Conservation of chain reversal regions in proteins

Chou, Peter Y.; Fasman, Gerald D.

doi:10.1016/s0006-3495(79)85260-1

Cited by 26 publications

(6 citation statements)

References 44 publications

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“…The secondary structures of the bacterial enzymes, predicted by the method of McLachlan [40], have been reported [41]. We have extended the secondary structure analysis to the mitochondrial Mn enzyme of yeast using the Chou and Fasman rules [42] (Fig. 6).…”

Section: Dna Sequence Analysismentioning

confidence: 99%

Nucleotide sequence analysis of the nuclear gene coding for manganese superoxide dismutase of yeast mitochondria, a gene previously assumed to code for the Rieske iron‐sulphur protein

Marres¹,

Loon

Oudshoorn³

et al. 1985

European Journal of Biochemistry

126

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We have previously reported the isolation of the gene coding for a 25‐kDa polypeptide present in a purified yeast QH2:cytochrome c oxidoreductase preparation, which was thus identified as the gene for the Rieske ironsulphur protein [Van Loon et al. (1983) Gene 26, 261–272]. Subsequent DNA sequence analysis reported here reveals, however, that the encoded protein is in fact manganese superoxide dismutase, a mitochondrial matrix protein. Comparison with the known amino acid sequence of the mature protein indicates that it is synthesized with an N‐terminal extension of 27 amino acids. In common with the N‐terminal extensions of other imported mitochondrial proteins, the presequence has several basic residues but lacks negatively charged residues. The function of these positive charges and other possible topogenic sequences are discussed. Sequences 5′ of the gene contain two elements that may be homologous to the suggested regulatory sites, UAS 1 and UAS 2 in the yeast CYC1‐gene [Guarente et al. (1984) Cell 36, 503–511]. The predicted secondary structures in manganese superoxide dismutase appear to be very similar to those reported for iron superoxide dismutase, suggesting similar three‐dimensional structures. Making use of the known three‐dimensional structure of the Fe enzyme, the Mn ligands are predicted.

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Section: Dna Sequence Analysismentioning

confidence: 99%

Nucleotide sequence analysis of the nuclear gene coding for manganese superoxide dismutase of yeast mitochondria, a gene previously assumed to code for the Rieske iron‐sulphur protein

Marres¹,

Loon

Oudshoorn³

et al. 1985

European Journal of Biochemistry

126

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“…Beta-turns in beta-hairpins, which are generally found on a protein surface, are a common structural feature in protein structures that play a key role in reversing the direction of the polypeptide chain and forming the compact globular state of a protein. 1,2 In addition, they often play a variety of functional roles in proteins, such as the binding sites in antibodies and active sites of enzymes. 3 Over the past two decades, the crucial roles of beta-hairpin turns in protein folding and stability have been reported in many protein and peptide engineering studies.…”

Section: Introductionmentioning

confidence: 99%

“…The main motivations of this study were as follows. (1) Many studies have examined the sequences and structures of beta-turns in proteins, but only a few studies focused on two residue beta-hairpin turns. Moreover, those studies were performed mainly 15-20 years ago, therefore a very small number of turn structures obtained from the Protein Data Bank (PDB) 15 was used in the analyses.…”

Section: Introductionmentioning

confidence: 99%

Structural and sequence features of two residue turns in beta-hairpins

2014

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Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences.

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“…β ‐turns are the most abundant secondary structural elements that connect the strands of β ‐hairpins . They play a key role in protein folding by assisting in folding the polypeptide chain back onto itself .…”

Section: Introductionmentioning

confidence: 99%

Redesigning the type II' β -turn in green fluorescent protein to type I': Implications for folding kinetics and stability

et al. 2014

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Both Type I' and Type II' β-turns have the same sense of the β-turn twist that is compatible with the β-sheet twist. They occur predominantly in two residue β-hairpins, but the occurrence of Type I' β-turns is two times higher than Type II' β-turns. This suggests that Type I' β-turns may be more stable than Type II' β-turns, and Type I' β-turn sequence and structure can be more favorable for protein folding than Type II' β-turns. Here, we redesigned the native Type II' β-turn in GFP to Type I' β-turn, and investigated its effect on protein folding and stability. The Type I' β-turns were designed based on the statistical analysis of residues in natural Type I' β-turns. The substitution of the native "GD" sequence of i+1 and i+2 residues with Type I' preferred "(N/D)G" sequence motif increased the folding rate by 50% and slightly improved the thermodynamic stability. Despite the enhancement of in vitro refolding kinetics and stability of the redesigned mutants, they showed poor soluble expression level compared to wild type. To overcome this problem, i and i + 3 residues of the designed Type I' β-turn were further engineered. The mutation of Thr to Lys at i + 3 could restore the in vivo soluble expression of the Type I' mutant. This study indicates that Type II' β-turns in natural β-hairpins can be further optimized by converting the sequence to Type I'.

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Conservation of chain reversal regions in proteins

Cited by 26 publications

References 44 publications

Nucleotide sequence analysis of the nuclear gene coding for manganese superoxide dismutase of yeast mitochondria, a gene previously assumed to code for the Rieske iron‐sulphur protein

Nucleotide sequence analysis of the nuclear gene coding for manganese superoxide dismutase of yeast mitochondria, a gene previously assumed to code for the Rieske iron‐sulphur protein

Structural and sequence features of two residue turns in beta-hairpins

Redesigning the type II' β -turn in green fluorescent protein to type I': Implications for folding kinetics and stability

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