Dobbs Lab - BCB Rotation Projects - Fall 2007

 

 

#1- Tools for cracking the protein-RNA recognition code:  RNABindR & PRIDB

 

Protein-RNA interactions are play critical roles in many essential biological processes. We are developing tools to investigate the molecular recognition code that mediates protein-RNA interactions. 

Dobbs lab projects involve collaborations with Honavar & Jernigan groups, and include:

1) design, implementation and evaluation of improved machine learning algorithms to predict RNA binding sites in proteins (& protein binding sites in RNAs); implement in our web-based server, RNABindR

2) design and implementation of a new database, Protein-RNA Interface Database (PRIDB), a comprehensive resource for analysis, characterization and visualization of structurally-characterized RNA-protein complexes (database will be modeled after PPIDB, see URL below)

:

         Web Resources:          RNABindR:       http://bindr.gdcb.iastate.edu/RNABindR/

                                                PPIDB:              http://ppidb.cs.iastate.edu/

 

         References:            Terribilini M, Sander JD, Lee JH, Zaback P, Jernigan RL, Honavar V, Dobbs D.

RNABindR: a server for analyzing and predicting RNA-binding sites in proteins.

Nucleic Acids Res. 2007 May 5; [Epub ahead of print]

http://nar.oxfordjournals.org/cgi/content/full/gkm294v1

 

         Preferred skills:         Some computer programming ability & basic biology

 

 

 

#2- Using structural information to re-engineer Zinc Finger DNA binding domains

             

We are using both computational and wet-lab experiments to design DNA binding proteins that specifically recognize unique sequences in genomic DNA. Our server, Zinc Finger Targeter (ZiFiT), is designed to facilitate the modular design of ZFPs as well as the discovery of "rules" that govern protein-DNA interactions. 

Dobbs lab projects involve collaborations with Voytas, Miller and Honavar groups, and include:

1) develop improved algorithms for site-specific ZFP design, e.g., by evaluating the use of structural information, in addition to sequence information

2) analyze and develop algorithms for distinguishing ZFPs that bind DNA vs RNA vs protein

3) develop high throughput DNA binding assays (e.g., SPR or microarray-based) to evaluate affinity & specificity of designed ZFPs

 

         Web Resources:          http://bindr.gdcb.iastate.edu/ZiFiT

                                                 http://www.zincfingers.org/

 

         Reference:                  Sander JD, Zaback P, Keith Joung J, Voytas DF, Dobbs D.

Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.

Nucleic Acids Res. 2007 May 25;

http://nar.oxfordjournals.org/cgi/content/full/gkm349v1

 

         Preferred skills:         Some computer programming ability & basic biology

 

 

#3- Predicting structure and functional sites in the human telomerase RNP complex

 

Telomerase is a ribonucleoprotein (RNP) enzyme that adds telomeric DNA repeat sequences to the ends of linear chromosomes. The enzyme plays pivotal roles in cellular senescence and aging, and because it provides a telomere maintenance mechanism for ~90% of human cancers, it is a promising target for cancer therapy. Despite its importance, a high-resolution structure of the telomerase enzyme has been elusive.

Dobbs lab projects involve collaborations with Ho, Honavar and Jernigan groups, and include:

            1) using threading and homology modeling to predict the structure of the telomerase reverse transcriptase enzyme, including its protein components (hTERT & dyskerin) and its RNA component (hTERC). 

2) using machine learning algorithms to predict which residues in the hTERT protein interact with DNA, RNA and other proteins.

 

         Web Resources:          http://www.genlink.wustl.edu/teldb/tel.html

                                    http://www4.utsouthwestern.edu/cellbio/shay-wright/intro/sw_intro.html                                                   

         Reference:                  Blackburn, EH, Greider, CW, and Szostak, JW

Telomeres and  telomerase: the path from maize, Tetrahymena and yeast to

human cancer & aging

Nature Medicine 12, 1133 - 1138 (2006).

http://www.nature.com/doifinder/10.1038/nm1006-1133

 

         Preferred skills:         Some computer programming ability & basic biology

 

 

#4- Deciphering SNARE complex interactions in Arabidopsis

 

Membrane fusion reactions within cells are catalyzed by members of the SNARE protein family and regulated by SM proteins. Expansion of the SNARE family in plants makes Arabidopsis a particularly attractive system for studying the specificity and functional specialization of SNARE family members. We are beginning to use computational modeling approaches, in conjunction with genetic and biochemical analyses, to investigate the mechanism and regulation of SNARE function and complex formation. Our overall goal is to understand how structural features of the SNARE proteins lead to specificity in membrane fusion pathways in vivo.

 

This Bassham/Dobbs rotation project also involves collaborations with Honavar, Jernigan, and Ho groups.  Specific projects include:

1) computational structure prediction: homology modeling of helical bundle interactions required for SNARE-catalyzed membrane fusion and analysis/prediction of both structural and phenotypic effects of mutations on helix association and SNARE functional specificity

2) machine learning: analysis and prediction of interactions between SM proteins and SNAREs in Arabidopsis; tools originally developed for prediction of MHC epitopes will be modified to investigate specific sequence and structural motifs that mediate specific SM-SNARE interactions

 

         Web Resources:          PepMIL:           http://ailab.cs.iastate.edu/PepMIL

           

References:            Chen Y, Y-K Shin and DC Bassham. 2005. YKT6 is a core constituent of membrane fusion machineries at the Arabidopsis trans-Golgi network. J Mol Biol 350:92-101.

 

         Preferred skills:         Some computer programming ability & basic biology