Biology subjects

Purdy, M. D.

Publications and source records attributed to Purdy, M. D..

5 recordsLinked to original sources

bioRxiv2024

A Collagen Triple Helix without the Super Helical Twist

Collagens are ubiquitous in biology functioning as the backbone of the extracellular matrix, forming the primary structural components of key immune system complexes, and fulfilling numerous other structural roles in a variety of systems. Despite this, there is limited understanding of how triple helices, the basic collagen structural units, pack into collagenous assemblies. Here we use a peptide self-assembly system to design collagenous assemblies based on the C1q collagen-like region. Using cryo-EM we solve a structure of one assembly to 3.5 [A] resolution and build an atomic model. From this, we identify a triple helix conformation with no superhelical twist, starkly in contrast to the canonical right-handed triple helix. This non-twisting region allows for unique hydroxyproline stacking between adjacent triple helices and also results in the formation of an exposed cavity with rings of hydrophobic amino acids packed symmetrically. We find no precedent for such an arrangement of collagen triple helices and have designed mutant assemblies to probe key stabilizing amino acid interactions in the complex. The mutations behave as predicted by our atomic model. Our findings, combined with the extremely limited experimental structural data on triple helix packing in the literature, suggest that collagen and collagen-like assemblies may adopt a far more varied conformational landscape than previously appreciated. We hypothesize that this is particularly likely adjacent to the termini of these helices and at discontinuities to the required Xaa-Yaa-Gly repeating primary sequence; a discontinuity found in the majority of this class of proteins and in many collagen-associated diseases.

biophysics↗

bioRxiv2022

CryoEM Structures of the Human HIV-1 Restriction Factor SERINC3 and Function as a Lipid Transporter

The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). CryoEM maps of full-length human SERINC3 and an ICL4 deletion construct reveal that hSERINC3 is comprised of two - helical bundles connected by a [~]40-residue, tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes flip phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. SERINC3 and SERINC5 reduce infectivity and expose PS on the surface of HIV-1 and also MLV, which is counteracted by Nef and GlycoGag, respectively. Antiviral activities by SERINCs and the scramblase TMEM16F correlate with the exposure of PS and with altered conformation of the envelope glycoprotein. We conclude that SERINCs are lipid transporters, and we demonstrate that lipid flipping is directly correlated with loss of infectivity. One Sentence SummaryThe HIV-1 restriction factor SERINC3 has a molecular design similar to non-ATP dependent lipid transporters, a function supported by the observation of flipping activity in proteoliposomes and exposure of phosphatidylserine on HIV-1 and MLV particles, which is correlated with loss of infectivity.

biophysics↗

bioRxiv2021

Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central tomaturation inhibition

The assembly and maturation of human immunodeficiency virus type-1 (HIV-1) requires proteolytic cleavage of the Gag polyprotein. The rate-limiting step resides at the junction between the capsid protein CA and spacer peptide 1, which assembles as a six-helix bundle (6HB). bevirimat (BVM), the first-in-class maturation inhibitor drug, targets the 6HB and impedes proteolytic cleavage, yet the molecular mechanisms of its activity, and relatedly, the escape mechanisms of mutant viruses, remain unclear. Here, we employed extensive molecular dynamics (MD) simulations and free energy calculations to quantitatively investigate molecular structure-activity relationships, comparing wild-type and mutant viruses in the presence and absence of BVM and inositol hexakisphosphate (IP6), an assembly cofactor. Our analysis shows that the efficacy of BVM is directly correlated with preservation of six-fold symmetry in the 6HB, which exists as an ensemble of structural states. We identified two primary escape mechanisms, and both lead to loss of symmetry, thereby facilitating helix uncoiling to aid access of protease. Our findings also highlight specific interactions that can be targeted for improved inhibitor activity and support the use of MD simulations for future inhibitor design.

biophysics↗

bioRxiv2021

A Constitutively Closed Pannexin1 Channel in Lipid Bilayer Nanodiscs Assembles as a Large-Pore Heptamer

Pannexin 1 (Panx1) channels are widely expressed and play important roles in apoptotic cell clearance, inflammation, blood pressure regulation, neurological disorders, opiate withdrawal, and cancer progression and metastasis. We performed (1) physicochemical analysis on a constitutively closed Panx1 channel (designated fPanx1{Delta}C) to examine the entire population of particles to detect multiple oligomeric states and (2) cryoEM in the membrane mimetics amphipol A8-35 and lipid bilayer nanodiscs. Our results reveal that the dominant if not exclusive oligomeric state of fPanx1{Delta}C is a heptamer, in solution and by cryoEM. The Panx1 heptamer provides further structural diversity within the family of large-pore channels, including hexameric LRRC8 (SWELL1) channels and connexin hemichannels, octameric CALHM1 channels and innexin hemichannels, and undecameric CALHM2 channels. Conserved structural themes are a large cytoplasmic vestibule with a diameter that corresponds roughly with the oligomeric state and a 4-helix bundle protomer, albeit with noncanonical helical packing for CALHM1 and CALHM2. In BriefThe 4-helix bundle protomer of a constitutively closed pannexin1 channel assembles as a heptamer in solution and by cryoEM.

biophysics↗

bioRxiv2017

MicroED Structures of HIV-1 Gag CTD-SP1 Reveal Binding Interactions with the Maturation Inhibitor Bevirimat

HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, three-dimensional microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-[A] MicroED structure revealed that a single BVM molecule stabilizes the 6-helix bundle via both electrostatic interactions with the dimethysuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design.\n\nOne-sentence summaryThe MicroED structure of HIV-1 Gag CTD-SP1 at 2.9 [A] resolution reveals the molecular basis for binding of the maturation inhibitor bevirimat that will inform further drug discovery efforts.

biophysics↗