Computational characterization of parallel dimeric and trimeric coiled-coils using effective amino acid indices

Chen Li; Xiao-Feng Wang; Zhen Chen; Ziding Zhang; Jiangning Song

doi:10.1039/c4mb00569d

High-resolution structures of a heterochiral coiled coil

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1507918112 ◽

2015 ◽

Vol 112 (43) ◽

pp. 13144-13149 ◽

Cited By ~ 18

Author(s):

David E. Mortenson ◽

Jay D. Steinkruger ◽

Dale F. Kreitler ◽

Dominic V. Perroni ◽

Gregory P. Sorenson ◽

...

Keyword(s):

Protein Interactions ◽

Structural Information ◽

Coiled Coil ◽

Coiled Coils ◽

Side Chain ◽

Amino Acid Residues ◽

Protein Protein Interactions ◽

Polypeptide Chains ◽

Packing Interactions

Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from d amino acids (d peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious protein–protein interactions. Coiled–coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled–coil interactions were predicted over 50 years ago by Crick, and limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report two independent crystal structures that elucidate coiled-coil packing between l- and d-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. However, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.

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Isolation and characterization of keratin-like proteins from cultured cells with fibroblastic morphology.

The Journal of Cell Biology ◽

10.1083/jcb.98.4.1231 ◽

1984 ◽

Vol 98 (4) ◽

pp. 1231-1237 ◽

Cited By ~ 50

Author(s):

R V Zackroff ◽

A E Goldman ◽

J C Jones ◽

P M Steinert ◽

R D Goldman

Keyword(s):

Amino Acid ◽

Secondary Structure ◽

Cultured Cells ◽

Coiled Coil ◽

Uranyl Acetate ◽

3T3 Cells ◽

Immunological Properties ◽

Molecular Weights ◽

Isolation And Characterization

Intermediate filaments (IF) isolated from a variety of cultured cells, conventionally described as fibroblasts, are composed predominantely of proteins of molecular weights of 54,000 and/or 55,000. Less than 15% of the protein found in native IF preparations from these cells is composed of three to four polypeptides of molecular weights 60,000-70,000. We have investigated some biochemical and immunological properties of these proteins isolated from BHK-21 and mouse 3T3 cells. They are capable of forming paracrystals that exhibit a light/dark banding pattern when negatively stained with uranyl acetate. The dark bands are composed of longitudinally aligned approximately 2-nm-diam filaments. The center-to-center spacing between either dark or light bands is 37-40 nm. These dimensions are consistent with the secondary structure of IF polypeptides and suggest that the dark bands represent lateral alignment of alpha-helical coiled-coil domains. Immunoblotting, secondary structure, as well as amino acid composition data indicate that the 60,000-70,000-mol-wt paracrystal polypeptides are similar to keratin. Thus, polypeptides with biochemical and immunological properties of epidermal keratin are present in cells normally considered to be fibroblasts.

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Oligomerization of hantaviral nucleocapsid protein: charged residues in the N-terminal coiled-coil domain contribute to intermolecular interactions

Journal of General Virology ◽

10.1099/vir.0.2008/004044-0 ◽

2008 ◽

Vol 89 (9) ◽

pp. 2167-2174 ◽

Cited By ~ 11

Author(s):

Agne Alminaite ◽

Vera Backström ◽

Antti Vaheri ◽

Alexander Plyusnin

Keyword(s):

Amino Acid ◽

Virus Assembly ◽

Coiled Coil ◽

Coiled Coils ◽

Substantial Contribution ◽

Protein Oligomerization ◽

Amino Acid Residues ◽

N Protein ◽

To Come ◽

Interacting Surfaces

The nucleocapsid (N) protein of hantaviruses (family Bunyaviridae) is the most abundant component of the virion; it encapsidates genomic RNA segments and participates in viral genome transcription and replication, as well as in virus assembly. During RNA encapsidation, the N protein forms intermediate trimers and then oligomers via ‘head-to-head, tail-to-tail’ interactions. In previous work, using Tula hantavirus (TULV) N protein as a model, it was demonstrated that an intact coiled-coil structure of the N terminus is crucial for the oligomerization capacity of the N protein and that the hydrophobic ‘a’ residues from the second α-helix are especially important. Here, the importance of charged amino acid residues located within the coiled-coil for trimer formation and oligomerization was analysed. To predict the interacting surfaces of the monomers, the previous in silico model of TULV coiled-coils was first upgraded, taking advantage of the recently published crystal structure of the N-terminal coiled-coil of the Sin Nombre virus N protein. The results obtained using a mammalian two-hybrid assay suggested that conserved, charged amino acid residues within the coiled-coil make a substantial contribution to N protein oligomerization. This contribution probably involves (i) the formation of interacting surfaces of the N monomers (residues D35 and D38, located at the tip of the coiled-coil loop, and R63 appear particularly important) and (ii) stabilization of the coiled-coil via intramolecular ionic bridging (with E55 as a key player). It is hypothesized that the tips of the coiled-coils are the first to come into direct contact and thus to initiate tight packing of the three structures.

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PURIFICATION AND PARTIAL CHEMICAL CHARACTERIZATION OF SHEEP NEUROPHYSIN

Acta Endocrinologica ◽

10.1530/acta.0.0740226 ◽

1973 ◽

Vol 74 (2) ◽

pp. 226-236 ◽

Cited By ~ 6

Author(s):

Michel Chrétien ◽

Claude Gilardeau

Keyword(s):

Amino Acid ◽

Polyacrylamide Gel Electrophoresis ◽

Chemical Characterization ◽

Terminal Amino Acid ◽

Amino Acid Determination ◽

Pituitary Glands ◽

Terminal Amino ◽

Partial Chemical ◽

Acid Determination

ABSTRACT A protein isolated from ovine pituitary glands has been purified, and its homogeneity assessed by NH2- and COOH-terminal amino acid determination, ultracentrifugation studies, and polyacrylamide gel electrophoresis after carboxymethylation. Its chemical and immunochemical properties are closely similar to those of beef and pork neurophysins, less similar to those of human neurophysins. It contains no tryptophan (like other neurophysins) or histidine (like all except bovine neurophysin-I and human neurophysins). It has alanine at the NH2-terminus and valine at the COOH-terminus. Its amino acid composition is similar to, but not identical with those of porcine and bovine neurophysins.

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