Hoffman Lab Home Page

Department of Molecular Biosciences at the University of Texas in Austin, Texas.
The Graduate Program in Biochemistry at UT Austin.
Molecular Biology Institute  at the 
University of Texas.

********************   Teaching   *************************

Spring 2014

CH370, Physical Methods of Biochemistry (Tues & Thurs 8 am)   course page for CH370 
CH387D,  Physical Methods of Biochemistry & Mol. Biology (Tues & Thurs 9:30 am)  course page for CH387D 
CH369,  Fundamentals of Biochemistry (TuTh 6 pm)  course page for CH369    register through UT    

**************   Biochemistry Graduate Student Information   ******************

Information for current Biochemistry graduate students 

********************* Research Interests  ***********************

Protein and RNA structure.  Biophysical methods including nuclear magnetic resonance (NMR) spectroscopy and x-ray crystallography.  

********************   Some of our publications   ************************

Terrell, C.R., Burks, E.A., Whitman, C.P. & Hoffman, D.W. (2013) Structural and kinetic characterization of the two 4-oxalocrotonate tautomerases in Methylibium petroleiphilum strain PM1. Arch. Biochem. Biophys., 537, 113-124.  abtstract at PubMed    full article  

Zheng, J., Fage, C.D., Demeler, B., Hoffman, D.W. & Keatinge-Clay, A.T. (2013) The missing linker: A dimerization motif located within polyketide synthase modules. ACS Chemical Biology, March 2013.  abstract at PubMed  

Paukstelis, P.J., Chari, N., Lambowitz, A.M., P & Hoffman, D. (2011) NMR structure of the C-terminal domain of a tyrosyl-tRNA synthetase that functions in group I intron splicing.  Biochemistry, 50, 3816-3826.  abstract at PubMed 

Lyon, A.M., Reveal, B.S., Macdonald, P.M. & Hoffman, D.W. (2009) Bruno protein contains an expanded RNA recognition motif.  Biochemistry, 48, 12202-12212.  abstract at PubMed   full article at Biochemistry  

Montemayor, E.J. & Hoffman, D.W. (2008) Crystal structure of spermidine/spermine N1-acetyltransferase in complex with spermine provides insights into substrate binding and catalysis.  Biochemistry, 47, 9145-9153.  Abstract at PubMed  Full article at Biochemistry

Chu, Y., Hoffman, D.W. & Iverson, B.L. (2009) A pseudocatenane structure formed between DNA and a cyclic bisintercalator.  J. Amer. Chem. Soc., 131, 3499-3508.  Abstract at PubMed   Full article at JACS

Tao, Zhihua, Gao, P., Hoffman, D.W. & Liu, H.w. (2008) Domain C of human poly-(ADP-ribose) polymerase-1 is important for enzyme activity and contains a novel zinc-ribbon motif.  Biochemistry, 47, 5804-5813.  
Abstract at PubMed   Link to article  

Monzingo, A.F., Dhaliwal, S., Dutt-Chadhuri, A., Lyon, A., Sadow, J.H., Hoffman, D.W., Robertus, J.D. & Browning, K.S. (2007) The structure of translation initiation factor eIF4E from wheat reveals a novel disulfide bond.  Plant Physiol., 143, 1504-1518.  Abstract at PubMed  Link to article  

Hoffman, D.W., Carroll, D., Martinez, N. & Hackert, M.L. (2005) Solution structure of a conserved domain of antizyme: An protein regulator of polyamines.  Biochemistry, 44, 11777-11785.  Abstract at PubMed   Full article at Biochemistry site   Picture of structure    Coordinates at PDB

Sidote, D.J., Heideker, J. & Hoffman, D.W. (2004) Crystal structure of the archaeal ribonuclease P protein aRpp29 from Archaeoglobus fulgidus. Biochemistry, 43, 14128-14138. Abstract at PubMed   Full article at Biochemistry site  Picture of structure  Coordinates at PDB

Laursen, B.S., Kjaergaard, A.C., Mortensen, K.K., Hoffman, D.W. & Sperling-Petersen, H.U. (2004) The N-terminal domain (IF2N) of bacterial translation initiaton factor IF2 is connected to the conserved C-terminal domains by a flexible linker. Protein Science,14,230-239.  Full article at Protein Science site   Abstract at PubMed

Sidote, D.J. & Hoffman, D.W. (2003) NMR structure of an archaeal homologue of RNase P protein Rpp29. Biochemistry, 42, 13541-13550.   Abstract at PubMed   Full article at Biochemistry site  Picture of structure   Coordinates at PDB

Dhaliwal, S. & Hoffman, D.W. (2003) The crystal structure of the N-terminal region of the alpha subunit of translation initiation factor 2 (eIF2a) from Saccharomyces cerevisiae provides a view of the loop containing serine-51, the site of phosphorylation by the eIF2a-specific kinases.  J. Mol. Biol.,334, 187-195. Abstract at PubMed   Full article at JMB web site   Picture of structure   Coordinates at PDB

Laursen, B.S., Mortensen, K.K., Sperling-Petersen, H.U. & Hoffman, D.W. (2003) A conserved structural motif at the N-terminus of bacterial translation initiation factor IF2.  J. Biol. Chem., 278,16320-16328. View abstract    Full article at JBC site

Wang, Y., Wills, N.M., Du, Z., Rangan, A., Atkins, J.F., Gesteland, R.F. & Hoffman, D.W. (2002) Comparative studies of frameshifting and non-frameshifting RNA pseudoknots: A mutational and NMR investigation of pseudoknots derived from the bacteriophage T2 gene 32 mRNA and the retroviral gag-pro frameshift site. RNA, 8,981-996. View abstract    Full article at "RNA" web site.

Cho, Seongeun & Hoffman, D.W. (2002) Structure of the beta subunit of translation initiation factor 2 from the archaeon Methanococcus jannaschii: A representative of the eIF2beta/eIF5 family of proteins.  Biochemistry, 41, 5730-5742. View abstract    Full article at "Biochemistry" site.

Dong, G., Nowakowski, J. & Hoffman, D.W. (2002) The structure of small protein B: The protein component of the tmRNA-SmpB system for ribosome rescue.  EMBO J., 21, 1845-1854. View abstract    Full article at "EMBO Journal" site

Li, W. & Hoffman, D.W. (2001) Structure and dynamics of translation initiation factor aIF-1A from the archeon Methanococcus jannaschii determined by NMR spectroscopy. Protein Science, 10, 2426-2438. View abstract

Hoffman, D.W. (2000) Resolution of the 1H-1H NOE spectrum of RNA into three dimensions using 15N-1H two-bond couplings. J. Biomolecular NMR., 16,165-169.   View abstract

Holland, J.A., Hansen, M.R., Du, Z. & Hoffman, D.W. (1999) Coaxial Stacking of Helical Stems in a Pseudoknot Motif:  An NMR Investigation of the Gene 32 Messenger RNA Pseudoknot of Bacteriophage
T2.  RNA, 5, 257-271. View abstract

Lillemoen, J. & Hoffman, D.W. (1998) An investigation of the dynamics of ribosomal protein L9 using heteronuclear NMR relaxation measurements.  J. Mol. Biol., 281, 539-551. View abstract

Du, Z. & Hoffman, D.W. (1997) An NMR and mutational study of the pseudoknot within the gene 32  mRNA of bacteriophage T2:  Insights into a family of structurally related RNA pseudoknots.  Nucl. Acids Res., 25,1130-1135. View abstract

Lillemoen, J., Cameron, C.S. & Hoffman, D.W. (1997) Stability and dynamics of ribosomal protein L9: An investigation of a molecular strut by amide proton exchange and circular dichroism. J. Mol. Biol., 268,  482-493.   View abstract

Du, Z., Giedroc, D.P. & Hoffman, D.W. (1996) Structure of the autoregulatory pseudoknot within the gene 32 mRNA of bacteriophages T2 and T6:  A model for a possible family of structurally related RNA pseudoknots.  Biochemistry, 35, 4187-4198.    View abstract

Hoffman, D.W., Cameron, C., Davies, White, S.W. & Ramakrishnan, V. (1996)  Ribosomal protein L9: A structure determination by the combined use of x-ray crystallography and NMR spectroscopy.  J. Mol. Biol., 264, 13, 1058-1071.   Link to article  

Hoffman, D.W., Davies, C. Gerchman, S.E., Kycia, H., Porter, S, White, S.W. & Ramakrishnan, V. (1994) Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein. EMBO J., 13, , 205-212.  Link to article

*******  Graduates (proof that it is possible to graduate!) & Post-docs   *********
Cassidy Terrell earned her PhD in Spring 2012, and will be an Assistant Professor at St. Olaf's College in Minnesota.
Nandini Chari earned her PhD in Spring 2010 and was a post-doc with Jon Robertus at UT Austin.
Angeline Lyon earned her PhD in August 2009 and is a post-doc with John Tesmer at U. Michigan.
Eric Montemayor earned his PhD in August 2008 and is a post-doc with John Hart at UT San Antonio.
Simrit Dhaliwal earned her PhD in December 2005 and did a post-doc in Arlen Johnson's lab at UT.
David Sidote earned his PhD in December 2004 and went to post-doc with Ann Stock at Rutgers.
Gang Dong earned his PhD and went to New Haven for a post-doc position with Karin Reinisch at Yale.
Seongeun Cho earned her PhD (May 2002) and moved to Sunnyvale, California, and then to a post-doc position at Rockefeller U. in New York.
Anu Rangan earned her PhD (December 2001) taught Cell Biology at UT, and then moved to India.
Priya Sivaraman (post-doc 2000-2001) became a patent specialist at a law firm in Austin, and later moved to California
Brian Laursen, exchange student, returned to Aarhus Denmark to finish his PhD, after visiting UT for fall semester 2001.
Yue Wang PhD, 2000, went on to medical school at Vanderbilt University.  She did a residency at Yale, fellowships at Johns Hopkins and Duke, and is now an opthamologist and eye surgeon in Melbourne, Florida.
Wei Li, MA, 1999, went on to graduate school in computer science at UT.
Chris Cameron, MA, 1997, took a position as a lecturer at Lenoir Community College in North Carolina.
Mark Hansen, post-doc 1997, went to Art Pardi's lab at U of Colorado, then Triad Pharma. in San Diego.
David Cohen, post-doc 1998, went to Burstein Technology, Irvine California.
Jason Holland, PhD, 1998, became an Assistant Professor at SUNY Oswego, and later joined the faculty at Central Missouri S.U. at Warrensburg.
Jarle Lillemoen, PhD, 1998, took a post-doc with Prof. Ken Johnson at UT Austin.
Zhihua Du, PhD, 1997, went to a post-doc with Prof. Tom James at UCSF.  He is currently an Assitant Professor in the Department of Chemistry and Biochemistry at Southern Illinois University.
********************* Molecular Structure Gallery  **********************
NMR structure of Antizyme isoform-1 from rat (Hoffman, Carroll, Martinez & Hackert, 2005)
Translation initiation factor eIF2 subunit alpha  (Dhaliwal & Hoffman, 2003)
RNaseP protein Rpp29 from Archaeoglobus fulgidus  (Sidote & Hoffman, 2003)
IF2 N-terminal domain (Laursen et al., 2003)
Translation initiation factor 2, subunit beta, N-terminal domain  (Cho & Hoffman, 2002)
Translation initiation factor 2, subunit beta, C-terminal domain (Cho & Hoffman, 2002)
SmpB from Aquifex aeolicus  (Gang Dong, Nowakowski & Hoffman, 2002)
Translation initiation factor 1A from M. jannaschii, NMR structure  (Li & Hoffman, 2001)
Ribosomal protein L9, Xray and NMR structure  (Hoffman et al., 1996) PDB entry 1DIV
Gene 32 mRNA pseudoknot  (Du et al., 1996; Holland et al., 1999)

*******************   Useful things for Protein NMR   *********************

The peptide NMR assignment problem
Typical proton NMR chemical shifts for amino acids
Typical NMR chemical shifts for proteins:  H-1, C-13 & N-15 nuclei
Identifying amino acids in protein NMR spectra
Distances and torsion angles in regular secondary structures
More distances in regular secondary structure
Typical NOE cross peaks in a helix
Typical NOE cross peaks in a beta strand
Typical NOE cross peaks in a beta sheet
Naming of atoms in isoleucine and tryptophan  (which I find tough to remember, so I made this diagram)
Naming of atoms in histidine
Using "Sparky" to evaluate volumes of peaks in 2-D spectra

********   Examples of scripts for processing NMR data using Nmrpipe   *********

Here are example scripts for processing with NMR Pipe
Phase correction of NMR spectra

*******************   Useful things for Crystallography  *********************

CNS things:

Dave H's molecular replacement tutorial using CNS, with sample input files.
Example of calculating a difference Patterson using CNS, with input files.
Multiple Isomorphous Replacement (MIR) using L9 as an example, with CNS input files.
Using phases calculated from one derivative to find heavy atom sites in a second derivative

Notes regarding Patterson maps:

Example of calculating a difference Patterson using CNS, with input files.

Denzo and Scalepack notes:

Using Denzo and Scalepack, and getting your data into CCP4 and/or CNS format.

CCP4 notes:

Multiple Isomorphous Replacement (MIR) with CCP4, using L9 as an example.
Molecular replacement of a dimer using CCP4, followed by refinement using CNS.

Misc. crystallography stuff:   Table of space group frequencies.

************************   Other useful links   *********************
Science Links

The NCBI Homepage includes PubMed, Blast, GenBank, Structural data.
UT Library  Electronic Journals on line
Hints for using the digital camera.

Miscellaneous Links

The Universe Today  is a good astronomy web site.
The Astronomy picture of the day is often interesting.
Caffeine content of common beverages (thanks to Michael Robertson).
My 3 hour marathon story - Austin, Feb. 2004

My rather boring personal blog is a web page for my non-science things.  The page is mostly about my hobbies, including running, bicycling, swimming, triathlons, and pinching pennies.  It is really quite dull.

Lobster Traps (a.k.a. Lobster Pots) Authentic New England lobster traps specially made in Massachusetts for recreational lobstermen (and lobsterwomen) can be purchased from David Hoffman (Dr. Hoffman's Dad).  Call David Hoffman at 781-444-9213 to order lobster traps, bouys, ropes, bait bags, etc.  Buoys can be custom painted.  For more information on lobster traps, see  David Hoffman's Lobster Trap Web Page.


  This page is maintained by David Hoffman, which explains why it is so simple.