Side-Chain Conformational Thermodynamics of Aspartic Acid Residue in the Peptides and Achatin-I in Aqueous Solution Tomohiro Kimura, Nobuyuki Matubayasi,

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Side-Chain Conformational Thermodynamics of Aspartic Acid Residue in the Peptides and Achatin-I in Aqueous Solution Tomohiro Kimura, Nobuyuki Matubayasi, Masaru Nakahara Biophysical Journal Volume 86, Issue 2, Pages 1124-1137 (February 2004) DOI: 10.1016/S0006-3495(04)74187-9 Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 1 (a) Molecular structures of Asp tripeptide (A) at the acidic pD, (N) at the neutral pD, and (B) at the basic pD. The arrows represent the dihedral angles analyzed. (b) Staggered side-chain conformers of Asp with respect to the dihedral angles analyzed. C represents the β-carboxyl carbon in the side chain. N represents the α-amino nitrogen or α-amide nitrogen in the peptide bond, and C represents the α-carboxyl carbon or α-carbonyl carbon in the peptide bond. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 2 1H NMR spectrum of (a) 10mM Asp tripeptide aqueous solution observed on a 270-MHz spectrometer and (b) 5mM Asp tetrapeptide aqueous solution observed on a 600-MHz spectrometer at 30°C (A) at the acidic pD, (N) at the neutral pD, and (B) at the basic pD. The 5-line signals with asterisks for the tripeptide correspond to the C-terminal protons. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 3 Probabilities (P) of side-chain conformers T, G+, and G− in Fig. 1 b for the Asp amino acid monomer and peptides (di-, tri-, and tetrapeptides) (A) at the acidic pD, (N) at the neutral pD, and (B) at the basic pD. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 4 Conformational energy changes ΔEgas0 (kJ mol−1) in the gas phase calculated by the MM2 for the trans-to-gauche transformation with respect to a pair of vicinal functional groups involved in Asp residues in peptides. One α-functional group was replaced by a hydrogen atom in the calculations as shown in the parentheses. In the cases where the α-amide group of a peptide bond is involved as for 2 and 4, not only the minimum but also the maximum values of ΔEgas0 due to the variation of the orientation of this group are shown. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 5 Sequence-position dependence of the conformational energy changes ΔEgas0 (kJ mol−1) in the gas phase. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 6 ln K against 1/T for the Asp side-chain conformational equilibria in Asp dipeptide. K=P(x)/P(T) is the equilibrium constant, where P(T) is the probability of conformer T, and P(x) is the probability of conformer G+ or G−. T is the absolute temperature. (a) At the acidic pD of 0.6 and (b) at the neutral pD of 7.4. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 7 Side-chain conformational changes in the standard free energy ΔG0, enthalpy ΔH0, and entropy −TΔS0 (kJ mol−1) from T to G+ or G− in Fig. 1 b of Asp amino acid monomer, di-, tri-, and tetrapeptides (A) at the acidic pD and (N) at the neutral pD. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 8 1H NMR spectrum of 2mM achatin-I (Gly-D-Phe-Ala-Asp) aqueous solution at 30°C (A) at the acidic pD of 0.7, (N) at the neutral pD of 7.5, and (B) at the basic pD of 13.8. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 9 Probabilities (P) of side-chain conformers T, G+, and G− in Fig. 1 b for the C-terminal Asp in achatin-I, (A) at the acidic pD, (N) at the neutral pD, and (B) at the basic pD. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 10 ln K against 1/T for the C-terminal Asp in achatin-I at the neutral pD. Biophysical Journal 2004 86, 1124-1137DOI: (10.1016/S0006-3495(04)74187-9) Copyright © 2004 The Biophysical Society Terms and Conditions