caa a22 4500 605513244 CHVBK 20210128100659.0 cr unu---uuuuu 210128e20150501xx s 000 0 eng 10.1007/s00894-015-2671-8 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2671-8 Conformational behavior of polyalanine peptides with and without protecting groups of varying chain lengths: population of PP-II structure! [Elektronische Daten] [Fateh Nandel, Mohan Garg, Mohd Shafique] Oculopharyngeal muscular dystrophy (OPMD), a polyalanine myopathy, occurs due to expansion of homo-polyalanine stretch in normal polyadenylating binding protein nuclear 1 (PABPN1) protein from Ala10 to Ala11-17. Therefore, the conformational behavior of polyalanine peptides with n = 10-17, with and without terminal protecting groups, have been investigated with different starting geometries in water by molecular dynamics simulation studies. Alanine peptides are shown to give rise to unordered structure irrespective of starting geometry and not more than two residues at a stretch have the same/similar set of φ, ψ values. However, the final structure with terminal protecting groups look like β-strand. Unprotected poly-Ala peptides adopt twisted β-hairpin/multi hairpin like structure with increasing chain length. The number of residues having φ, ψ values in collagen region is found to be less in peptides with unprotected termini as compared to peptides with protected termini of same chain length. The results have been supported by recent synchrotron radiation circular dichroism spectroscopy of polyproline II and unordered secondary structures. Opening of the helical structure in poly-Ala peptides with protecting groups has been shown to take place from C-terminal and in peptides without protecting groups opening of helix starts from both terminals. Further, opening of helix takes more time in poly-Ala peptides without terminal protecting groups. The deviations in amide bond planarity have been discussed and compared with available experimental and computational results. Springer-Verlag Berlin Heidelberg, 2015 β-hairpin nationallicence Collagen type nationallicence Non-planar amide bonds nationallicence OPMD nationallicence Polyalanine nationallicence Nandel Fateh Department of Biophysics, Panjab University, 160014, Chandigarh, India aut Garg Mohan Department of Biophysics, Panjab University, 160014, Chandigarh, India aut Shafique Mohd Department of Biophysics, Panjab University, 160014, Chandigarh, India aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/5(2015-05-01), 1-12 1610-2940 21:5<1 2015 21 894 https://doi.org/10.1007/s00894-015-2671-8 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2671-8 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Nandel Fateh Department of Biophysics, Panjab University, 160014, Chandigarh, India aut NATIONALLICENCE 700 1- Garg Mohan Department of Biophysics, Panjab University, 160014, Chandigarh, India aut NATIONALLICENCE 700 1- Shafique Mohd Department of Biophysics, Panjab University, 160014, Chandigarh, India aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/5(2015-05-01), 1-12 1610-2940 21:5<1 2015 21 894