Characterization and computational simulation of human Syx, a RhoGEF implicated in glioblastoma

Ryan J. Boyd, Tien L. Olson, James D. Zook, Derek Stein, Manuel Aceves, Wan Hsin Lin, Felicia M. Craciunescu, Debra T. Hansen, Panos Z. Anastasiadis, Abhishek Singharoy, Petra Fromme

Research output: Contribution to journalArticlepeer-review

Abstract

Structural discovery of guanine nucleotide exchange factor (GEF) protein complexes is likely to become increasingly relevant with the development of new therapeutics targeting small GTPases and development of new classes of small molecules that inhibit protein-protein interactions. Syx (also known as PLEKHG5 in humans) is a RhoA GEF implicated in the pathology of glioblastoma (GBM). Here we investigated protein expression and purification of ten different human Syx constructs and performed biophysical characterizations and computational studies that provide insights into why expression of this protein was previously intractable. We show that human Syx can be expressed and isolated and Syx is folded as observed by circular dichroism (CD) spectroscopy and actively binds to RhoA as determined by co-elution during size exclusion chromatography (SEC). This characterization may provide critical insights into the expression and purification of other recalcitrant members of the large class of oncogenic—Diffuse B-cell lymphoma (Dbl) homology GEF proteins. In addition, we performed detailed homology modeling and molecular dynamics simulations on the surface of a physiologically realistic membrane. These simulations reveal novel insights into GEF activity and allosteric modulation by the plekstrin homology (PH) domain. These newly revealed interactions between the GEF PH domain and the membrane embedded region of RhoA support previously unexplained experimental findings regarding the allosteric effects of the PH domain from numerous activity studies of Dbl homology GEF proteins. This work establishes new hypotheses for structural interactivity and allosteric signal modulation in Dbl homology RhoGEFs.

Original languageEnglish (US)
Article numbere22378
JournalFASEB Journal
Volume36
Issue number7
DOIs
StatePublished - Jul 2022

Keywords

  • Dbl homology
  • DH domain
  • GEF
  • glioblastoma
  • lipid binding protein
  • membrane-associated protein
  • molecular dynamics
  • oncogene
  • PH domain
  • PIP
  • protein dynamics
  • protein engineering
  • protein–protein interactions
  • RhoA
  • RhoGEF
  • small GTPase
  • structure-guided drug design

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Genetics

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