Local repulsion in protein structures as revealed by a charge distribution analysis of all amino acid sequences from the<i>Saccharomyces cerevisiae</i>genome

Ke, Runcong; Mitaku, Shigeki

doi:10.1088/0953-8984/17/31/007

Cited by 7 publications

(5 citation statements)

References 7 publications

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“…10 A ). The resulting distribution of charges is comparable to what has been observed for the entire proteome of Saccharomyces cerevisiae ( 55 ) and indicates that peripheral membrane-binding proteins do not display a distribution of net charges skewed toward positive values. In fact, approximately one-third of the protein families classified as peripheral/monotopic in OPM have on average three or fewer basic amino acids within 10 Å of the membrane surface in their predicted membrane-bound state.…”

Section: Discussionsupporting

confidence: 78%

A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding

Fuglebakk

et al. 2016

Biophysical Journal

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Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) is a secreted virulence factor that binds specifically to phosphatidylcholine (PC) bilayers containing negatively charged phospholipids. BtPI-PLC carries a negative net charge and its interfacial binding site has no obvious cluster of basic residues. Continuum electrostatic calculations show that, as expected, nonspecific electrostatic interactions between BtPI-PLC and membranes vary as a function of the fraction of anionic lipids present in the bilayers. Yet they are strikingly weak, with a calculated ΔGel below 1 kcal/mol, largely due to a single lysine (K44). When K44 is mutated to alanine, the equilibrium dissociation constant for small unilamellar vesicles increases more than 50 times (∼2.4 kcal/mol), suggesting that interactions between K44 and lipids are not merely electrostatic. Comparisons of molecular-dynamics simulations performed using different lipid compositions reveal that the bilayer composition does not affect either hydrogen bonds or hydrophobic contacts between the protein interfacial binding site and bilayers. However, the occupancies of cation-π interactions between PC choline headgroups and protein tyrosines vary as a function of PC content. The overall contribution of basic residues to binding affinity is also context dependent and cannot be approximated by a rule-of-thumb value because these residues can contribute to both nonspecific electrostatic and short-range protein-lipid interactions. Additionally, statistics on the distribution of basic amino acids in a data set of membrane-binding domains reveal that weak electrostatics, as observed for BtPI-PLC, might be a less unusual mechanism for peripheral membrane binding than is generally thought.

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Section: Discussionsupporting

confidence: 78%

A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding

Fuglebakk

et al. 2016

Biophysical Journal

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“…A previous analysis of the autocorrelation of the charge distribution in proteins from Saccharomyces cerevisiae showed no significant periodicity but only a broad positive correlation. 8) In contrast, we found a significant charge periodicity of 28 residues for total proteins in the human genome. This finding suggests that the number of PCP28 has increased in the process of evolution from single-celled eukaryotes to humans.…”

Section: Resultscontrasting

confidence: 56%

“…Figure 4 shows the distribution of the net electric charge of the two types of proteins. We previously analyzed the distribution of the net electric charge of all amino acid sequences from the genomes of Saccharomyces cerevisiae and Drosophila melanogaster, 8,9) leading to the Gaussian distribution of approximately zero. The net charge distribution of non-PCP28 from the human genome also had a Gaussian distribution of approximately zero, indicating that the total charge of this type of protein is almost randomly distributed.…”

Section: Resultsmentioning

confidence: 99%

Human Genome Encodes Many Proteins with Charge Periodicity of 28 Residues

Sakiyama

Sawada

et al. 2007

jjap

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We discuss the signatures of non-Gaussianity in the curvaton model where the potential includes also a non-quadratic term. In such a case the non-linearity parameter f NL can become very small, and we show that non-Gaussianity is then encoded in the non-reducible non-linearity parameter g NL of the trispectrum, which can be very large. Thus the place to look for the non-Gaussianity in the curvaton model may be the trispectrum rather than the bispectrum. We also show that g NL measures directly the deviation of the curvaton potential from the purely quadratic form. While g NL depends on the strength of the non-quadratic terms relative to the quadratic one, we find that for reasonable cases roughly g NL ∼ O(−10 4 )-O(−10 5 ), which are values that may well be accessible by future observations. Keywords: cosmological perturbation theory, cosmology of theories beyond the SM, physics of the early universe ArXiv ePrint: 0807.3069

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“…Similarly, the electrostatic interactions are predominant in disordered proteins. Earlier work 36 suggests that the electrostatic interactions in proteins are predominantly repulsive. Due to strong repulsive forces, a disordered protein cannot fold to a single minimally frustrated native conformation.…”

Section: Resultsmentioning

confidence: 99%

Globular–disorder transition in proteins: a compromise between hydrophobic and electrostatic interactions?

Baruah

Biswas

2016

Phys. Chem. Chem. Phys.

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The charge-hydrophobicity correlation of globular and disordered proteins is explored using a generalized self-consistent field theoretical method combined with Monte Carlo simulations. Globular and disordered protein sequences with varied mean net charge and mean hydrophobicity are designed by theory, while Metropolis Monte Carlo generates a suitable ensemble of conformations. Results imply a transition of the dominant interactions between globular and disordered proteins across the charge-hydrophobicity boundary. It is observed that the charge-hydrophobicity boundary actually represents a trade-off between the repulsive and attractive interactions in a protein sequence. The attractive interactions predominate on the globular side of the boundary, while the repulsive interactions prevail on the disordered side. For globular proteins, core forming hydrophobic interactions are dominant leading to a minimally frustrated native conformation. For disordered proteins, the repulsive electrostatic interactions prevail yielding a minimally frustrated region comprising of an expanded, dynamic conformational ensemble. Thus, protein disorder, like protein folding, satisfies the principle of minimal frustration. All results are compared to real globular and disordered proteins. Thus this algorithm may be useful to probe the conformational characteristics of disordered proteins.

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Local repulsion in protein structures as revealed by a charge distribution analysis of all amino acid sequences from theSaccharomyces cerevisiaegenome

Cited by 7 publications

References 7 publications

A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding

A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding

Human Genome Encodes Many Proteins with Charge Periodicity of 28 Residues

Globular–disorder transition in proteins: a compromise between hydrophobic and electrostatic interactions?

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