WARWICKER Jim

Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold

Published date : 17 Oct 2017

An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions.

type
Journal Paper
journal
PLOS ONE, 10 Oct 2017, doi: 10.1371/journal.pone.018592
Impact Factor
2.806

Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"

Published date : 24 Jul 2017

BACKGROUND:
Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane's hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein's biological functions.

RESULTS:

type
Journal Paper
journal
BMC Biology 2017 Jul 24;15(1):66. doi: 10.1186/s12915-017-0404-4
Impact Factor
6.779

Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

Published date : 20 Oct 2016

Critical regulatory pathways are replete with instances of intra- and interfamily protein-protein interactions due to the pervasiveness of gene duplication throughout evolution. Discerning the specificity determinants within these systems has proven a challenging task. Here, we present an energetic analysis of the specificity determinants within the Bcl-2 family of proteins (key regulators of the intrinsic apoptotic pathway) via a total of ∼20 μs of simulation of 60 distinct protein-protein complexes.

type
Journal Paper
journal
Structure, Vol 24, Issue 11, pg 2024-2033, 1 Nov 2016, doi: 10.1016/j.str.2016.09.006
Impact Factor
5.237