ROBERT CUKIER

Summary

Affiliation: Michigan State University
Country: USA

Publications

  1. ncbi A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper
    Robert I Cukier
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 1322, USA
    J Chem Phys 134:045104. 2011
  2. ncbi Apo adenylate kinase encodes its holo form: a principal component and varimax analysis
    Robert I Cukier
    Department of Chemistry and the Quantitative Biology Modeling Initiative, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 113:1662-72. 2009
  3. ncbi Theory and simulation of proton-coupled electron transfer, hydrogen-atom transfer, and proton translocation in proteins
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing, MI 48824 1322, USA
    Biochim Biophys Acta 1655:37-44. 2004
  4. ncbi Quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing, MI 48824 1322, USA
    Biochim Biophys Acta 1656:189-202. 2004
  5. ncbi A targeted reweighting method for accelerating the exploration of high-dimensional configuration space
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
    J Chem Phys 123:234908. 2005
  6. ncbi A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing, MI 48824 1322, USA
    Biochim Biophys Acta 1706:134-46. 2005
  7. ncbi Proton-coupled electron transfer
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing 48824 1322, USA
    Annu Rev Phys Chem 49:337-69. 1998
  8. ncbi Structural character and energetics of tyrosyl radical formation by electron/proton transfers of a covalently linked histidine-tyrosine: a model for cytochrome C oxidase
    Yuxiang Bu
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 1322, USA
    J Phys Chem B 109:22013-26. 2005
  9. ncbi Water chain formation and possible proton pumping routes in Rhodobacter sphaeroides cytochrome c oxidase: a molecular dynamics comparison of the wild type and R481K mutant
    Steve A Seibold
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
    Biochemistry 44:10475-85. 2005
  10. ncbi Factors determining the deriving force of DNA formation: geometrical differences of base pairs, dehydration of bases, and the arginine assisting
    Lixiang Sun
    Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P R China
    J Phys Chem B 111:1802-8. 2007

Research Grants

Collaborators

  • Ping Li
  • William L Smith
  • Claire Vieille
  • Denise A Mills
  • Dianxiang Xing
  • Lishan Yao
  • Yuxiang Bu
  • Steve A Seibold
  • Honggao Yan
  • Shihai Yan
  • Hongfeng Lou
  • Huifang Li
  • Stepan Sklenak
  • Li Su
  • Feng Xiang
  • Lixiang Sun
  • Huichun Liu
  • Liang Zhang
  • Jinmei Zhang
  • Jiayan Liu
  • Harini Krishnamurthy
  • Inseok Song
  • Caroline J Rieke
  • Adam Kimple
  • Shelagh Ferguson-Miller
  • Terry Ball
  • Rajeewa D Abeysinghe
  • Caroline Jill Rieke
  • Renee Micielli
  • Linda C Hsi

Detail Information

Publications31

  1. ncbi A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper
    Robert I Cukier
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 1322, USA
    J Chem Phys 134:045104. 2011
    ..The interface formation time scale is sufficiently short that using HTREM_MS as a screening tool to validate leucine zipper design methods may be feasible...
  2. ncbi Apo adenylate kinase encodes its holo form: a principal component and varimax analysis
    Robert I Cukier
    Department of Chemistry and the Quantitative Biology Modeling Initiative, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 113:1662-72. 2009
    ..In this sense, apo AKE does encode in its fluctuations information about holo-like conformations...
  3. ncbi Theory and simulation of proton-coupled electron transfer, hydrogen-atom transfer, and proton translocation in proteins
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing, MI 48824 1322, USA
    Biochim Biophys Acta 1655:37-44. 2004
    ..Protonation of the glutamate is found to occur in agreement with experimental results...
  4. ncbi Quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing, MI 48824 1322, USA
    Biochim Biophys Acta 1656:189-202. 2004
    ..Rather, there are chains spanning Glu286 to the vicinity of Asn140, and other more robust and ramified water structures that connect Asp132 with waters close to Asn140...
  5. ncbi A targeted reweighting method for accelerating the exploration of high-dimensional configuration space
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
    J Chem Phys 123:234908. 2005
    ..The targeted reweighting is found to be essential to permit the original all-helical conformation to bend and generate turn structures while still maintaining the alpha-helical segments...
  6. ncbi A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing, MI 48824 1322, USA
    Biochim Biophys Acta 1706:134-46. 2005
    ..The water hydrogen-bonded to the hydroxyl of Tyr288 is extremely persistent and well positioned to participate in O2 reduction. The third water is located where O2 is often suggested to reside in mechanistic studies of O2 reduction...
  7. ncbi Proton-coupled electron transfer
    R I Cukier
    Department of Chemistry, Michigan State University, East Lansing 48824 1322, USA
    Annu Rev Phys Chem 49:337-69. 1998
    ....
  8. ncbi Structural character and energetics of tyrosyl radical formation by electron/proton transfers of a covalently linked histidine-tyrosine: a model for cytochrome C oxidase
    Yuxiang Bu
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 1322, USA
    J Phys Chem B 109:22013-26. 2005
    ..The cation effect demonstrates that the cationized cross-linked His-Tyr should be the best candidate to mimic the covalently ring-linked histidine-tyrosine structure in CcO...
  9. ncbi Water chain formation and possible proton pumping routes in Rhodobacter sphaeroides cytochrome c oxidase: a molecular dynamics comparison of the wild type and R481K mutant
    Steve A Seibold
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
    Biochemistry 44:10475-85. 2005
    ..The results suggest a possible gating mechanism for proton movement that includes key residues W172 and Y175 on the loop and F282 on helix VI...
  10. ncbi Factors determining the deriving force of DNA formation: geometrical differences of base pairs, dehydration of bases, and the arginine assisting
    Lixiang Sun
    Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P R China
    J Phys Chem B 111:1802-8. 2007
    ..Arg668 cannot prevent the extension of the GT mispair, as well as the GC correct base pair, and GA and GG mispairs. This may be attributed to the small geometry difference between the GT base pair and the correct AT base pair...
  11. ncbi Exploration on regulating factors for proton transfer along hydrogen-bonded water chains
    Shihai Yan
    Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P R China
    Chemphyschem 8:944-54. 2007
    ..The most favorable condition for the proton transfer along the H-bonded water wire is the four-water contained chain with side water attached near to the acceptor fragment in polar solvent under higher temperature...
  12. ncbi A molecular dynamics study comparing a wild-type with a multiple drug resistant HIV protease: differences in flap and aspartate 25 cavity dimensions
    Steve A Seibold
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 1322, USA
    Proteins 69:551-65. 2007
    ..The migration of water to the active site aspartates is monitored. Water molecules move in and out of the active site and individual waters hydrogen bond to both aspartate carboxylate oxygens, with residence times in the ns time regime...
  13. ncbi Ca2+ selectivity of the sarcoplasmic reticulum Ca2+-ATPase at the enzyme-water interface and in the Ca2+ entrance channel
    Feng Xiang
    Key Laboratory for Colloid and Interface Chemistry of Ministry of Education, The Modeling and Simulation Chemistry Division, Shandong University, Jinan 250100, P R China
    J Phys Chem B 111:12282-93. 2007
    ..Furthermore, the corresponding theoretical investigations have demonstrated that the increase of the ligand electronegativity can enhance their discrimination between these two cations effectively...
  14. ncbi Hamiltonian and distance replica exchange method studies of Met-enkephalin
    Li Su
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 1322, USA
    J Phys Chem B 111:12310-21. 2007
    ..The two-dimensional PMF constructed from the first two PCA modes captures most of the significant backbone conformational space of Met-enkephalin...
  15. ncbi Remarkable metal counterion effect on the internucleotide J-couplings and chemical shifts of the N-H...N hydrogen bonds in the W-C base pairs
    Huifang Li
    The Center for Modeling and Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People s Republic of China
    J Phys Chem B 112:9174-81. 2008
    ..N H-bond units may provide a new approach to the determination of H-bond structure and strength in Watson-Crick base pairs, and provide an alternative probe of the heterogeneity of DNA sequences...
  16. ncbi Histidine 386 and its role in cyclooxygenase and peroxidase catalysis by prostaglandin-endoperoxide H synthases
    Steve A Seibold
    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 0606, USA
    J Biol Chem 278:46163-70. 2003
    ..Being less bulky than AA, linoleic acid is apparently unable to reopen this constriction...
  17. pmc A molecular dynamics study of the ligand release path in yeast cytosine deaminase
    Lishan Yao
    Department of Chemistry, Michigan State University Center for Biological Modeling, East Lansing, Michigan 48824, USA
    Biophys J 92:2301-10. 2007
    ....
  18. ncbi Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations
    Hongfeng Lou
    Department of Chemistry and the Quantitative Biology Modeling Initiative, Michigan State University, East Lansing, Michigan 48824 1322, USA
    J Phys Chem B 110:24121-37. 2006
    ..Therefore, apo AKE can fluctuate from its open form to conformations that are quite similar to its closed form X-ray structure, even in the absence of its substrates...
  19. ncbi Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist
    Huichun Liu
    Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P R China
    Chemphyschem 8:304-14. 2007
    ..The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes...
  20. ncbi Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates
    Harini Krishnamurthy
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48224 1322, USA
    Proteins 58:88-100. 2005
    ....
  21. ncbi A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminase
    Lishan Yao
    Department of Chemistry, MSU Center for Biological Modeling, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 109:7500-10. 2005
    ..The simulations also reveal small motions of the C-terminus and the loop that contains Phe114 that may be important for reactant binding and product release...
  22. ncbi Catalytic mechanism of yeast cytosine deaminase: an ONIOM computational study
    Stepan Sklenak
    Center for Biological Modeling and Departments of Biochemistry and Chemistry, Michigan State University, East Lansing, MI 48824, USA
    J Am Chem Soc 126:14879-89. 2004
    ..The rate determining step in the oxygen exchange is the formation of the gem-diol intermediate, which is also the rate determining step for the overall yCD-catalyzed deamination reaction...
  23. ncbi Electron bridging dihydrogen bond in the imidazole-contained anion derivatives
    Shihai Yan
    Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People s Republic of China
    J Chem Phys 124:124314. 2006
    ..The H...H interaction can be formed by X-Hdelta+ and Hdelta- -Y polar molecules in Hdelta+...Hdelta- and Hdelta+...e...Hdelta+ of two forms...
  24. ncbi Mechanism of dihydroneopterin aldolase: a molecular dynamics study of the apo enzyme and its product complex
    Lishan Yao
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 110:1443-56. 2006
    ..An analysis of the various components that contribute to the exit path energy and entropy provides insight into the energy-entropy compensation for product release...
  25. ncbi Proton character of the peptide unit in the Ca2+-binding sites of calcium pump
    Huifang Li
    School of Chemistry, Qufu Normal University, Qufu, 273165, PRC
    J Phys Chem B 110:11005-13. 2006
    ..Ionization states of the acidic residues forming the Ca2+-binding sites may influence the activity of the amide H of the MPU and further affect the transport tendency of the peptide unit proton in the direction opposite to Ca2+...
  26. ncbi Molecular dynamics of apo-adenylate kinase: a principal component analysis
    Hongfeng Lou
    Department of Chemistry and the Quantitative Biology Modeling Initiative, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 110:12796-808. 2006
    ..A pair of residues is suggested for labeling that would be useful for monitoring distance fluctuations by energy transfer experiments...
  27. ncbi Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks
    Jinmei Zhang
    Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P R China
    J Phys Chem B 111:8335-41. 2007
    ..Thus, the expanded G bases may be considered as DNA genetic motifs, and they may serve as building blocks for potential biological applications and the development of molecular electronic devices...
  28. ncbi Prostaglandin endoperoxide H synthases: peroxidase hydroperoxide specificity and cyclooxygenase activation
    Jiayan Liu
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
    J Biol Chem 282:18233-44. 2007
    ..However, no cross-talk between the POX and COX sites of monomers was detected in a PGHS-2 heterodimer comprised of a Q203R monomer having an inactive POX site and a G533A monomer with an inactive COX site...
  29. ncbi Theoretical prediction of the p53 gene mutagenic mechanism induced by trans-4-hydroxy-2-nonenal
    Dianxiang Xing
    Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People s Republic of China
    J Phys Chem B 111:5362-71. 2007
    ..Our mutational results have interpreted well a part of the discrete experimental observations, but the mutagenic process itself has not previously been characterized, through either computation or experiment...
  30. ncbi Catalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics study
    Lishan Yao
    Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 111:4200-10. 2007
    ..The Zn-O2 bond can be broken without the assistance of water during the release of xanthine...
  31. ncbi A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase
    Lishan Yao
    Department of Chemistry, and MSU Center for Biological Modeling, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 110:26320-6. 2006
    ..In the work presented here, the combined ONIOM MD method is used to show that the barrier for bond cleavage is small, approximately 3 kcal/mol, and, consequently, should not be the rate-limiting step in the reaction...

Research Grants1

  1. Proton-coupled electron translocation in metalloenzymes
    ROBERT CUKIER; Fiscal Year: 2006
    ..Contemporaneously, we will explore PTR by simulation methodologies that we are developing, which combine quantum mechanics and molecular dynamics to quantitatively describe proton translocation. ..