A simple method for displaying the hydropathic character of a protein

Kyte, Jack; Doolittle, Russell F.

doi:10.1016/0022-2836(82)90515-0

Cited by 21,465 publications

(12,849 citation statements)

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“…To determine whether the characteristics of the initial peptide could explain the mitoribosome profiles we inspected the hydropathicity predictions of the initial 10 amino acids of transcripts described above. Using ExPASy programmes where a positive score indicates hydrophobicity 36, 37 , these products were predicted to generate hydrophobic peptides. The most hydrophobic was the translation product of MTND4 with a hydrophobicity score of 1.84, followed by MTND3 (1.80), then MTCO2 and MTND2 both with a score 0.47.…”

Section: Resultsmentioning

confidence: 99%

Using mitoribosomal profiling to investigate human mitochondrial translation

et al. 2017

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Background: Gene expression in human mitochondria has various idiosyncratic features. One of these was recently revealed as the unprecedented recruitment of a mitochondrially-encoded tRNA as a structural component of the large mitoribosomal subunit. In porcine particles this is mt-tRNA Phe whilst in humans it is mt-tRNA Val. We have previously shown that when a mutation in mt-tRNA Val causes very low steady state levels, there is preferential recruitment of mt-tRNA Phe. We have investigated whether this altered mitoribosome affects intra-organellar protein synthesis. Methods: By using mitoribosomal profiling we have revealed aspects of mitoribosome behaviour with its template mt-mRNA under both normal conditions as well as those where the mitoribosome has incorporated mt-tRNA Phe. Results: Analysis of the mitoribosome residency on transcripts under control conditions reveals that although mitochondria employ only 22 mt-tRNAs for protein synthesis, the use of non-canonical wobble base pairs at codon position 3 does not cause any measurable difference in mitoribosome occupancy irrespective of the codon. Comparison of the profile of aberrant mt-tRNA Phe containing mitoribosomes with those of controls that integrate mt-tRNA Val revealed that the impaired translation seen in the latter was not due to stalling on triplets encoding either of these amino acids. The alterations in mitoribosome interactions with start codons was not directly attributable to the either the use of non-cognate initiation codons or the presence or absence of 5’ leader sequences, except in the two bicistronic RNA units, RNA7 and RNA14 where the initiation sites are internal. Conclusions: These data report the power of mitoribosomal profiling in helping to understand the subtleties of mammalian mitochondrial protein synthesis. Analysis of profiles from the mutant mt-tRNA Val cell line suggest that despite mt-tRNA Phe being preferred in the porcine mitoribosome, its integration into the human counterpart results in a suboptimal structure that modifies its interaction with mt-mRNAs.

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Section: Resultsmentioning

confidence: 99%

Using mitoribosomal profiling to investigate human mitochondrial translation

et al. 2017

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“…If available, a three-dimensional model of the protein would indicate the accessibility of the sites for interaction. Hydrophilicity [22,23], flexibility [24] and surface accessibility [25] may also assist in the prediction. Additional information is helpful, but not essential for the prediction of interaction sites.…”

Section: Novel Methods For Prediction Of Interaction Sitesmentioning

confidence: 99%

Prediction of potential protein‐protein interaction sites from amino acid sequence

Kini

Evans

1996

FEBS Letters

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“…In fact, cysteine is intermediate between alanine and valine both in volume 14 and in the Kyte and Doolittle hydropathy scale. 15 Moreover, hydrogen bonds between the Cys thiol and backbone carbonyl oxygens' would be expected to be much weaker than those commonly observed from the Ser or Thr alcohol, due to the poorer pK A match of the thiol proton. The BLOSUM62 matrix 16 shows that the highest probability substitution throughout evolution of Cys is for Ala (log-odds of zero), followed by Ile, Leu, Met, Ser, Thr, and Val (log-odds of À1).…”

Section: Introductionmentioning

confidence: 99%

Cysteine‐free rop: A four‐helix bundle core mutant has wild‐type stability and structure but dramatically different unfolding kinetics

et al. 2010

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Cysteine residues can complicate the folding and storage of proteins due to improper formation of disulfide bonds or oxidation of residues that are natively reduced. Wild-type Rop is a homodimeric four-helix bundle protein and an important model for protein design in the understanding of protein stability, structure and folding kinetics. In the native state, Rop has two buried, reduced cysteine residues in its core, but these are prone to oxidation in destabilized variants, particularly upon extended storage. To circumvent this problem, we designed and characterized a Cys-free variant of Rop, including solving the 2.3 Å X-ray crystal structure. We show that the C38A C52V variant has similar structure, stability and in vivo activity to wild-type Rop, but that it has dramatically faster unfolding kinetics like virtually every other mutant of Rop that has been characterized. This cysteine-free Rop has already proven useful for studies on solution topology and on the relationship of core mutations to stability. It also suggests a general strategy for removal of pairs of Cys residues in proteins, both to make them more experimentally tractable and to improve their storage properties for therapeutic or industrial purposes.

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A simple method for displaying the hydropathic character of a protein

Cited by 21,465 publications

References 58 publications

Using mitoribosomal profiling to investigate human mitochondrial translation

Using mitoribosomal profiling to investigate human mitochondrial translation

Prediction of potential protein‐protein interaction sites from amino acid sequence

Cysteine‐free rop: A four‐helix bundle core mutant has wild‐type stability and structure but dramatically different unfolding kinetics

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