J Phys Chem B. 2017 Jun 08;121(22):5483-5498. doi: 10.1021/acs.jpcb.7b01867. Epub 2017 May 24.

Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.

The journal of physical chemistry. B

Shahid M Nayeem, Francesco Oteri, Marc Baaden, Shashank Deep

PMID: 28497965 DOI: 10.1021/acs.jpcb.7b01867

Abstract

Transforming growth factors (TGF-βs) are proteins that regulate cell growth by binding to their receptors. In contrast to transforming growth factor (TGF) β1, TGF-β3 homodimer is believed to exist also in an open conformation, in which both of its monomers are loosely packed against each other. At the origin of this difference is the H3-helix. Its sequence and degree of structuration seem to govern the outcome of TGF dimerization. We docked two monomers of TGF-β3 with intact and altered H3 α-helix against each other using HADDOCK. TGF-β3 monomer with an intact H3-helix exclusively forms closed conformations of homodimer, whereas the open conformation may coexist with the closed one when a part of the H3 α-helix is destabilized. We quantify the difference in its conformational preference for the open versus the closed structure by calculating the binding energy between monomers using the MMPBSA approach. We compare the wild type (wt) TGFβ3/TGFβ1 homodimers in the Protein Data Bank to a swapped mutant where all residues of the H3-helix were mutated to the respective TGFβ1/TGFβ3 sequence. Swapping stabilizes the closed conformation and destabilizes the open conformation of TGFβ3. Further detailed insight is derived from molecular dynamics simulation studies suggesting that Val 61 of the H3-helix may act as an anchor residue for the closed conformation of TGFβ3. Computational alanine scanning mutagenesis confirms that several residues of the H3-helix are the hot residues for the closed conformation of TGFβ3. These observations may bear relevance to general conformational transitions in proteins and specifically in the TGFβ superfamily.

Substances

• Transforming Growth Factor beta3

MeSH terms

• Molecular Dynamics Simulation*
• Protein Conformation, alpha-Helical
• Transforming Growth Factor beta3 / chemistry
• Transforming Growth Factor beta3 / genetics

Publication Types

• Journal Article
• Research Support, Non-U.S. Gov't