Geodesic
Structure of looped regions in $\beta-\alpha$- and $\alpha-\beta$-arches in abcd-units of globular proteins
Matematičeskaâ biologiâ i bioinformatika, Tome 11 (2016) no. 2, pp. 159-169 
E. V. Brazhnikov; A. M. Kargatov; A. V. Efimov. Structure of looped regions in $\beta-\alpha$- and $\alpha-\beta$-arches in abcd-units of globular proteins. Matematičeskaâ biologiâ i bioinformatika, Tome 11 (2016) no. 2, pp. 159-169. http://geodesic.mathdoc.fr/item/MBB_2016_11_2_a2/
@article{MBB_2016_11_2_a2,
     author = {E. V. Brazhnikov and A. M. Kargatov and A. V. Efimov},
     title = {Structure of looped regions in $\beta-\alpha$- and $\alpha-\beta$-arches in abcd-units of globular proteins},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
     pages = {159--169},
     year = {2016},
     volume = {11},
     number = {2},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MBB_2016_11_2_a2/}
}
TY  - JOUR
AU  - E. V. Brazhnikov
AU  - A. M. Kargatov
AU  - A. V. Efimov
TI  - Structure of looped regions in $\beta-\alpha$- and $\alpha-\beta$-arches in abcd-units of globular proteins
JO  - Matematičeskaâ biologiâ i bioinformatika
PY  - 2016
SP  - 159
EP  - 169
VL  - 11
IS  - 2
UR  - http://geodesic.mathdoc.fr/item/MBB_2016_11_2_a2/
LA  - ru
ID  - MBB_2016_11_2_a2
ER  - 
%0 Journal Article
%A E. V. Brazhnikov
%A A. M. Kargatov
%A A. V. Efimov
%T Structure of looped regions in $\beta-\alpha$- and $\alpha-\beta$-arches in abcd-units of globular proteins
%J Matematičeskaâ biologiâ i bioinformatika
%D 2016
%P 159-169
%V 11
%N 2
%U http://geodesic.mathdoc.fr/item/MBB_2016_11_2_a2/
%G ru
%F MBB_2016_11_2_a2

Voir la notice de l'article provenant de la source Math-Net.Ru

Conformations of about 600 looped regions (loops) in $\beta-\alpha$- and $\alpha-\beta$-arches of a structural motif occurring in the abCd-unit of proteins were analyzed. On the whole, 258 abCd-units with a reverse turn of the polypeptide chain (236 PDB files) and 69 abCd-units with a direct turn (65 PDB files) were selected in non-homologous proteins. Four types of arches were studied: $\beta-\alpha$- and $\alpha-\beta$-ones at a direct turn of the chain; $\beta-\alpha$- and $\alpha-\beta$-ones at a reverse turn of the chain. For each type of arches, frequencies of loops occurrence of different lengths were determined and corresponding histograms were plotted. It was found that abCd-units with loops up to three amino acid residues long occur most frequently (57%). In $\beta-\alpha$-arches with a direct turn of the chain, loops consisting of two amino acid residues occur most often (44%) and in 86% cases they have the $\beta_m\alpha\beta\alpha_n$-conformation. They have no Gly and Pro residues, and in position $\beta$ there is an Asn residue. In such type of arches, the loops of one residue ($\beta_m\varepsilon\alpha_n$- or $\beta_m\alpha_L\alpha_n$-conformation) contain the Gly residue most frequently. $\alpha-\beta$-Arches with a direct turn of the chain have most commonly (18%) loops of four amino acid residues. In this case, there is no predominant conformation of the loops. In $\beta-\alpha$-arches with a reverse turn of the chain, most common are loops of seven amino acid residues (17%), and most part of them (88%) have the $\beta_m\alpha_L\beta\beta\alpha\alpha\beta\beta\alpha_n$-conformation. $\alpha-\beta$-Arches with a reverse turn of the chain contain most frequently (32%) loops of one amino acid residue (all Gly ones) with arch conformations $\alpha_m\varepsilon\beta_n$ or $\alpha_n\alpha_L\beta_n$. The above structural analysis of the abCd-unit has useful information for prediction of the three-dimensional structure of proteins and for molecular simulation of the de novo design of protein structures.

[1] Phillips D. C., “The hen egg-white lysozyme molecule”, Proc. Natl. Acad. Sci. USA, 57 (1967), 483–495 | DOI

[2] Ptitsyn O. B., “Stadiinyi mekhanizm samoorganizatsii belkovykh molekul”, Dokl. AN SSSR, 210 (1973), 1213–1215

[3] Wetlaufer D. B., “Nucleation, rapid folding, and globular intrachain regions in proteins”, Proc. Natl. Acad. Sci. USA, 70 (1973), 697–701 | DOI

[4] Efimov A. V., Boshkova E. A., “Dva mekhanizma svorachivaniya belkov. Teoreticheskii analiz”, Bioorg. khim., 40 (2014), 665–672 | DOI

[5] Rudnev V. P., Pankratov A. N., Kulikova L. I., Dedus F. F., Tikhonov D. A., Efimov A. V., “Konformatsionnyi analiz strukturnykh motivov tipa $\alpha$-$\alpha$-ugolok v vychislitelnom eksperimente molekulyarnoi dinamiki”, Matematicheskaya biologiya i bioinformatika, 9:2 (2014), 575–584 | DOI

[6] Gordeev A. B., Kargatov A. M., Efimov A. V., “PCBOST: Protein classification based on structural trees”, Biochemical and Biophysical Research Communications, 397 (2010), 470–471 | DOI

[7] Efimov A. V., “Supervtorichnaya struktura $\beta$-belkov”, Molekulyarnaya biologiya, 16 (1982), 799–806

[8] Efimov A. V., “Structure of $\alpha$-$\alpha$-hairpins with short connections”, Protein Engineering, 4 (1991), 245–250 | DOI

[9] Brazhnikov E. V., Efimov A. V., “Struktura $\alpha$-spiralnykh shpilek s korotkimi peretyazhkami v globulyarnykh belkakh”, Molekulyarnaya biologiya, 35 (2001), 100–108

[10] Efimov A. V., “Novaya supervtorichnaya struktura belkov: $\alpha$-$\alpha$-ugolok”, Molekulyarnaya biologiya, 18 (1984), 1524–1537

[11] Efimov A. V., “Structure of coiled $\beta$-$\beta$-hairpins and $\beta$-$\beta$-corners”, FEBS Lett., 284 (1991), 288–292 | DOI

[12] Boshkova E. A., Brazhnikov E. V., Efimov A. V., “Vzaimosvyaz mezhdu strukturoi i aminokislotnoi posledovatelnostyu silno skruchennykh i izognutykh $\beta$-shpilek v globulyarnykh belkakh”, Molekulyarnaya. biologiya, 50:5 (2016), 777-782 | DOI

[13] Edwards M. S., Sternberg J. E., Thornton J. M., “Structural and sequence patterns in the loops of $\beta\alpha\beta$ units”, Protein Engineering, 1 (1987), 173–181 | DOI

[14] Efimov A. V., “Standartnye struktury v belkovykh molekulakh. I. $\alpha$-$\beta$-Shpilki”, Molekulyarnaya biologiya, 20 (1986), 329–339

[15] Efimov A. V., “Standartnye struktury v belkovykh molekulakh. II. $\beta$-$\alpha$-Shpilki”, Molekulyarnaya biologiya, 20 (1986), 340–345

[16] Efimov A. V., “Standard structures in proteins”, Progr. Biophys. Mol. Biol., 60 (1997), 201–239 | DOI

[17] Gordeev A. B., Efimov A. V., “Novoe strukturnoe drevo $(\alpha+\beta)$-belkov, soderzhaschikh abCd-edinitsy”, Molekulyarnaya biologiya, 43 (2009), 521–526

[18] Tatusova T. A., Madden T. L., “Blast 2 sequences — a new tool for comparing protein and nucleotide sequences”, FEMS Microbiol. Lett., 174 (1999), 247–250 | DOI

[19] Sayle R., Milner-White J., “RasMol: biomolecular graphics for all”, Trends Biochem. Sci., 20 (1995), 374–376 | DOI

[20] Koradi R., Billeter M., Wuthrich K., “MOLMOL: a program for display and analysis of macromolecular structures”, J. Mol. Graph., 14 (1996), 51–55 | DOI