Barnali (Neel) Chaudhuri
Research Scientist, Hauptman-Woodward Institute
Assistant Professor, Department of Structural Biology, SUNY Buffalo

EDUCATION
Ph.D.,  1998, Uppsala University, Sweden
M. Sc., 1991, Indian Institute of Technology, Kharagpur, India
B. Sc., 1988, Presidency College, Calcutta University, India

Research Interests

Our principal research interest is to investigate how biological macromolecules function as molecular machines by virtue of their structural design.

Understanding bacterial mitosis

The goal of this project is to understand how the segrosome, the mitotic-like chromosome trafficking device, segregates newly replicated chromosomes in the pre-divisional bacterial cell. Bacterial chromosome segregation cassette or the segrosome (ParABS) is composed of two proteins (ParA and ParB) and a set of centromere-like DNA sequences typically found near the origin of replication (parS). ParBs self-associate on the parS-proximal chromosomal DNA to form the partition assembly, a large nucleoprotein filament of unknown nature spanning several kilobases. The partition assembly serves to recruit ParA (an ATPase that forms a spindle-like filament to drive segregation) as well as SMC (Structural Maintenance of Chromosome that condenses DNA) proteins in several bacteria. It is quite possible that the pulling force for chromosome movement is generated by nucleotide-dependent depolymerization and shrinkage of the ParA filament tethered to the DNA via the partition assembly. Nevertheless, mechanism of the bacterial segrosome-mediated chromosome movement is not settled yet.

We are using a rigorous hybrid approach to elucidate the architectures of the ParB-DNA and the ParA filaments. Spatial organizations of these filaments will be elucidated using experiment-derived information on shape, size, periodicity, internal topology, interface and exposed surfaces – much like solving a puzzle. In addition, we will find out how these two filaments interact with each other, leading to DNA segregation. We are using a number of techniques including solution X-ray and neutron scattering with hydrogen/deuterium contrast variation, structural mass spectrometry, transmission electron microscopy, and single molecule technique as well as bulk-phase biochemistry.

Selected publications

The evidence of large-scale DNA-induced compaction in the mycobacterial chromosomal ParB
Barnali Chaudhuri, Rebecca Dean (in press, Journal of Molecular Biology)
http://www.sciencedirect.com/science/article/pii/S0022283611008497

Chaudhuri BN, Gupta S, Urban VS, Chance MR, D'Mello R, Smith L, Lyons K, Gee J. A combined global and local approach to elucidate spatial organization of the mycobacterial ParB-parS partition assembly. Biochemistry. 2010 Dec 13. [Epub ahead of print] [Pub Med ID: 21142182]
http://www.ncbi.nlm.nih.gov/pubmed/21142182

A computational method to predict genetically encoded rare amino acids in proteins.
Chaudhuri BN, Yeates TO. Genome Biol. 2005;6(9):R79.

Crystal structure of the apo forms of 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: A hinge at the base of the catalytic cleft.
Chaudhuri BN, Chan S, Perry LJ, Yeates TO. J Biol Chem. 2004

The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.
Chaudhuri BN, Sawaya MR, Kim CY, Waldo GS, Park MS, Terwilliger TC, Yeates TO. Structure (Camb). 2003 Jul;11(7):753-64.

Toward understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerolphosphate synthase: crystal structures of a ternary complex and the free enzyme.
Chaudhuri, BN, Lange, SC., Myers, RS., Chittur, SV., Davisson, VJ. & Smith, JL. Biochemistry. 2003, 42:7003-12

Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel through a (b/a)8 Barrel Joins Two Active Sites.
Chaudhuri, BN, Lange, SC., Myers, RS., Chittur, SV., Davisson, VJ. & Smith, JL. Structure (Camb). 2001, 10, 987-97.