Biomedical subjects

William F Degrado

Publications and source records attributed to William F Degrado.

10 recordsLinked to original sources

PubMed2005

An atomic environment potential for use in protein structure prediction.

We describe the derivation and testing of a knowledge-based atomic environment potential for the modeling of protein structural energetics. An analysis of the probabilities of atomic interactions in a dataset of high-resolution protein structures shows that the probabilities of non-bonded inter-atomic contacts are not statistically independent events, and that the multi-body contact frequencies are poorly predicted from pairwise contact potentials. A pseudo-energy function is defined that measures the preferences for protein atoms to be in a given microenvironment defined by the number of contacting atoms in the environment and its atomic composition. This functional form is tested for its ability to recognize native protein structures amongst an ensemble of decoy structures and a detailed relative performance comparison is made with a number of common functions used in protein structure prediction.

Algorithms↗

PubMed2005

X-ray structure of a water-soluble analog of the membrane protein phospholamban: sequence determinants defining the topology of tetrameric and pentameric coiled coils.

Phospholamban (PLB) is a pentameric transmembrane protein that regulates the Ca(2+)-dependent ATPase SERCA2a in sarcoplasmic reticulum membranes. We previously described the computational design of a water-soluble variant of phospholamban, WSPLB, which reproduced many of the structural and functional properties of the native membrane-soluble protein. While the full-length WSPLB forms a pentamer in solution, a truncated variant forms very stable tetramers. To obtain insight into the tetramer-pentamer cytoplasmic switch, we solved the crystal structure of the truncated construct, WSPLB 21-52. This peptide has a heptad sequence repeat with Leu residues at a- and Ile at d-positions from residues 31-52. The crystal structure revealed that WSPLB 21-52 adopted an antiparallel tetrameric coiled coil. This topology contrasts with the parallel topology of an analogue of the coiled-coil of GCN4 with the same Leu(a) Ile(d) repeat. Analysis of these structures revealed how the nature of the partially exposed residues at e- and g-positions influence the topology formed by the bundle. We also constructed a model for the pentameric form of PLB using the coiled-coil parameters derived from a single monomer in the tetrameric structure. This model suggests that both buried and interfacial hydrogen bonds are important for stabilizing the parallel pentamer.

Amino Acid Sequence↗

PubMed2005

De novo design of a redox-active minimal rubredoxin mimic.

Metal-binding sites in metalloproteins frequently occur at the interfaces of elements of secondary structure, which has enabled the retrostructural analysis of natural proteins and the de novo design of helical bundles that bind metal ion cofactors. However, the design of metalloproteins containing beta-structure is less well developed, despite the frequent occurrence of beta-conformations in natural metalloproteins. Here, we describe the design and construction of a beta-protein, RM1, that forms a stable, redox-active 4-Cys thiolate Fe(II/III) site analogous to the active site of rubredoxin. The protein folds into a beta-structure in the presence and absence of metal ions and binds Fe(II/III) to form a redox-active site that is stable to repeated cycles of oxidation and reduction, even in an aerobic environment.

Binding Sites↗

PubMed2005

Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle.

A peptide designed to form a homo-oligomeric transmembrane helical bundle was reconstituted into lipid bilayers and studied by using (2)H NMR (nuclear magnetic resonance) with magic angle spinning to confirm that the helical interface corresponds to the interface intended in the design. The peptide belongs to a family of model peptides derived from a membrane-solubilized version of the water-soluble coiled-coil GCN4-P1. The variant studied here contains two asparagines thought to engage in interhelical hydrogen bonding critical to the formation of a stable trimer. For the NMR studies, three different peptides were synthesized, each with one of three consecutive leucines in the transmembrane region deuterium labeled. Prior to NMR data collection, polarized infrared spectroscopy was used to establish that the peptides were reconstituted in lipid bilayers in a transmembrane helical conformation. The (2)H NMR line shapes of the three different peptides are consistent with a trimer structure formed by the designed peptide that is stabilized by inter-helical hydrogen bonding of asparagines at positions 7 and 14.

Amino Acid Sequence↗

PubMed2005

The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment.

The M2 protein from influenza A virus is a 97-amino-acid protein with a single transmembrane helix that forms proton-selective channels essential to virus function. The hydrophobic transmembrane domain of the M2 protein (M2TM) contains a sequence motif that mediates the formation of functional tetramers in membrane environments. A variety of structural models have previously been proposed which differ in the degree of helix tilt, with proposed tilts ranging from approximately 15 degrees to 38 degrees . An important issue for understanding the structure of M2TM is the role of peptide-lipid interactions in the stabilization of the lipid bilayer bound tetramer. Here, we labeled the N terminus of M2TM with a nitroxide and studied the tetramer reconstituted into lipid bilayers of different thicknesses using EPR spectroscopy. Analyses of spectral changes provide evidence that the lipid bilayer does influence the conformation. The structural plasticity displayed by M2TM in response to membrane composition may be indicative of functional requirements for conformational change. The various structural models for M2TM proposed to date--each defined by a different set of criteria and in a different environment--might provide snapshots of the distinct conformational states sampled by the protein.

Electron Spin Resonance Spectroscopy↗

PubMed2005

A push-pull mechanism for regulating integrin function.

Homomeric and heteromeric interactions between the alphaIIb and beta3 transmembrane domains are involved in the regulation of integrin alphaIIbbeta3 function. These domains appear to interact in the inactivated state but separate upon integrin activation. Moreover, homomeric interactions may increase the level of alphaIIbbeta3 activity by competing for the heteromeric interaction that specifies the resting state. To test this model, a series of mutants were examined that had been shown previously to either enhance or disrupt the homomeric association of the alphaIIb transmembrane domain. One mutation that enhanced the dimerization of the alphaIIb transmembrane domain indeed induced constitutive alphaIIbbeta3 activation. However, a series of mutations that disrupted homodimerization also led to alphaIIbbeta3 activation. These results suggest that the homo- and heterodimerization motifs overlap in the alphaIIb transmembrane domain, and that mutations that disrupt the alphaIIb/beta3 transmembrane domain heterodimer are sufficient to activate the integrin. The data also imply a mechanism for alphaIIbbeta3 regulation in which the integrin can be shifted from its inactive to its active state by destabilizing an alphaIIb/beta3 transmembrane domain heterodimer and by stabilizing the resulting alphaIIb and beta3 transmembrane domain homodimers.

Animals↗

PubMed2004

Volatile anesthetic modulation of oligomerization equilibria in a hexameric model peptide.

To determine if occupancy of interfacial pockets in oligomeric proteins by volatile anesthetic molecules can allosterically regulate oligomerization equilibria, variants of a three-helix bundle peptide able to form higher oligomers were studied with analytical ultracentrifugation, hydrogen exchange and modeling. Halothane shifted the oligomerization equilibria towards the oligomer only in a mutation predicted to create sufficient volume in the hexameric pocket. Other mutations at this residue, predicted to create a too small or too polar pocket, were unaffected by halothane. Inhaled anesthetic modulation of oligomerization interactions is a novel and potentially generalizable biophysical basis for some anesthetic actions.

Allosteric Regulation↗

PubMed2004

Simulated evolution of emergent chiral structures in polyalanine.

The relationship between monomer chirality and polymer structure has been studied using both theoretical and experimental methods. Atomistic models, such as the ones employed in computational protein folding and design, can be used to study the relationship between monomer chirality and the properties of polypeptides. Using a simulated evolution approach that combines side-chain epimerization with backbone flexibility, we recapitulate the relationship between basic forces that drive secondary structure formation and sequence homochirality. Additionally, we find heterochiral motifs including a C-terminal helix capping interaction and stable helix-reversals that result in bent helix structures. Our studies show that simulated evolution of chirality with backbone flexibility can be a powerful tool in the design of novel heteropolymers with tuned stereochemical properties.

Amino Acid Sequence↗

PubMed2004

Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers.

The role of an ortho-alkylthioether group in controlling the conformation around the ring-N bonds of meta-connected arylamide oligomers is studied. Density functional theory (DFT) geometries of model compounds, including acetanilide, an ether acetanilide, and a thioether acetanilide, and their corresponding diamides, show that for either monoamide or diamide the alkyl side chain of the thioether should be perpendicular to the aryl plane, whereas for the ether monoamide, the alkyl side chain is in the aryl plane. DFT ring-N torsional potentials and constrained geometries of the model compounds demonstrate that carbonyl-S repulsion leads to a high torsional barrier and that intramolecular N-H...S and C-H...O hydrogen bonds and ring-amide conjugation lead to N-H having a preferred orientation in the benzene plane pointing towards S. The N-H bond lengthens and the ortho-ring C-H bond shortens in a regular pattern in the approach to the preferred orientation. Calculated IR frequencies for the N-H stretch show a clear red shift between model compounds without and with the thioether side chain.

Amides↗

PubMed2004

Association of a model transmembrane peptide containing gly in a heptad sequence motif.

A peptide containing glycine at a and d positions of a heptad motif was synthesized to investigate the possibility that membrane-soluble peptides with a Gly-based, left-handed helical packing motif would associate. Based on analytical ultracentrifugation in C14-betaine detergent micelles, the peptide did associate in a monomer-dimer equilibrium, although the association constant was significantly less than that reported for the right-handed dimer of the glycophorin A transmembrane peptide in similar detergents. Fluorescence resonance energy transfer (FRET) experiments conducted on peptides labeled at their N-termini with either tetramethylrhodamine (TMR) or 7-nitrobenz-2-oxa-1,3-diazole (NBD) also indicated association. However, analysis of the FRET data using the usual assumption of complete quenching for NBD-TMR pairs in the dimer could not be quantitatively reconciled with the analytical ultracentrifugation-measured dimerization constant. This led us to develop a general treatment for the association of helices to either parallel or antiparallel structures of any aggregation state. Applying this treatment to the FRET data, constraining the dimerization constant to be within experimental uncertainty of that measured by analytical ultracentrifugation, we found the data could be well described by a monomer-dimer equilibrium with only partial quenching of the dimer, suggesting that the helices are most probably antiparallel. These results also suggest that a left-handed Gly heptad repeat motif can drive membrane helix association, but the affinity is likely to be less strong than the previously reported right-handed motif described for glycophorin A.

Amino Acid Motifs↗