Accession Number:

ADA455856

Title:

Development of Combined Computational and Experimental Approaches for Using Molecular Engineering in the Design, Construction, and Analysis of Integrated Biosensor Microsystems

Descriptive Note:

Final rept.

Corporate Author:

DUKE UNIV MEDICAL CENTER DURHAM NC DEPT OF BIOCHEMISTRY

Personal Author(s):

• Hellinga, Homme W.

Report Date:

2006-08-30

Pagination or Media Count:

6.0

Abstract:

Structure-based protein design methods constitute the basis for this project. These methods aim to describe molecular recognition using semi-empirical potential functions that capture van der Waals, hydrogen-bonding, electrostatic, and solvation contributions. These descriptions are combined with representations of the dominant degrees of freedom in a protein design calculations the sequence and structure of amino acid side-chains placed within the three-dimensional frame work of a parent protein the scaffold, and the translationsrotational degrees of freedom of a ligand. Discrete combinatorial optimization algorithms are then used to identify a combination of amino acids and docked ligand conformation that represents the global energy minimum of the potential function. Computationally generated solutions are then tested experimentally by making the specified mutations in the gene encoding the parent protein using oligonucleotide-directed mutagenesis, producing the mutant protein by heterologous over-expression in E. coli followed by protein purification and appropriate biochemical assays to test for the presence of the desired function.

Descriptors:

• *PROTEINS
• *DEGREES OF FREEDOM
• *LIGANDS
• *AMINO ACIDS
• COMPUTATIONS
• BIOLOGICAL AGENTS
• BIOASSAY
• CHEMICAL AGENTS
• THREE DIMENSIONAL
• DEOXYRIBONUCLEIC ACIDS
• DETECTION
• VALIDATION

Subject Categories:

• Biochemistry
• Chemical, Biological and Radiological Warfare

Distribution Statement:

APPROVED FOR PUBLIC RELEASE