A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure
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2008
Članak u časopisu (Objavljena verzija)
Metapodaci
Prikaz svih podataka o dokumentuApstrakt
The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: alpha-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their C beta and C gamma atoms that predicts their preference for a particular secondary structure. All alpha-helix preferrers have neither polar heteroatoms on C beta and C gamma atoms, nor branching or aromatic group on the C beta atom. All strand preferrers have aromatic groups or branching groups on the C beta atom. All turn and bend preferrers have a polar heteroatom on the C beta or C gamma atoms or do not have a C beta atom at all. These new rules could be helpful in making predictions about non-natur...al amino acids.
Ključne reči:
amino acid / protein / protein secondary structure / statistical correlationIzvor:
Journal of Molecular Modeling, 2008, 14, 8, 769-775Izdavač:
- Springer, New York
Finansiranje / projekti:
- Proučavanje odnosa reaktivnosti, nekovalentnih interakcija i strukture molekula i modelovanje hemijskih sistema (RS-MESTD-MPN2006-2010-142037)
- Automatsko rezonovanje i napredne obrade velikih količina podataka i teksta (RS-MESTD-MPN2006-2010-144030)
DOI: 10.1007/s00894-008-0313-0
ISSN: 1610-2940
PubMed: 18504624
WoS: 000257330700014
Scopus: 2-s2.0-47249128045
Kolekcije
Institucija/grupa
Hemijski fakultet / Faculty of ChemistryTY - JOUR AU - Malkov, Sasa N. AU - Živković, Miodrag V. AU - Beljanski, Milos V. AU - Hall, Michael B. AU - Zarić, Snežana D. PY - 2008 UR - https://cherry.chem.bg.ac.rs/handle/123456789/953 AB - The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: alpha-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their C beta and C gamma atoms that predicts their preference for a particular secondary structure. All alpha-helix preferrers have neither polar heteroatoms on C beta and C gamma atoms, nor branching or aromatic group on the C beta atom. All strand preferrers have aromatic groups or branching groups on the C beta atom. All turn and bend preferrers have a polar heteroatom on the C beta or C gamma atoms or do not have a C beta atom at all. These new rules could be helpful in making predictions about non-natural amino acids. PB - Springer, New York T2 - Journal of Molecular Modeling T1 - A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure VL - 14 IS - 8 SP - 769 EP - 775 DO - 10.1007/s00894-008-0313-0 ER -
@article{ author = "Malkov, Sasa N. and Živković, Miodrag V. and Beljanski, Milos V. and Hall, Michael B. and Zarić, Snežana D.", year = "2008", abstract = "The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: alpha-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their C beta and C gamma atoms that predicts their preference for a particular secondary structure. All alpha-helix preferrers have neither polar heteroatoms on C beta and C gamma atoms, nor branching or aromatic group on the C beta atom. All strand preferrers have aromatic groups or branching groups on the C beta atom. All turn and bend preferrers have a polar heteroatom on the C beta or C gamma atoms or do not have a C beta atom at all. These new rules could be helpful in making predictions about non-natural amino acids.", publisher = "Springer, New York", journal = "Journal of Molecular Modeling", title = "A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure", volume = "14", number = "8", pages = "769-775", doi = "10.1007/s00894-008-0313-0" }
Malkov, S. N., Živković, M. V., Beljanski, M. V., Hall, M. B.,& Zarić, S. D.. (2008). A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. in Journal of Molecular Modeling Springer, New York., 14(8), 769-775. https://doi.org/10.1007/s00894-008-0313-0
Malkov SN, Živković MV, Beljanski MV, Hall MB, Zarić SD. A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. in Journal of Molecular Modeling. 2008;14(8):769-775. doi:10.1007/s00894-008-0313-0 .
Malkov, Sasa N., Živković, Miodrag V., Beljanski, Milos V., Hall, Michael B., Zarić, Snežana D., "A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure" in Journal of Molecular Modeling, 14, no. 8 (2008):769-775, https://doi.org/10.1007/s00894-008-0313-0 . .