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 PubMedDhaliwal, 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
******************* 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
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.
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