title: Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures.
abstract: In peptoids due to the absence of amide protons, the backbone is devoid of hydrogen bond donor, linked by tertiary amide, which can be iso-energetic between cis and trans-amide bond geometry. The peptoids can be realized with cis amide bond if the side chain of ith residue can engage the carbonyl group of ith-1 residue in CH--O interactions. Simulations studies both in water and DMSO have been carried out. The peptoid Ac-(N(tle))(7) -NMe(2) can adopt degenerate conformations with alternate φ, ψ values of inverse PP-I and PP-I type structure's, or vice versa in water. In DMSO, Ac-(N(tle))(7)-NMe(2) also adopts inverse PP-I type structure. Like polyproline, molecule adopting a rigid structure can be used as molecular markers or spacers in biological studies.The peptoid Ac-(N(ala)-N(tle))(3)-NMe(2) with alternate trans and cis amide bond geometry for N(ala) and N(tle) residue corresponding to inverse PP-II/PP-II type and for N(tle) residue of PP-I type.
authors.affiliation: Department of Biophysics, Panjab University, Chandigarh, 160014, India, fateh_nandel@yahoo.com.
authors.forename: Fateh Singh
authors.initials: FS
authors.lastname: Nandel
authors.forename: Radhika Rani
authors.initials: RR
authors.lastname: Jaswal
authors.forename: Avneet
authors.initials: A
authors.lastname: Saini
authors.forename: Vibhuti
authors.initials: V
authors.lastname: Nandel
authors.forename: Mohd
authors.initials: M
authors.lastname: Shafique
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry*; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D034444:Peptoids / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
chemical_list: D000577:Amides; D034444:Peptoids; D012997:Solvents; D014867:Water; D004121:Dimethyl Sulfoxide