Search results | J. Murrey Atkins Library

Title: A virtual pebble game to ensemble average graph rigidity
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2015
Subjects--Topical: Probabilities, Proteins
Description: Background: The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensemble of constraint topologies...

Title: Calculating ensemble averaged descriptions of protein rigidity without sampling
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Biology, Proteins
Description: Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently cal...

Title: Changes in Lysozyme flexibility upon mutation are frequent, large and long-ranged
Author: Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Bioinformatics, Statistics
Description: We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility ...

Title: Conformational entropy of an ideal cross-linking polymer chain
Author: Jacobs, Donald J., Vorov, Oleg, Livesay, Dennis R.
Date Created: 2008
Subjects--Topical: Proteins, Entropy
Description: We present a novel analytical method to calculate conformational entropy of ideal cross-linking polymers from the configuration integral by employing a Mayer series expansion. Mayer-functions describing chemical bonds within the chain and for cros...

Title: Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
Author: Jacobs, Donald J., Livesay, Dennis R.
Date Created: 2008
Subjects--Topical: Bacteria, Proteins
Description: Background: Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two do...

Title: Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Chatelier's principle
Author: Jacobs, Donald J., Li, Tong, Livesay, Dennis R.
Date Created: 2014
Subjects--Topical: Immunoglobulins, Biology
Description: Le Chatelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Chatelier's principle states t...

Title: Rigidity emerges during antibody evolution in three distinct antibody systems: evidence from QSFR analysis of fab fragments
Author: Jacobs, Donald J., Li, Tong, Livesay, Dennis R.
Date Created: 2015
Subjects--Topical: Immunoglobulins, Biology
Description: The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assess...

Title: Variations within class-a beta-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity
Author: Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
Date Created: 2013
Subjects--Topical: Biology, Bacteria
Description: The bacterial enzyme beta-lactamase hydrolyzes the beta-lactam ring of penicillin and chemically related antibiotics, rendering them ineffective. Due to rampant antibiotic overuse, the enzyme is evolving new resistance activities at an alarming ra...