Biomedical subjects

John M Rosenberg

Publications and source records attributed to John M Rosenberg.

4 recordsLinked to original sources

PubMed2004

Machine-learning techniques for macromolecular crystallization data.

Systematizing belief systems regarding macromolecular crystallization has two major advantages: automation and clarification. In this paper, methodologies are presented for systematizing and representing knowledge about the chemical and physical properties of additives used in crystallization experiments. A novel autonomous discovery program is introduced as a method to prune rule-based models produced from crystallization data augmented with such knowledge. Computational experiments indicate that such a system can retain and present informative rules pertaining to protein crystallization that warrant further confirmation via experimental techniques.

Algorithms↗

PubMed2004

Adaptive integration method for Monte Carlo simulations.

We present an adaptive sampling method for computing free energies, radial distribution functions, and potentials of mean force. The method is characterized by simplicity and accuracy, with the added advantage that the data are obtained in terms of quasicontinuous functions. The method is illustrated and tested with simulations on a high density fluid, including a stringent consistency test involving an unusual thermodynamic cycle that highlights its advantages.

Algorithms↗

PubMed2003

A kinesin switch I arginine to lysine mutation rescues microtubule function.

Switch I and II are key active site structural elements of kinesins, myosins, and G-proteins. Our analysis of a switch I mutant (R210A) in Drosophila melanogaster kinesin showed a reduction in microtubule affinity, a loss in cooperativity between the motor domains, and an ATP hydrolysis defect leading to aberrant detachment from the microtubule. To investigate the conserved arginine in switch I further, a lysine substitution mutant was generated. The R210K dimeric motor has lost the ability to hydrolyze ATP; however, it has rescued microtubule function. Our results show that R210K has restored microtubule association kinetics, microtubule affinity, ADP release kinetics, and motor domain cooperativity. Moreover, the active site at head 1 is able to distinguish ATP, ADP, and AMP-PNP to signal head 2 to bind the microtubule and release mantADP with kinetics comparable with wild-type. Therefore, the structural pathway of communication from head 1 to head 2 is restored, and head 2 can respond to this signal by binding the microtubule and releasing mantADP. Structural modeling revealed that lysine could retain some of the hydrogen bonds made by arginine but not all, suggesting a structural hypothesis for the ability of lysine to rescue microtubule function in the Arg210 mutant.

Adenosine Diphosphate↗

PubMed2003

Motor domain mutation traps kinesin as a microtubule rigor complex.

Conventional kinesin is a highly processive, microtubule-based motor protein that drives the movement of membranous organelles in neurons. Using in vivo genetics in Drosophila melanogaster, Glu164 was identified as an amino acid critical for kinesin function [Brendza, K. M., Rose, D. J., Gilbert, S. P., and Saxton, W. M. (1999) J. Biol. Chem. 274, 31506-31514]. Glu164 is located at the beta-strand 5a/loop 8b junction of the catalytic core and projects toward the microtubule binding face in close proximity to key residues on beta-tubulin helix alpha12. Substitution of Glu(164) with alanine (E164A) results in a dimeric kinesin with a dramatic reduction in the microtubule-activated steady-state ATPase (5 s(-1) per site versus 22 s(-1) per site for wild-type). Our analysis shows that E164A binds ATP and microtubules with a higher affinity than wild-type kinesin. The rapid quench and stopped-flow results provide evidence that ATP hydrolysis is significantly faster and the precise coordination between the motor domains is disrupted. The data reveal an E164A intermediate that is stalled on the microtubule and cannot bind and hydrolyze ATP at the second head.

Adenosine Diphosphate↗