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Former Graduate Students and Publications

Katherine Rank

2008-2013
Current position: Senior Scientist, Pharmaceutical Product Development, LLC (PPD)
Publications:

1: Cope J, Rank KC, Gilbert SP, Rayment I, Hoenger A. Kar3Vik1 uses a minus-end directed powerstroke for movement along microtubules. PLoS One. 2013;8(1):e53792.

2: Crosby HA, Rank KC, Rayment I, Escalante-Semerena JC. Structural insights into the substrate specificity of the Rhodopseudomonas palustris protein acetyltransferase RpPat: identification of a loop critical for recognition by RpPat. J Biol Chem. 2012 Nov 30;287(49):41392-404. 

3: Rank KC, Rayment I. Functional asymmetry in kinesin and dynein dimers. Biol Cell. 2013 Jan;105(1):1-13.

4: Crosby HA, Rank KC, Rayment I, Escalante-Semerena JC. Structure-guided expansion of the substrate range of methylmalonyl coenzyme A synthetase (MatB) of Rhodopseudomonas palustris. Appl Environ Microbiol. 2012 Sep;78(18):6619-29. 

5: Rank KC, Chen CJ, Cope J, Porche K, Hoenger A, Gilbert SP, Rayment I. Kar3Vik1, a member of the kinesin-14 superfamily, shows a novel kinesin microtubule binding pattern. J Cell Biol. 2012 Jun 25;197(7):957-70.

At least two papers more to be published in the near future.


Sean Newmister

2007-2012
Current Position: Postdoctoral Fellow, University of Michigan
Publications:

1: Moore TC, Newmister SA, Rayment I, Escalante-Semerena JC. Structural insights into the mechanism of four-coordinate Cob(II)alamin formation in the active site of the Salmonella enterica ATP:Co(I)rrinoid adenosyltransferase enzyme: critical role of residues Phe91 and Trp93. Biochemistry. 2012 Dec 4;51(48):9647-57.

2: Newmister SA, Chan CH, Escalante-Semerena JC, Rayment I. Structural insights into the function of the nicotinate mononucleotide:phenol/p-cresolphosphoribosyltransferase (ArsAB) enzyme from Sporomusa ovata. Biochemistry. 2012 Oct 30;51(43):8571-82.

3: Newmister SA, Otte MM, Escalante-Semerena JC, Rayment I. Structure and mutational analysis of the archaeal GTP:AdoCbi-P guanylyltransferase (CobY) from Methanocaldococcus jannaschii: insights into GTP binding and dimerization. Biochemistry. 2011 Jun 14;50(23):5301-13.

4: Khatibi PA, Newmister SA, Rayment I, McCormick SP, Alexander NJ, Schmale DG 3rd. Bioprospecting for trichothecene 3-O-acetyltransferases in the fungal genus Fusarium yields functional enzymes with different abilities to modify the mycotoxin deoxynivalenol. Appl Environ Microbiol. 2011 Feb;77(4):1162-70

At least one more paper to be published in the near future.


Jeremiah Frye

2003-2010
Current Position: Postdoctoral Fellow, St Jude Children’s Research Hospital, Memphis TN
Publications:

1: Klenchin VA, Frye JJ, Jones MH, Winey M, Rayment I. Structure-function analysis of the C-terminal domain of CNM67, a core component of the Saccharomyces cerevisiae spindle pole body. J Biol Chem. 2011 May 20;286(20):18240-50. 

2: Frye J, Klenchin VA, Rayment I. Structure of the tropomyosin overlap complex from chicken smooth muscle: insight into the diversity of N-terminal recognition. Biochemistry. 2010 Jun 15;49(23):4908-20. 

3: Frye JJ, Klenchin VA, Bagshaw CR, Rayment I. Insights into the importance of hydrogen bonding in the gamma-phosphate binding pocket of myosin: structural and  functional studies of serine 236. Biochemistry. 2010 Jun 15;49(23):4897-907.


Graeme Garvey

2003-2008
Current Position: Biochemistry Discovery Scientist, Monsanto Vegetables
Publications:

1: Garvey GS, McCormick SP, Alexander NJ, Rayment I. Structural and functional characterization of TRI3 trichothecene 15-O-acetyltransferase from Fusarium sporotrichioides. Protein Sci. 2009 Apr;18(4):747-61.

2: Garvey GS, McCormick SP, Rayment I. Structural and functional characterization of the TRI101 trichothecene 3-O-acetyltransferase from Fusarium sporotrichioides and Fusarium graminearum: kinetic insights to combating Fusarium head blight. J Biol Chem. 2008 Jan 18;283(3):1660-9. 

3: Garvey GS, Rocco CJ, Escalante-Semerena JC, Rayment I. The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function. Protein Sci. 2007 Jul;16(7):1274-84.


Eric Wise

2000-2004
Current Position: Pediatrician, Michigan
Publications: 2000-2004

1: Wise EL, Yew WS, Akana J, Gerlt JA, Rayment I. Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2005 Feb 15;44(6):1816-23. 

2: Yew WS, Akana J, Wise EL, Rayment I, Gerlt JA. Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2005 Feb 15;44(6):1807-15. 

3: Wise EL, Akana J, Gerlt JA, Rayment I. Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution. Acta Crystallogr D Biol Crystallogr. 2004 Sep;60(Pt 9):1687-90. 

4: Wise EL, Yew WS, Gerlt JA, Rayment I. Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2004 Jun 1;43(21):6438-46.

5: Yew WS, Wise EL, Rayment I, Gerlt JA. Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: mechanistic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2004 Jun 1;43(21):6427-37. 

6: Wise EL, Rayment I. Understanding the importance of protein structure to nature's routes for divergent evolution in TIM barrel enzymes. Acc Chem Res. 2004 Mar;37(3):149-58. 

7: Wise EL, Yew WS, Gerlt JA, Rayment I. Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily. Biochemistry. 2003 Oct 28;42(42):12133-42. 

8: Wise EL, Graham DE, White RH, Rayment I. The structural determination of phosphosulfolactate synthase from Methanococcus jannaschii at 1.7-A resolution: an enolase that is not an enolase. J Biol Chem. 2003 Nov 14;278(46):45858-63. Epub 2003 Sep 2. 

9: Wise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I. Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2002 Mar 26;41(12):3861-9.


Cheom-Gil Cheong

1997-2002
Current Position: Research Associate, Duke University
Publications:

1: Cheong CG, Escalante-Semerena JC, Rayment I. Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes. Biochemistry. 2002 Jul 23;41(29):9079-89.

2: Cheong CG, Escalante-Semerena JC, Rayment I. Capture of a labile substrate by expulsion of water molecules from the active site of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella enterica. J Biol Chem. 2002 Oct 25;277(43):41120-7. 

3: Cheong CG, Bauer CB, Brushaber KR, Escalante-Semerena JC, Rayment I. Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica. Biochemistry. 2002 Apr 16;41(15):4798-808.

4: Cheong CG, Escalante-Semerena JC, Rayment I. Structural investigation of the biosynthesis of alternative lower ligands for cobamides by nicotinate mononucleotide: 5,6-dimethylbenzimidazole phosphoribosyltransferase from Salmonella enterica. J Biol Chem. 2001 Oct 5;276(40):37612-20. 

5: Cheong CG, Escalante-Semerena JC, Rayment I. The three-dimensional structures of nicotinate mononucleotide:5,6- dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella typhimurium complexed with 5,6-dimethybenzimidazole and its reaction products determined to 1.9 A resolution. Biochemistry. 1999 Dec 7;38(49):16125-35.


Douglas Davies

1994-2000
Current Position: Senior Director of Structural Studies, deCode biostructures
Publications:

1: Davies DR, Goryshin IY, Reznikoff WS, Rayment I. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science. 2000 Jul 7;289(5476):77-85.

2: Reznikoff WS, Bhasin A, Davies DR, Goryshin IY, Mahnke LA, Naumann T, Rayment I, Steiniger-White M, Twining SS. Tn5: A molecular window on transposition. Biochem Biophys Res Commun. 1999 Dec 29;266(3):729-34.

3: Davies DR, Mahnke Braam L, Reznikoff WS, Rayment I. The three-dimensionalstructure of a Tn5 transposase-related protein determined to 2.9-A resolution. J Biol Chem. 1999 Apr 23;274(17):11904-13.


Thomas B. Thompson

1995-2000
Current Position: Professor, University of Cincinnati
Publications:

1: Thompson TB, Katayama K, Watanabe K, Hutchinson CR, Rayment I. Structural and functional analysis of tetracenomycin F2 cyclase from Streptomyces glaucescens. A type II polyketide cyclase. J Biol Chem. 2004 Sep 3;279(36):37956-63. 

2: Bauer CB, Fonseca MV, Holden HM, Thoden JB, Thompson TB, Escalante-Semerena JC, Rayment I. Three-dimensional structure of ATP:corrinoid adenosyltransferase from Salmonella typhimurium in its free state, complexed with MgATP, or complexed with hydroxycobalamin and MgATP. Biochemistry. 2001 Jan 16;40(2):361-74. 

3: Thompson TB, Garrett JB, Taylor EA, Meganathan R, Gerlt JA, Rayment I. Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate. Biochemistry. 2000 Sep 5;39(35):10662-76. 

4: Thomas MG, Thompson TB, Rayment I, Escalante-Semerena JC. Analysis of the adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase (CobU) enzyme of Salmonella typhimurium LT2. Identification of residue His-46 as the site of guanylylation. J Biol Chem. 2000 Sep 8;275(36):27576-86. 

5: Thompson TB, Thomas MG, Escalante-Semerena JC, Rayment I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site. Biochemistry. 1999 Oct 5;38(40):12995-3005. 

6: Thompson TB, Thomas MG, Escalante-Semerena JC, Rayment I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 A resolution,. Biochemistry. 1998 May 26;37(21):7686-95. 

7: Fisher AJ, Thompson TB, Thoden JB, Baldwin TO, Rayment I. The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions. J Biol Chem. 1996 Sep 6;271(36):21956-68. 

8: Baldwin, T. O., Ziegler, M. M., Clark, A. C., Sinclair, J. F., Raushel, F. M., Rayment, I., Holden, H. M., Fisher, A. J., Thompson, T. B., and Thoden, J. B. Structure and folding of bacterial luciferase. in Flavins and Flavoproteins 1996, Editors Stevenson, K.J., Massey, V., and Williams, C. H., University of Calgary press.


Joe Wedekind

1991-1995
Current Position: Professor, University of Rochester Medical Center
Publications:

1: Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA. The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry. 1996 Dec 24;35(51):16489-501. 

2: Reed GH, Poyner RR, Larsen TM, Wedekind JE, Rayment I. Structural and mechanistic studies of enolase. Curr Opin Struct Biol. 1996 Dec;6(6):736-43. Review. 

3: Wedekind JE, Frey PA, Rayment I. The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer. Biochemistry. 1996 Sep 10;35(36):11560-9. 

4: Larsen TM, Wedekind JE, Rayment I, Reed GH. A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution. Biochemistry. 1996 Apr 9;35(14):4349-58.

5: Wedekind JE, Frey PA, Rayment I. Three-dimensional structure of galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.8 Å resolution. Biochemistry. 1995 Sep 5;34(35):11049-61. 

6: Ruzicka FJ, Wedekind JE, Kim J, Rayment I, Frey PA. Galactose-1-phosphate uridylyltransferase from Escherichia coli, a zinc and iron metalloenzyme. Biochemistry. 1995 Apr 25;34(16):5610-7.

7: Wedekind JE, Reed GH, Rayment I. Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the MgII--enzyme complex from yeast at 1.9 Å resolution. Biochemistry. 1995 Apr 4;34(13):4325-30. 

8: Wedekind JE, Poyner RR, Reed GH, Rayment I. Chelation of serine 39 to Mg2+ latches a gate at the active site of enolase: structure of the bis(Mg2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-Å resolution. Biochemistry. 1994 Aug 9;33(31):9333-42. 

9: Wedekind JE, Frey PA, Rayment I. Crystallization and preliminary crystallographic analysis of galactose-1-phosphate uridylyltransferase from Escherichia coli. Acta Crystallogr D Biol Crystallogr. 1994 May 1;50(Pt3):329-31.