P. Shing Ho, Ph.D. - Publications

Biochemistry and Biophysics Colorado State University, Fort Collins, CO 
DNA structure and function, Halogen bonding

80 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Vander Zanden CM, Czarny RS, Ho EN, Robertson AB, Ho PS. Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function. Nucleic Acids Research. PMID 32095813 DOI: 10.1093/nar/gkaa117  1
2019 Riel AMS, Rowe RK, Ho EN, Carlsson AC, Rappé AK, Berryman OB, Ho PS. Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry. Accounts of Chemical Research. PMID 31318520 DOI: 10.1021/acs.accounts.9b00189  0.56
2018 Carlsson AC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. Increasing enzyme stability and activity through hydrogen bond enhanced halogen bonds. Biochemistry. PMID 29921126 DOI: 10.1021/acs.biochem.8b00603  1
2017 Ford MC, Saxton M, Ho PS. Sulfur as An Acceptor to Bromine in Biomolecular Halogen Bonds. The Journal of Physical Chemistry Letters. PMID 28796521 DOI: 10.1021/acs.jpclett.7b01725  0.52
2016 Vander Zanden CM, Rowe RK, Broad AJ, Robertson AB, Ho PS. The effect of hydroxymethylcytosine on the structure and stability of Holliday junctions. Biochemistry. PMID 27653243 DOI: 10.1021/acs.biochem.6b00801  1
2015 Ford MC, Ho PS. Computational Tools To Model Halogen Bonds in Medicinal Chemistry. Journal of Medicinal Chemistry. PMID 26465079 DOI: 10.1021/acs.jmedchem.5b00997  1
2014 Scholfield MR, Ford MC, Vander Zanden CM, Billman MM, Ho PS, Rappé AK. Force Field Model of Periodic Trends in Biomolecular Halogen Bonds. The Journal of Physical Chemistry. B. PMID 25338128 DOI: 10.1021/jp509003r  1
2013 Vander Zanden CM, Carter M, Ho PS. Determining thermodynamic properties of molecular interactions from single crystal studies. Methods (San Diego, Calif.). 64: 12-8. PMID 23933330 DOI: 10.1016/j.ymeth.2013.07.039  1
2013 Carter M, Voth AR, Scholfield MR, Rummel B, Sowers LC, Ho PS. Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions. Biochemistry. 52: 4891-903. PMID 23789744 DOI: 10.1021/bi400590h  1
2013 Scholfield MR, Zanden CM, Carter M, Ho PS. Halogen bonding (X-bonding): a biological perspective. Protein Science : a Publication of the Protein Society. 22: 139-52. PMID 23225628 DOI: 10.1002/pro.2201  1
2012 Carter M, Rappé AK, Ho PS. Scalable Anisotropic Shape and Electrostatic Models for Biological Bromine Halogen Bonds. Journal of Chemical Theory and Computation. 8: 2461-73. PMID 26588975 DOI: 10.1021/ct3001969  1
2011 Carter M, Ho PS. Assaying the energies of biological halogen bonds Crystal Growth and Design. 11: 5087-5095. DOI: 10.1021/cg200991v  1
2010 Hays FA, Teegarden A, Jones ZJR, Harms M, Raup D, Watson J, Cavaliere E, Ho PS. How sequence defines structure: A crystallographic map of DNA structure and conformation (Proceedings of the National Academy of Sciences of the United States of America (2005) 102 (7157-7162) DOI: 10.1073/pnas.0409455102) Proceedings of the National Academy of Sciences of the United States of America. 107: 4486. DOI: 10.1073/pnas.1000618107  1
2009 Voth AR, Khuu P, Oishi K, Ho PS. Halogen bonds as orthogonal molecular interactions to hydrogen bonds. Nature Chemistry. 1: 74-9. PMID 21378804 DOI: 10.1038/nchem.112  1
2009 Khuu P, Ho PS. A rare nucleotide base tautomer in the structure of an asymmetric DNA junction. Biochemistry. 48: 7824-32. PMID 19580331 DOI: 10.1021/bi900829b  1
2009 Ho PS. Thermogenomics: thermodynamic-based approaches to genomic analyses of DNA structure. Methods (San Diego, Calif.). 47: 159-67. PMID 18848994 DOI: 10.1016/j.ymeth.2008.09.007  1
2007 Full SJ, Deinzer ML, Ho PS, Greenwood JA. Phosphoinositide binding regulates alpha-actinin CH2 domain structure: analysis by hydrogen/deuterium exchange mass spectrometry. Protein Science : a Publication of the Protein Society. 16: 2597-604. PMID 17965186 DOI: 10.1110/ps.073146807  1
2007 Khuu P, Sandor M, DeYoung J, Ho PS. Phylogenomic analysis of the emergence of GC-rich transcription elements. Proceedings of the National Academy of Sciences of the United States of America. 104: 16528-33. PMID 17925442 DOI: 10.1073/pnas.0707203104  1
2007 Voth AR, Ho PS. The role of halogen bonding in inhibitor recognition and binding by protein kinases. Current Topics in Medicinal Chemistry. 7: 1336-48. PMID 17692024 DOI: 10.2174/156802607781696846  1
2007 Daniels M, Hart LP, Ho PS, Ballini JP, Vigny P, Brochon JC. Intrinsic fluorescence of B and Z forms of poly d(G-m5C).poly d(G-m5C), a synthetic double-stranded DNA: spectra and lifetimes by the maximum entropy method. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 6: 883-93. PMID 17668119 DOI: 10.1039/b615670c  1
2007 Voth AR, Hays FA, Ho PS. Directing macromolecular conformation through halogen bonds. Proceedings of the National Academy of Sciences of the United States of America. 104: 6188-93. PMID 17379665 DOI: 10.1073/pnas.0610531104  1
2006 Khuu PA, Voth AR, Hays FA, Ho PS. The stacked-X DNA Holliday junction and protein recognition. Journal of Molecular Recognition : Jmr. 19: 234-42. PMID 16575941 DOI: 10.1002/jmr.765  1
2006 Hays FA, Schirf V, Ho PS, Demeler B. Solution formation of Holliday junctions in inverted-repeat DNA sequences. Biochemistry. 45: 2467-71. PMID 16489738 DOI: 10.1021/bi052129x  1
2005 Hays FA, Teegarden A, Jones ZJ, Harms M, Raup D, Watson J, Cavaliere E, Ho PS. How sequence defines structure: a crystallographic map of DNA structure and conformation. Proceedings of the National Academy of Sciences of the United States of America. 102: 7157-62. PMID 15870206 DOI: 10.1073/pnas.0409455102  1
2005 Mok MC, Martin RC, Dobrev PI, Vanková R, Ho PS, Yonekura-Sakakibara K, Sakakibara H, Mok DW. Topolins and hydroxylated thidiazuron derivatives are substrates of cytokinin O-glucosyltransferase with position specificity related to receptor recognition. Plant Physiology. 137: 1057-66. PMID 15728338 DOI: 10.1104/pp.104.057174  1
2004 Champ PC, Maurice S, Vargason JM, Camp T, Ho PS. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research. 32: 6501-10. PMID 15598822 DOI: 10.1093/nar/gkh988  1
2004 Auffinger P, Hays FA, Westhof E, Ho PS. Halogen bonds in biological molecules. Proceedings of the National Academy of Sciences of the United States of America. 101: 16789-94. PMID 15557000 DOI: 10.1073/pnas.0407607101  1
2004 Hays FA, Jones ZJ, Ho PS. Influence of minor groove substituents on the structure of DNA Holliday junctions. Biochemistry. 43: 9813-22. PMID 15274635 DOI: 10.1021/bi049461d  1
2004 Watson J, Hays FA, Ho PS. Definitions and analysis of DNA Holliday junction geometry. Nucleic Acids Research. 32: 3017-27. PMID 15173384 DOI: 10.1093/nar/gkh631  1
2004 Yan X, Watson J, Ho PS, Deinzer ML. Mass spectrometric approaches using electrospray ionization charge states and hydrogen-deuterium exchange for determining protein structures and their conformational changes. Molecular & Cellular Proteomics : McP. 3: 10-23. PMID 14623985 DOI: 10.1074/mcp.R300010-MCP200  1
2003 Hays FA, Watson J, Ho PS. Caution! DNA crossing: crystal structures of Holliday junctions. The Journal of Biological Chemistry. 278: 49663-6. PMID 14563836 DOI: 10.1074/jbc.R300033200  1
2003 Hays FA, Vargason JM, Ho PS. Effect of sequence on the conformation of DNA holliday junctions. Biochemistry. 42: 9586-97. PMID 12911300 DOI: 10.1021/bi0346603  1
2002 Eichman BF, Ortiz-Lombardía M, Aymamí J, Coll M, Ho PS. The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions. Journal of Molecular Biology. 320: 1037-51. PMID 12126623 DOI: 10.1016/S0022-2836(02)00540-5  1
2002 Vargason JM, Ho PS. The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution. The Journal of Biological Chemistry. 277: 21041-9. PMID 11919197 DOI: 10.1074/jbc.M201357200  1
2001 Kim MY, Maier CS, Reed DJ, Ho PS, Deinzer ML. Intramolecular interactions in chemically modified Escherichia coli thioredoxin monitored by hydrogen/deuterium exchange and electrospray ionization mass spectrometry. Biochemistry. 40: 14413-21. PMID 11724553 DOI: 10.1021/bi0115941  1
2001 Ho PS, Eichman BF. The crystal structures of DNA Holliday junctions. Current Opinion in Structural Biology. 11: 302-8. PMID 11406378 DOI: 10.1016/S0959-440X(00)00219-0  1
2001 Vargason JM, Henderson K, Ho PS. A crystallographic map of the transition from B-DNA to A-DNA. Proceedings of the National Academy of Sciences of the United States of America. 98: 7265-70. PMID 11390969 DOI: 10.1073/pnas.121176898  1
2001 Eichman BF, Mooers BH, Alberti M, Hearst JE, Ho PS. The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions. Journal of Molecular Biology. 308: 15-26. PMID 11302703 DOI: 10.1006/jmbi.2001.4567  1
2001 Bash RC, Vargason JM, Cornejo S, Ho PS, Lohr D. Intrinsically bent DNA in the promoter regions of the yeast GAAL1-10 and GAL80 genes. The Journal of Biological Chemistry. 276: 861-6. PMID 11013248 DOI: 10.1074/jbc.M007070200  1
2001 Vargason JM, Ho PS. Response to NG and Dickerson Nature Structural Biology. 8: 107-108.  1
2000 Vargason JM, Eichman BF, Ho PS. The extended and eccentric E-DNA structure induced by cytosine methylation or bromination. Nature Structural Biology. 7: 758-61. PMID 10966645 DOI: 10.1038/78985  1
2000 Eichman BF, Vargason JM, Mooers BH, Ho PS. The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Proceedings of the National Academy of Sciences of the United States of America. 97: 3971-6. PMID 10760268 DOI: 10.1073/pnas.97.8.3971  1
1999 Eichman BF, Schroth GP, Basham BE, Ho PS. The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA. Nucleic Acids Research. 27: 543-50. PMID 9862978 DOI: 10.1093/nar/27.2.543  1
1998 Harwood SH, Li L, Ho PS, Preston AK, Rohrmann GF. AcMNPV late expression factor-5 interacts with itself and contains a zinc ribbon domain that is required for maximal late transcription activity and is homologous to elongation factor TFIIS. Virology. 250: 118-34. PMID 9770426 DOI: 10.1006/viro.1998.9334  1
1997 Ho PS, Mooers BH. Z-DNA crystallography . Biopolymers. 14: 65-90. PMID 19174848 DOI: 10.1002/(SICI)1097-0282(1997)44:1<65::AID-BIP5>3.0.CO;2-Y  1
1997 Mooers BH, Eichman BF, Ho PS. The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals. Journal of Molecular Biology. 269: 796-810. PMID 9223642 DOI: 10.1006/jmbi.1997.1100  0.88
1996 Howell ML, Schroth GP, Ho PS. Sequence-dependent effects of spermine on the thermodynamics of the B-DNA to Z-DNA transition. Biochemistry. 35: 15373-82. PMID 8952489 DOI: 10.1021/bi961881i  1
1996 Rasmussen C, Leisy DJ, Ho PS, Rohrmann GF. Structure-function analysis of the Autographa californica multinucleocapsid nuclear polyhedrosis virus homologous region palindromes. Virology. 224: 235-45. PMID 8862418 DOI: 10.1006/viro.1996.0525  1
1995 Robert CH, Ho PS. Significance of bound water to local chain conformations in protein crystals. Proceedings of the National Academy of Sciences of the United States of America. 92: 7600-4. PMID 11607570 DOI: 10.1073/pnas.92.16.7600  1
1995 Basham B, Schroth GP, Ho PS. An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA. Proceedings of the National Academy of Sciences of the United States of America. 92: 6464-8. PMID 7604014 DOI: 10.1073/pnas.92.14.6464  0.96
1995 Mooers BH, Schroth GP, Baxter WW, Ho PS. Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA. Journal of Molecular Biology. 249: 772-84. PMID 7602589 DOI: 10.1006/jmbi.1995.0336  0.96
1995 Schroth GP, Ho PS. Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA. Nucleic Acids Research. 23: 1977-83. PMID 7596826 DOI: 10.1093/nar/23.11.1977  1
1994 Ho PS. The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proceedings of the National Academy of Sciences of the United States of America. 91: 9549-53. PMID 7937803  1
1993 Kagawa TF, Howell ML, Tseng K, Ho PS. Effects of base substituents on the hydration of B- and Z-DNA: correlations to the B- to Z-DNA transition. Nucleic Acids Research. 21: 5978-86. PMID 8290360  1
1993 Schroth GP, Kagawa TF, Ho PS. Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG). Biochemistry. 32: 13381-92. PMID 8257675 DOI: 10.1021/bi00212a002  0.64
1992 Schroth GP, Chou PJ, Ho PS. Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. The Journal of Biological Chemistry. 267: 11846-55. PMID 1601856  1
1992 Schroth GP, Siino JS, Cooney CA, Th'ng JP, Ho PS, Bradbury EM. Intrinsically bent DNA flanks both sides of an RNA polymerase I transcription start site. Both regions display novel electrophoretic mobility. The Journal of Biological Chemistry. 267: 9958-64. PMID 1577826  1
1992 Loret EP, Georgel P, Johnson WC, Ho PS. Circular dichroism and molecular modeling yield a structure for the complex of human immunodeficiency virus type 1 trans-activation response RNA and the binding region of Tat, the trans-acting transcriptional activator. Proceedings of the National Academy of Sciences of the United States of America. 89: 9734-8. PMID 1409690 DOI: 10.1073/pnas.89.20.9734  1
1991 Ho PS, Kagawa TF, Tseng KH, Schroth GP, Zhou GW. Prediction of a crystallization pathway for Z-DNA hexanucleotides. Science (New York, N.Y.). 254: 1003-6. PMID 1948069  1
1991 Geierstanger BH, Kagawa TF, Chen SL, Quigley GJ, Ho PS. Base-specific binding of copper(II) to Z-DNA. The 1.3-A single crystal structure of d(m5CGUAm5CG) in the presence of CuCl2. The Journal of Biological Chemistry. 266: 20185-91. PMID 1939079  0.96
1991 Kagawa TF, Geierstanger BH, Wang AH, Ho PS. Covalent modification of guanine bases in double-stranded DNA. The 1.2-A Z-DNA structure of d(CGCGCG) in the presence of CuCl2. The Journal of Biological Chemistry. 266: 20175-84. PMID 1939078  0.96
1990 Ho PS, Zhou G, Clark LB. Polarized electronic spectra of Z-DNA single crystals Biopolymers. 30: 151-163. PMID 2224047 DOI: 10.1002/bip.360300115  1
1990 Zhou G, Ho PS. Stabilization of Z-DNA by demethylation of thymine bases: 1.3-Å single-crystal structure of d(m5CGUAm5CG) Biochemistry. 29: 7229-7236. PMID 2207101  1
1990 Green SA, Simpson DJ, Zhou G, Ho PS, Blough NV. Intramolecular quenching of excited singlet states by stable nitroxyl radicals Journal of the American Chemical Society. 112: 7337-7346.  1
1989 Kagawa TF, Stoddard D, Zhou GW, Ho PS. Quantitative analysis of DNA secondary structure from solvent-accessible surfaces: the B- to Z-DNA transition as a model. Biochemistry. 28: 6642-51. PMID 2790019  1
1989 Zhou G, Ho PS, van Holde KE. An analytic solution to the Monod-Wyman-Changeux model and all parameters in this model. Biophysical Journal. 55: 275-280. PMID 2713440  1
1988 Ho PS, Quigley GJ, Tilton RF, Rich A. Hydration of methylated and nonmethylated B-DNA and Z-DNA Journal of Physical Chemistry. 92: 939-945.  1
1987 Ellison MJ, Fenton MJ, Ho PS, Rich A. Long-range interactions of multiple DNA structural transitions within a common topological domain. The Embo Journal. 6: 1513-22. PMID 3608986  1
1987 Ho PS, Frederick CA, Saal D, Wang AH, Rich A. The interactions of ruthenium hexaammine with Z-DNA: crystal structure of a Ru(NH3)6+3 salt of d(CGCGCG) at 1.2 A resolution. Journal of Biomolecular Structure & Dynamics. 4: 521-34. PMID 3271453 DOI: 10.1080/07391102.1987.10507657  1
1986 Ho PS, Ellison MJ, Quigley GJ, Rich A. A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. The Embo Journal. 5: 2737-44. PMID 3780676  1
1986 Kelleher RJ, Ellison MJ, Ho PS, Rich A. Competitive behavior of multiple, discrete B-Z transitions in supercoiled DNA. Proceedings of the National Academy of Sciences of the United States of America. 83: 6342-6. PMID 3462699  1
1986 Liang N, Kang CH, Ho PS, Margoliash E, Hoffman BM. Long-range electron transfer from iron(II)-cytochrome c to (zinc-cytochrome c peroxidase)(+) within the 1:1 complex Journal of the American Chemical Society. 108: 4665-4666.  1
1985 Ho PS, Frederick CA, Quigley GJ, van der Marel GA, van Boom JH, Wang AH, Rich A. G.T wobble base-pairing in Z-DNA at 1.0 A atomic resolution: the crystal structure of d(CGCGTG). The Embo Journal. 4: 3617-23. PMID 4092690  1
1985 Peterson-Kennedy SE, McGourty JL, Ho PS, Sutoris CJ, Liang N, Zemel H, Blough NV, Margoliash E, Hoffman BM. Long-Range Electron Transfer at Fixed and Known Distance within Protein Complexes Coordination Chemistry Reviews. 64: 125-133. DOI: 10.1016/0010-8545(85)80046-1  1
1985 Ho PS, Sutoris C, Liang N, Margoliash E, Hoffman BM. Species specificity of long-range electron transfer within the complex between zinc-substituted cytochrome c peroxidase and cytochrome c Journal of the American Chemical Society. 107: 1070-1071.  1
1985 McGourty JL, Peterson-Kennedy SE, Ho PS. Long-range electron transfer in zinc-substituted hemoproteins: Tunnelling; species specificity Federation Proceedings. 44: No. 8014.  1
1984 Ho PS, Hoffman BM, Solomon N, Kang CH, Margoliash E. Kinetics and energetics of intramolecular electron transfer in yeast cytochrome c peroxidase. Biochemistry. 23: 4122-8. PMID 6091738  1
1983 Martinsen J, Irwin MJ, Ho PS, Hoffman BM, Klotz IM. Oxidation state of binuclear iron site in azidosemimethemerythrin. Biochemical and Biophysical Research Communications. 112: 954-6. PMID 6303342 DOI: 10.1016/0006-291X(83)91710-2  1
1983 Ho PS, Hoffman BM, Kang CH, Margoliash E. Control of the transfer of oxidizing equivalents between heme iron and free radical site in yeast cytochrome c peroxidase. The Journal of Biological Chemistry. 258: 4356-63. PMID 6300084  1
1980 Yoder CH, Ryan CM, Martin GF, Ho PS. Reactions of the ambidentate substrate chloromethyldimethylchlorosilane with amines and amides Journal of Organometallic Chemistry. 190: 1-7. DOI: 10.1016/S0022-328X(00)82874-0  1
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