From: Song, James (NIH/NLM/NCBI) [E]
Sent: Wednesday, June 18, 2008 4:00 PM
To: NLM/NCBI List ncbi-seminar
Cc: Song, James (NIH/NLM/NCBI) [E]
Subject: CBB Seminar on 6/24, Tuesday, 11 AM

Date: 06/24/2008, Tuesday, 11 AM

Location: Building 38A, B2 Library

 

Speaker: James S. Song

 

TITLE

Evolutionary models of the ABC domain and the periplasmic binding domain superfamilies. 

 

ABSTRACT

 

I will present the classification of and phylogenetic relationships among ancient subfamilies in the periplasmic-binding protein superfamily involved in the active transport, as the primary receptors for chemotaxis and transport of many sugar based solutes.  Using powerful tools of the alignment refiner Cn3D and the protein domain hierarchy editor CDTree, subfamilies present in diverse organisms were created by inferences derived from the multiple sequence alignments, phylogenetic trees, and the domain architectures of the proteins involved.  Furthermore, subfamilies, including as yet uncharacterized proteins, were annotated with molecular and cellular function and conserved sites, as available in the literature and evident from protein 3D structure. To discuss the structural and functional relationships between these two essential domains, I will introduce our fully annotated published model of the largest transporter gene family, the ATP-binding cassette (ABC) transporter superfamily. 

 

 

==============================

James S. Song, Ph.D.

Computational Biology Branch

Building 38A, Room 5N-511E

NIH/NLM/NCBI

Bethesda, MD 20894

Office: (301) 435-5928

E-mail: song@ncbi.nlm.nih.gov

==============================