Omnipresence of the polyproline II helix in fibrous and globular proteins

Ng, Esipova; Tumanyan, V. G.

doi:10.1016/j.sbi.2016.10.012

Cited by 15 publications

(6 citation statements)

References 72 publications

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“…The quotes on hydrogen bond indicate that the N–H–O angles are not restricted so as to indicate a true hydrogen bond. However, the 1–3 HB definition turns out to be a good indication of the PPII structure. , We find that for this work, there are essentially no 1–4 HBs, but many 1–3 distances that do correspond in some cases to the PPII helix geometry.…”

Section: Methodsmentioning

confidence: 61%

“…It is of interest to interrogate hydrogen bonding and PPII structure patterns as these are residue specific versus, for example, overall geometric measures. The α helical HBs are defined as residue i to i + 4 N–H to O distances less than 3.5 Å and for PPII characterization , residue i to i + 3 N–H to O distances less than 3.5 Å. For all of the peptides, there are no α helical (1–4) HBs.…”

Section: Resultsmentioning

confidence: 99%

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Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain

Cukier

2018

J. Phys. Chem. B

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Intrinsically disordered proteins (IDPs), involved in regulatory pathways and cell signaling, sample a range of conformations. Constructing structural ensembles of IDPs is a difficult task for both experiment and simulation. In this work, we produce potential IDP ensembles using an existing database of pair residue φ and ψ angle probabilities chosen from turn, coil, and bend parts of sequences from the Protein Data Bank. For all residue pair types, a k-means-based discretization is used to create a set of rotamers and their probabilities in this pair Ramachandran space. For a given sequence, a Markov-based probabilistic algorithm is used to create Ramachandran space database-Markov ensembles that are converted to Cartesian coordinates of the backbone atoms. From these Cartesian coordinates and φ and ψ dihedral angles of a sequence, various observables: the radius of gyration and shape parameters, the distance probability distribution that is related to the small-angle X-ray scattering intensity, atom-atom contact percentages, local structural information, NMR three-bond J couplings, CA chemical shifts, and residual dipolar couplings are evaluated. A benchmark set of ensembles for 16 residue, regular sequences is constructed and used to validate the method and to explore the implications of the database for some of the above-mentioned observables. Then, we examine a set of nonapeptides of the form EGAAXAASS where X denotes residues of different characters. These peptides were studied by NMR, and subsequent molecular dynamics (MD) simulations were carried out using various force fields to find which one best agrees with the NMR data. Our analysis of these peptides shows that the combination of the database and the Markov algorithm yields ensembles that agree very well with the NMR and MD results for the above-listed observables. Thus, this database-Markov method is a promising method to generate IDP conformational ensembles.

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Section: Methodsmentioning

confidence: 61%

Section: Resultsmentioning

confidence: 99%

Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain

Cukier

2018

J. Phys. Chem. B

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“…An extended site II was identified as a major site interacting with calnexin. Part of this site is formed by a left-handed polyproline-II helix (PPII) GLY71-GLN77, which is known as a preferable structure for protein-protein interactions [30] [31]. A range of interaction sites are present in calnexin in different models.…”

Section: Resultsmentioning

confidence: 99%

Modelling interaction between HIV-1 Nef and calnexin

Adzhubei

Anashkina

Tkachev

et al. 2018

Aids

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“…Nevertheless, almost all are based on combinations of a-helices or β-sheets or both, but largely ignore polyproline II (PPII) helices (2). In nature, PPII helices are common as they are the main component of collagen, the most abundant human protein, and most globular proteins contain at least one turn of PPII helix (3)(4)(5). Moreover, a small protein class, recently reviewed (6), which includes snow flea antifreeze proteins (sfAFP) (7), bacteriophage tail spike proteins (8), the enzyme acetophenone carboxylase (9), the universally conserved translation factor Obg (10) and the recently discovered anaplastic lymphoma kinase (11) consist of or contain glycine-rich PPII helical bundle domains.…”

Section: Introductionmentioning

confidence: 99%

Insight into Polyproline II Helical Bundle Stability and Folding from NMR Spectroscopic Characterization of the Snow Flea Antifreeze Protein Denatured State

Treviño

Moya

Sánchez

et al. 2022

Preprint

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The use of PPII helices in protein design is currently hindered by limitations in our understanding of their conformational stability and folding. Recent studies of the snow flea antifreeze protein (sfAFP), a useful model system composed of six PPII helices, suggested that a low denatured state entropy contributes to folding thermodynamics. To get atomic level information on the conformational ensemble and entropy of the reduced denatured state of sfAFP, we have analyzed its chemical shifts and {1H}-15N relaxation parameters by NMR spectroscopy at three experimental conditions. No significant populations of preferred secondary structure were detected. The stiffening of certain N-terminal residues at neutral versus acidic pH leads us to suggest that favorable charge-charge interactions could bias the conformational ensemble to favor the formation of the two disulfide bonds during nascent folding. Despite a high content of flexible glycine residues, the mobility of the sfAFP denatured ensemble is similar for denatured α/β proteins both on fast ps/ns as well as slower μs/ms timescales. These results are in line with a conformational entropy in the denatured ensemble resembling that of typical proteins and suggest that new structures based on PPII helical bundles should be amenable to protein design.

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Omnipresence of the polyproline II helix in fibrous and globular proteins

Cited by 15 publications

References 72 publications

Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain

Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain

Modelling interaction between HIV-1 Nef and calnexin

Insight into Polyproline II Helical Bundle Stability and Folding from NMR Spectroscopic Characterization of the Snow Flea Antifreeze Protein Denatured State

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