Prediction of chain flexibility in proteins

Karplus, P.A.; Schulz, Georg E.

doi:10.1007/bf01195768

Cited by 1,086 publications

(510 citation statements)

References 13 publications

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“…The amino acid propensities calculated here for the buried surface exhibit a strong inverse correlation of -0.84 with the mean B,,, flexibility parameters used to predict mobility (Karplus & Schulz, 1985). Similarly, the amino acid propensities for "empty" cavities at intradomain, interdomain, and intersubunit surfaces show correlations of -0.67, -0.74, and -0.41, respectively, with the Karplus and Schulz parameters.…”

Section: Mobility Of Cavity Atoms and Solventmentioning

confidence: 53%

Cavities and packing at protein interfaces

1994

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An analysis of internal packing defects or "cavities" (both empty and water-containing) within protein structures has been undertaken and includes 3 cavity classes: within domains, between domains, and between protein subunits. We confirm several basic features common to all cavity types but also find a number of new characteristics, including those that distinguish the classes. The total cavity volume remains only a small fraction of the total protein volume and yet increases with protein size. Water-filled "cavities" possess a more polar surface and are typically larger. Their constituent waters are necessary to satisfy the local hydrogen bonding potential. Cavitysurrounding atoms are observed to be, on average, less flexible than their environments. Intersubunit and interdomain cavities are on average larger than the intradomain cavities, occupy a larger fraction of their resident surfaces, and are more frequently water-filled. We observe increased cavity volume at domain-domain interfaces involved with shear type domain motions. The significance of interfacial cavities upon subunit and domain shape complementarity and the protein docking problem, as well as in their structural and functional role in oligomeric proteins, will be discussed. The results concerning cavity size, polarity, solvation, general abundance, and residue type constituency should provide useful guidelines for protein modeling and design.

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Section: Mobility Of Cavity Atoms and Solventmentioning

confidence: 53%

Cavities and packing at protein interfaces

1994

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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 addition, the epitope 147-154 belongs to part of the RNA binding site of La/SSB protein. All four epitopes presented features of high antigenicity [23], had high ratios of hydrophilic amino acids, commonly found in B cell epitopes [24], and moderate to high flexibilities [25]. The epitopes HKAFKGSI (147-154) and VTWEVLEGE-VEKEALKKI (301-318) possessed features of putative T cell epitopes by three of four methods used for T cell epitope predictability [26][27][28].…”

Section: Alanine Substitutions Predicted Features and Molecular Simimentioning

confidence: 99%

Fine specificity of autoantibodies to La/SSB: epitope mapping, and characterization

Tzioufas

Yiannaki

Sakarellos‐Daitsiotis

et al. 1997

Clinical and Experimental Immunology

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SUMMARYThe B cell epitope mapping of La/SSB was performed using 20 mer synthetic peptides overlapping by eight amino acids covering the whole sequence of the protein. IgG, purified from sera of five patients with systemic lupus erythematosus (SLE) and four sera from patients with primary Sjögren's syndrome (pSS) were tested against the overlapping synthetic peptides. Peptides highly reactive with purified IgG were those spanning the regions 145-164, 289-308, 301-320 and 349-368 364 . Predicted features and molecular similarities of the defined epitopes were investigated using protein databases. The La epitope 147 HKAFKGSI 154 presented 83·3% similarity with the 139 HKGFKGVD 146 region of human myelin basic protein (MBP) and 72% similarity with the fragment YKNFKGTI of human DNA topoisomerase II. Peptides corresponding to these sequences cross-reacted with anti-La/SSB antibodies. Sixty-three sera with anti-La/SSB antibodies from patients with pSS or SLE, 35 sera without anti-La/SSB antibodies from patients with SS or SLE and 41 sera from age/sex-matched healthy blood donors were tested against biotinylated synthetic epitope analogues in order to determine their sensitivity and specificity for the detection of anti-La/SSB antibodies. Anti-La/SSB were detected with various frequencies ranging from 20% to epitope 147 HKAFKGSI 154 to 100% to epitope 349 GSGKGKVQGKKTKF 364 . The overall sensitivity and specificity using all assays with the synthetic peptides were found to be 93·6% and 85·6%, respectively. In conclusion, antibodies to La/SSB constitute a heterogeneous population, directed against different linear B cell epitopes of the molecule. The epitope 147 HKAFKGSI 154 presents molecular similarity with fragments of two other autoantigens, i.e. human MBP and DNA topoisomerase II. Finally, synthetic epitope analogues exhibit high sensitivity and specificity for the detection of anti-La/SSB antibodies.

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Prediction of chain flexibility in proteins

Cited by 1,086 publications

References 13 publications

Cavities and packing at protein interfaces

Cavities and packing at protein interfaces

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

Fine specificity of autoantibodies to La/SSB: epitope mapping, and characterization

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