M 0-90 with T=10 . Zwitterionic AAA and the alanine dipeptide variety from 5-85

M 0-90 with T=10 . Zwitterionic AAA and the alanine dipeptide variety from 5-85 with T=5 .J Phys Chem B. Author manuscript; available in PMC 2014 April 11.Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptFigure 7.3J(HN,H)[Hz] from the central (left panel) and C-terminal residue amide (right panel) plotted as a function of temperature for cationic AAA (circles), zwitterionic AAA (squares) and also the AdP (triangles). The solid lines outcome from the two-state thermodynamic model fitting procedure described in the text.J Phys Chem B. Author manuscript; obtainable in PMC 2014 April 11.Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author CXCR7 Activator Accession ManuscriptJ Phys Chem B. Author manuscript; obtainable in PMC 2014 April 11.Figure eight.Ramachandran plots for (A) the cationic and (B) zwitterionic AAA and (C) AdP obtained by MD simulations utilizing the OPLS force field and SPC/E water model.Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptJ Phys Chem B. Author manuscript; offered in PMC 2014 April 11.Figure 9.Distribution of durations, N(t), of the (A) pPII, (B) -strand, and (C) helical conformations for cationic AAA (black circles) and AdP (red circles) derived by MD. The solid line represents exponential fits (see Table 7).Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptJ Phys Chem B. Author manuscript; accessible in PMC 2014 April 11.Figure 10.Radial distribution functions, g(r), of water molecules (working with H- and O-atoms of water) about the amide proton of your central residue of cationic AAA and AdP (see Figure 1, atoms depicted in blue), derived by MD. Distributions with the (B) cationic AAA and (C) AdP conformations with respect for the dihedral angle along with the distance among the nitrogen atom on the third residue and also the side-chain atom C in the central residue in AAA as well as the corresponding distance in AdP (see Figure 1, the two atoms depicted in red).Toal et al.PageTableCenter (,)-coordinates and respective mole fractions with the two-dimensional Gaussian sub-distributions made use of for simulation of Vibrational Spectra and J-coupling CB1 Agonist web constants for Cationic AAA (AAA+), Zwitterionic AAA (AAA+-), Anionic AAA(AAA-), Alanine dipeptide (AdP), and cationic GAG (GAG+).Conformation pPII -strand right-hand helical inverse -turn form II -turn variety I’ -turn inverse -turn AAA+ 0.84 (-69,145) 0.08 (-125,160) 0.04 (-60,-30) 0.04 (-85,78) AAA+- 0.84 (-69,145) 0.08 (-125,160) 0.04 (-60,-30) 0.04 (-85,78) AAA- 0.84 (-69,130) 0.08 (-125,150) 0.04 (-60,-30) 0.04 (-85,78) 0.03 (-60,120) 0.03 (20,40) 0.04 (20,-60) 0.03 (-60,-120) AdP 0.74 (-69,160) 0.16 (-115,160) 0.04 (-60,-30) GAG+ 0.72 (-69,155) 0.18 (-115,155) 0.03 (-60,-30)NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptJ Phys Chem B. Author manuscript; accessible in PMC 2014 April 11.Toal et al.PageTableComparison of experimental50 and calculated J-coupling constants in Hertz for cationic AAA.COUPLING CONSTANT3J(HNH) 3J(HNC’) 3J(HC’) 3J(C’C’) 3J(HNC) 1J(NC)NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptEXPERIMENTAL five.68 1.13 1.84 0.25 2.39 11.CALCULATED 5.63 1.09 1.57 0.59 two.ten 11.J Phys Chem B. Author manuscript; available in PMC 2014 April 11.Toal et al.PageTableComparison of experimental and calculated 3J(HNH) coupling constants of zwitterionic AAA along with the alanine dipeptide. All values are expressed in units of Hertz.3J(HNH)NIH-PA Author.