Contact info:
Lawrence Berkeley National Laboratory
Physical Biosciences Division
One Cyclotron Road
Mail Stop: Calvin Lab - 350
Berkeley, California 94720
USA

Location: 3-0350 Calvin
Phone: (510) 486-4332/-4588
Fax: (510) 486-6059
Email: R_Kim@lbl.gov

Web site: The Kim Group

Research Emphases

Biochemical proteome
An analysis of the genomic sequences of many organisms indicates that a large fraction of the encoded proteins cannot be assigned particular molecular and/or cellular functions. Since the molecular function of a gene product is tightly coupled to its three-dimensional structure, determining the structure or its folding pattern may provide important insight into its molecular function, which, in turn, may help to place it in a particular cellular pathway. However, structure determination and the experimental verification of the molecular function inferred by the structure require cloning and expression of the genes, and purification of the proteins in the proteome, the protein complement of a genome. Biochemical and molecular biological approaches are used to develop high throughput methods for determining structure-function relationship of a proteome.

Structure-function relationship of hyperthermal proteins
Many microorganisms live in extreme environments such as hyperthermal vents, volcanoes, salty lakes, hot springs, and frozen glaciers. The objective of this program is to discover the structural and biochemical basis for understanding the unusual stabilities and biochemical properties of the proteins from these organisms, and to find their application for industrial and medical purposes.

Publications

2005:

Das, D., Oganesyan, N., Yokota, H., Pufan, R., Kim, R., Kim, S. –H. (2005) Crystal structure of the conserved hypothetical protein MPN330 (GI: 1674200) from Mycoplasma pneumoniae PROTEINS: Struc. Func. Bioinf. 58:504-508.

Chen S., Shin D. H., Pufan, R., Kim, R., Kim, S.–H. (2005) Crystal Structure of Methenyltetrahydrofolate Synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 ? Resolution. PROTEINS: Struc. Func. Bioinf. 56: 839-842.

2004:

Pajon, A., Ionides, J., Diprose, J., Fillon, J., Fogh, R., Ashton, A. W., Berman, H., Boucher, W., Cygler, M., Deulery, E., Esnouf, R., Janin, J., Kim, R., Krimm, I., Lawson, C. L., Oeuillet, E., Poupon, A., Raymond, S., Stevens, T., van Tilbeurgh, H., Westbrook, J., Wood, P., Ulrich, E., Vranken, W., Xueli, L., Laue, E., Stuart, D. I., Henrick, K. (2004) Design of a data model for developing laboratory information management and analysis systems for protein production. PROTEIN: Struc. Func. Bioinf. 58: 278-84.

Oganesyan, N., Kim, S. –H., Kim, R. (2004) On-column Chemical Refolding of Proteins. PharmaGenomics 4: 22-26

Oganesyan, V., Ramona P., DeGiovanni, A., Yokota, H. A., Kim, R., Kim, S. –H. (2004) Structure of the putative DNA-binding protein SP_1288 from Streptococcus pyogenes. Acta Cryst. Sec D60: 1266-1271

Shin, D. H., Brandsen J., Jancarik, J., Yokota H., Kim, R., Kim, S.-H. (2004) Structural Analyses of Peptide Release Factor 1 from Thermotoga maritima Reveal Domain Flexibility Required for Its Interaction with the Ribosome. J. Mol. Biol. 341: 227-239.

Shin, D. H., Lou Y., Jancarik J., Yokota H., Kim, R., Kim, S.-H. (2004) Crystal structure of YjeQ from Thermotoga maritima contains a circularly permuted GTPase domain. Proc. Natl. Acad. Sci. USA 101: 13198-13203.

Busso, D., Kim, R., Kim, S.-H. (2004) Using an Escherichia coli cell-free extract to screen for soluble expression of recombinant proteins. J. Struct. Funct. Genomics 5: 69-74.

Xu, Q. S., Shin, D.-H., Pufan, R., Yokota, H., Kim, R., Kim, S.-H. (2004) Crystal structure of a phosphotransacetylase from Streptococcus pyogenes. PROTEINS: Struct. Funct. and Bioinf. 55: 479-481

Nguyen, H., Martinez, B., Oganesyan, N., Kim, R. (2004) An automated small-scale protein expression and purification screening provides beneficial information for protein production. J. Struct. Funct. Genomics 5: 23-27

Liu, J., Yokota. H., Kim R., Kim S. –H. (2004) A Conserved Hypothetical Protein From Mycoplasma genitalium Shows Structural Homology to NusB Proteins. PROTEINS: Struct. Funct. and Bioinf. 55: 1082 – 1086

Adams, M., Joachimiak, A., Kim, R., Montelione, G. T., Norvell, J. (2004) 2003 NIH Protein Structure Initiative Workship in Protein Production and Crystallization for Structural and Functional Genomics. J. Struct. Funct. Genomics. 5: 1-2

Chen, S., Jancarik, J., Yokota H., Kim, R., Kim, S. –H. (2004) Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif. Proteins 4: 785-791

Shin, D. H., Choi I. G., Busso D., Jancarik J., Yokota H., Kim, R., Kim, S. –H. (2004) Structure of OsmC from Escherichia coli: a salt-shock-induced protein. Acta Crystallogr. D 60: 903-911

2003:

Shin, D. H., Nguyen H., Jancarick, J., Yokota H., Kim R., Kim S.-H. (2003) Crystal Structure of NusA from Thermotoga maritima and Functional Implication of the N-Terminal Domain. Biochem. 42: 13429-1343

Liu, J., Wang, W., Shin, D. H., Yokota, H., Kim, R., Kim, S. – H. (2003) Crystal Structure of tRNA (m1G37) Methyltransferase from Aquifex aeolicus at 2.6Å Resolution: A Novel Methyltransferase Fold. PROTEINS: Struct. Funct. and Genetics 53: 326-328

Kim, S. H., Shin, D. H., Choi, I. G., Schulze-Gahmen, U., Chen, S., Kim, R. (2003) Structure-based functional inference in structural genomics. J. Struct. Funct. Genomics 4: 129-135

Busso, D., Kim, R. (2003) Screening and increasing soluble expression of recombinant proteins using the RTS 100 E. coli HY in a 96-Well Format. Cell-Free Protein Expression James R. Swartz (Ed.) 109-116

Choi, I. G., Shin, D. H., Brandsen, J., Jancarik, J., Busso, D., Yokota, H., Kim, R., Kim, S. – H. (2003) Crystal structure of a stress inducible protein from Mycoplasma pneumoniae at 2.85 Å resolution. J. Struct. Funct. Genomics 4: 31-34

Oganesyan, V., Busso, D., Brandsen, J., Chen, S., Jancarik, J., Kim, R., Kim, S. -H. (2003) Structure of the hypothetical protein AQ1354 from Aquifex aeolicus. Acta Crystallogr D. 59: 1219-1223

Kim, R. (2003) Native Agarose Gel Electrophoresis of Multiprotein Complexes. Proteins and Proteomics, A Laboratory Manual. Ed. R. J. Simpson. Cold Spring Harbor Laboratory Press p. 713-716

Wang, W., Kim, R., Jancarik, J., Yokota, H., Kim, S. –H. (2003) Crystal structure of a flavin-binding protein from Thermotoga maritima. PROTEINS: Struct. Funct. and Genetics. 52: 633-635

Rubin, S. M., Pelton, J. G., Yokota, H., Kim, R., Wemmer, D. E. (2003) Solution structure of a putative ribosome binding protein from Mycoplasma pneumoniae and comparison to a distant homolog. J. Struct. Funct. Genomics 4: 235-243