corporation, 3 Polaris Way, Aliso Viejo, California 92698, Applied Thermodynamics, University of Kaiserslautern, D-67653, Kaiserslautern, Germany, Dow Chemical Company, South Charleston, West Virginia 25303, AstraZeneca Pharmaceutical Ltd., Macclesfield, Cheshire, SK10 2NA, U. K
| | - James D. Olson
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904-4741, CAPEC, Technical University of Denmark, DK-2800, Lyngby, Denmark, Fluor Corporation, 3 Polaris Way, Aliso Viejo, California 92698, Applied Thermodynamics, University of Kaiserslautern, D-67653, Kaiserslautern, Germany, Dow Chemical Company, South Charleston, West Virginia 25303, AstraZeneca Pharmaceutical Ltd., Macclesfield, Cheshire, SK10 2NA, U. K
| | - Peter A. Crafts
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904-4741, CAPEC, Technical University of Denmark, DK-2800, Lyngby, Denmark, Fluor Corporation, 3 Polaris Way, Aliso Viejo, California 92698, Applied Thermodynamics, University of Kaiserslautern, D-67653, Kaiserslautern, Germany, Dow Chemical Company, South Charleston, West Virginia 25303, AstraZeneca Pharmaceutical Ltd., Macclesfield, Cheshire, SK10 2NA, U. K
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14
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Abstract
Excessive hydrogen peroxide is harmful for almost all cell components, so its rapid and efficient removal is of essential importance for aerobically living organisms. Conversely, hydrogen peroxide acts as a second messenger in signal-transduction pathways. H(2)O(2) is degraded by peroxidases and catalases, the latter being able both to reduce H(2)O(2) to water and to oxidize it to molecular oxygen. Nature has evolved three protein families that are able to catalyze this dismutation at reasonable rates. Two of the protein families are heme enzymes: typical catalases and catalase-peroxidases. Typical catalases comprise the most abundant group found in Eubacteria, Archaeabacteria, Protista, Fungi, Plantae, and Animalia, whereas catalase-peroxidases are not found in plants and animals and exhibit both catalatic and peroxidatic activities. The third group is a minor bacterial protein family with a dimanganese active site called manganese catalases. Although catalyzing the same reaction (2 H(2)O(2)--> 2 H(2)O+ O(2)), the three groups differ significantly in their overall and active-site architecture and the mechanism of reaction. Here, we present an overview of the distribution, phylogeny, structure, and function of these enzymes. Additionally, we report about their physiologic role, response to oxidative stress, and about diseases related to catalase deficiency in humans.
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Affiliation(s)
- Marcel Zamocky
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Applied Life Sciences, Vienna, Austria.
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15
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Iranzo O, Cabello C, Pecoraro V. Heterochromia in Designed Metallopeptides: Geometry-Selective Binding of CdII in a De Novo Peptide. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701729] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Lippow SM, Tidor B. Progress in computational protein design. Curr Opin Biotechnol 2007; 18:305-11. [PMID: 17644370 PMCID: PMC3495006 DOI: 10.1016/j.copbio.2007.04.009] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Accepted: 04/17/2007] [Indexed: 11/25/2022]
Abstract
Current progress in computational structure-based protein design is reviewed in the areas of methodology and applications. Foundational advances include new potential functions, more efficient ways of computing energetics, flexible treatments of solvent, and useful energy function approximations, as well as ensemble-based approaches to scoring designs for inclusion of entropic effects, improvements to guaranteed and to stochastic search techniques, and methods to design combinatorial libraries for screening and selection. Applications include new approaches and successes in the design of specificity for protein folding, binding, and catalysis, in the redesign of proteins for enhanced binding affinity, and in the application of design technology to study and alter enzyme catalysis. Computational protein design continues to mature and advance.
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Affiliation(s)
- Shaun M Lippow
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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17
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Narasimhulu KV, Carmieli R, Goldfarb D. Single Crystal 55Mn ENDOR of Concanavalin A: Detection of Two Mn2+ Sites with Different 55Mn Quadrupole Tensors. J Am Chem Soc 2007; 129:5391-402. [PMID: 17408266 DOI: 10.1021/ja0662826] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Concanavalin A is a member of the plant hemeagglutinin (or plant lectin) family that contains two metal binding sites; one, called S1, is occupied by Mn2+ and the other, S2, by Ca2+. 55Mn electron-nuclear double resonance (ENDOR) measurements were performed on a single crystal of concanavalin A at W-band (95 GHz, ~3.5 T) to determine the 55Mn nuclear quadrupole interaction in a protein binding site and its relation to structural parameters. Such measurements are easier at a high field because of the high sensitivity for size-limited samples and the reduction of second-order effects on the spectrum which simplifies spectral analysis. The analysis of the 55Mn ENDOR rotation patterns showed that two chemically inequivalent Mn2+ types are present at low temperatures, although the high-resolution X-ray structure reported only one site. Their quadrupole coupling constants, e2Qq/h, are significantly different; 10.7 +/- 0.6 MHz for Mand only -2.7 +/-0.6 MHz for M. The ENDOR data also refined the hyperfine coupling determined earlier by single-crystal EPR measurements, yielding a small but significant difference between the two: -262.5 MHz for M and -263.5 MHz for M. The principal z-axis for M is not aligned with any of the Mn-ligand directions, but is 25 off the Mn-asp10 direction, and its orientation is different than that of the zero-field splitting (ZFS) interaction. Because of the small quadrupole interaction of M the orientation dependence was very mild, leading to larger uncertainties in the asymmetry parameter. Nonetheless, there too z is not along the Mn-ligand bonds and is rotated 90 with respect to MnA. These results show, that similar to the ZFS, the quadrupolar interaction is highly sensitive to small differences in the coordination sphere of the Mn2+, and the resolution of the two types is in agreement with the earlier observation of a two-site conformational dynamic detected through the ZFS interaction, which is frozen out at low temperatures and averaged at room temperature. To account for the structural origin of the different e2Qq/h values, the electric field gradient tensor was calculated using the point-charge model. The calculations showed that a relatively small displacement of the oxygen ligand of asp10 can lead to differences on the order observed experimentally.
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Iranzo O, Cabello C, Pecoraro VL. Heterochromia in designed metallopeptides: geometry-selective binding of CdII in a de novo peptide. Angew Chem Int Ed Engl 2007; 46:6688-91. [PMID: 17582808 PMCID: PMC5242183 DOI: 10.1002/anie.200701729] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Olga Iranzo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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Dal Peraro M, Spiegel K, Lamoureux G, De Vivo M, DeGrado WF, Klein ML. Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J Struct Biol 2006; 157:444-53. [PMID: 17188512 DOI: 10.1016/j.jsb.2006.10.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 10/19/2006] [Accepted: 10/19/2006] [Indexed: 10/24/2022]
Abstract
Almost half of the proteome of living organisms is constituted of metalloproteins. Unfortunately, the ability of the current generation of molecular dynamics pairwise-additive forcefields to properly describe metal pockets is severely lacking due to the intrinsic difficulty of handling polarization and charge transfer contributions. In order to improve the description of metalloproteins, a simple reparameterization strategy is proposed herein that does not involve artificial constraints. Specifically, a non-bonded quantum mechanical-based model is used to capture the mean polarization and charge transfer contributions to the interatomic forces within the metal site. The present approach is demonstrated to provide enough accuracy to maintain the integrity of the metal pocket for a variety of metalloproteins during extended (multi-nanosecond) molecular dynamics simulations. The method enables the sampling of small conformational changes and the relaxation of local frustrations in NMR structures.
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Affiliation(s)
- M Dal Peraro
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA.
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