Statistical physics and biological information : hydrophobicity patterns in protein design and differential motif finding in DNA

(cont.) is dictated by the solvent accessibility of structures. The distinct intrinsic tendencies of sequence and structure profiles are most pronounced at long periods, where sequence hydrophobicity fluctuates less, while solvent accessibility fluctuates more than average. Correlations between the two profiles can be interpreted as the Boltzmann weight of the solvation energy at room temperature. Chapter 4 shows that correlations in solvent accessibility along protein structures play a key role in the designability phenomenon, for both lattice and natural proteins. Without such correlations, as predicted by the Random Energy Model (REM), all structures will have almost equal values of designability. By using a toy, Ising-based model, we show that changing the correlations moves between a regime with no designability and a regime exhibiting the designability phenomenon, where a few highly designable structures emerge. Understanding how gene expression is regulated is one of the main goals of molecular cell biology. To reach this goal, the recognition and identification of DNA motifs--short patterns in biological sequences--is essential. Common examples of motifs include transcription factor binding sites in promoter regions of co-regulated genes and exonic and intronic splicing enhancers ...

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Physics.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2004

Author dc:creator

• Yahyanejad, Mehdi, 1975-

Advisor dc:contributor.advisor

• Christopher B. Burge and Mehran Kardar.

• Physics.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

en_US

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/28647

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/28647