A synthetic polypeptide with a compact structure and its self‐organization

Ануфриева, Е. В.; Bychkova, Valentina E.; Krakovyak, M. G.; Паутов, В. Д.; Ptitsyn, Oleg B.

doi:10.1016/0014-5793(75)80953-7

Cited by 27 publications

(24 citation statements)

References 7 publications

(9 reference statements)

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“…Random protein sequences are nearly as structured or more structured than natural sequences. This finding, based on disorder prediction and prediction of secondary structure, is consistent with several experimental examinations of sequences from random co-polymerization of mixed amino-acid N -carboxyanhydrides [ 6 , 7 ], random three residue types (Q, R, and L) of 70–90 amino acid residues [ 8 ], random 120-amino-acid sequences of 20 and 12 residue types [ 9 ], random 50-residue proteins [ 10 ], and random 71-residue proteins [ 11 ]. These experimental studies showed that random sequences have compact structures, cooperative unfolding, secondary structures, and/or protected from serine protease thrombin.…”

Section: Discussionsupporting

confidence: 90%

“…Artificial proteins with random sequences have been studied experimentally. Random co-polymerization of mixed amino-acid N -carboxyanhydrides was shown to produce compact structures similar to proteins [ 6 , 7 ]. Random sequences of three residue types (Q, R, and L) of 70–90 amino acid residues were expressed in E. coli and shown to have secondary structures and cooperative unfolding [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

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Natural protein sequences are more intrinsically disordered than random sequences

Cao

Yang

et al. 2016

Cell. Mol. Life Sci.

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Most natural protein sequences have resulted from millions or even billions of years of evolution. How they differ from random sequences is not fully understood. Previous computational and experimental studies of random proteins generated from noncoding regions yielded inclusive results due to species-dependent codon biases and GC contents. Here, we approach this problem by investigating 10,000 sequences randomized at the amino acid level. Using well-established predictors for protein intrinsic disorder, we found that natural sequences have more long disordered regions than random sequences, even when random and natural sequences have the same overall composition of amino acid residues. We also showed that random sequences are as structured as natural sequences according to contents and length distributions of predicted secondary structure, although the structures from random sequences may be in a molten globular-like state, according to molecular dynamics simulations. The bias of natural sequences toward more intrinsic disorder suggests that natural sequences are created and evolved to avoid protein aggregation and increase functional diversity.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Natural protein sequences are more intrinsically disordered than random sequences

Cao

Yang

et al. 2016

Cell. Mol. Life Sci.

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“…According to a wide-spread conception, the formation of the protein globular structure requires the amino acid sequence strategically chosen in the course of evolution (see, for example, Flory, 1969). However, it has been shown in our laboratory (Bychkova et al 1975;Anufrieva et al 1975;Bychkova et al 1980;Semisotnov et al 1980) that it is possible to isolate from random copolymers of non-polar residue (leucine) with polar residue (glutamic acid) the non-aggregating fractions which, at deionization of glutamic acid residues, are able to acquire globular structures possessing a high degree of helicity.…”

Section: =mentioning

confidence: 95%

Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding?

Ptitsyn

Finkelstein

1980

Quart. Rev. Biophys.

195

113

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(A) Evolutionary similarities of protein structures Two decades have passed from the time that the three dimensional structure of the first globular protein, sperm whale myoglobin, was decoded (Kendrew et al. 1960). Its structure, which now looks so simple and habitual, then seemed to be unusually complicated. The decoding of the subsequent proteins, lysozyme (Blake et al. 1965), ribonuclease (Kartha, Bello & Harker, 1967), chymotrypsin (Matthews et al. 1967), carboxypeptidase (Lipscomb et al. 1969) redoubled the feeling of amazement and even of some confusion before the extremely complicated, intricate and, above all, absolutely unlike protein structures. Some consolation against this background was the evident and far-reaching similarity between the three-dimensional structures of myoglobin and hemoglobin subunits (Perutz, Kendrew & Watson, 1965) and an analogous similarity between the structures of chymotrypsin and other serine proteases, elastase (Shotton & Watson, 1970) and trypsin (Stroud, Kay & Dickerson, 1972). However this similarity was easily explained by the far-reaching homology between the primary structures of myoglobin and hemoglobin and between the primary structures of serine proteases.

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“…Using Eqs. (3) and (4) it is possible to calculate from these dependences the average time of "slow" relaxation processes r and the relative contribution of "fast" relaxation processes to the decrease in luminescence polarization f. [The correction distinguishing Eq. (4') from Eq.…”

Section: Separation Of "Fast" and "Slow" Relaxation Processes For Coimentioning

confidence: 99%

Polarized luminescence and mobility of tryptophan residues in polypeptide chains

et al. 1981

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SynopsisPolarized luminescence was used to study the mobility of tryptophan residues in polypeptide chains of different chemical composition and structural organization. It has been shown that the luminescence depolarization of tryptophan residues in coillike, helical, and p-structural polypeptide chains is mainly caused by "fast" torsional vibrations and "slow" rotational isomerization of indole groups of tryptophan side chains. The characteristics of these types of motions are practically the same for tryptophan residues included in coillike chains of different chemical structure. Helix-coil transitions in copolymers of glutamic acid and lysine with tryptophan (Glu, Trp) and (Lys, Trp) (where side groups of tryptophan residues weakly interact with the surrounding side groups) do not appreciably change the amplitude of torsional vibrations or rotational isomerization. At the same time, in the helical state of glutamic acid-leucine-tryptophan copolymers (Glu, Leu, Trp) and in the p-structural state of (Lys, Trp) copolymers (where direct interactions of Trp side groups with other side groups are possible), the amplitudes of the torsional vibrations are smaller and the rotational isomerization times larger than in the coil. The transition of (Glu, Leu, Trp) polypeptide chains into a compact state is accompanied by a marked decrease of both "fast" and "slow" intramolecular mobility and by an increase of the contribution made by the rotation of the macromolecule as a whole, as shown by the decrease of the luminescence polarization.

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A synthetic polypeptide with a compact structure and its self‐organization

Cited by 27 publications

References 7 publications

Natural protein sequences are more intrinsically disordered than random sequences

Natural protein sequences are more intrinsically disordered than random sequences

Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding?

Polarized luminescence and mobility of tryptophan residues in polypeptide chains

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