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Protein Side Chain Absorptions in the Infrared Finger Print Region Excerpted from: Lauren DeFlores, Multi‐mode Vibrational Spectroscopy of Peptides and Proteins, Ch. 6 (PhD Thesis, Massachusetts Institute of Technology, 2008) See also: Andreas Barth and Christian Zscherp, “What vibrations tell us about proteins,” Quarterly Reviews of Biophysics 35 (2002) 369–430 Andreas Barth, “The infrared absorption of amino acid side chains,” Progress in Biophysics & Molecular Biology 74 (2000) 141–173 Table 1. Extinction coefficients and peak frequencies of amino acids that absorb between 1200 cm‐1 and 1800 cm‐1 in H2O and D2O. Frequencies are tabulated as a function of pH relative to the pKa value determined from the isolated amino acid. For vibrations with no pH dependence appear in the central column. Table 1a. Side Chain Absorptions in H2O Amino Acid cm-1 (H20) < pKs low pH Arginine ARG R 460 320 Aspartic Acid ASP D Asparagine ASN N Cysteine CYS C Glutamic Acid GLU E Glutamine GLN Q Histindine HIS H 250 70 Lysine LYS K 80 85 Phenylalanine PHE F Proline PRO P Tryptophan TRP W Tyrosine TYR Y 120 85 385 200 1652 1630 1631 1575, 1594 1626 1526 1617 1598 1515 1250 cm-1 (H20) 280 320 150 220 370 230 80 - 1716 1375 1677 1617 2551 1712 1680 1595 1410 1494 1460 1432 1450 1622 1509 1496 1462 1427 - cm-1 (H20) > pKs high pH - - 235 256 - 1577 1402 1558 1404 1439 1601 1499 1270 - 460 316 160 700 580 - Mode pKs asCN3H5+ sCN3H5+ C=O asCOOsCOOsCH3 C=O NH2 SH C=O asCOOsCOOC=O NH2 CN C=C (H2+) C=C (H) CH3, CN (-) asNH3+ sNH3+ CC ring asCH3 CN CH2 CC, C=C CN, CH, NH CC, CH CH, CC, CN dNH, CC, CH CC, CH CC CC, CH CC, CH CO, CC CO, CC 11.6 - 12.6 4.0 - 4.8 9.0-9.5 4.4 - 4.6 6.0-7.0 10.4-11.1 9.8 - 10.4 Table 1b. Side Chain Absorptions in D2O Amino Acid Arginine ARG R Aspartic Acid ASP D Asparagine ASN N Cysteine CYS C Glutamic Acid GLU E Glutamine GLN Q Histindine HIS H Lysine LYS K Tryptophan TRP W Tyrosine TYR Y cm-1 (D2O) <pKs low pH 460 1605 500 1586 35 1600 70 1569, 1575 1200 1170 160 1615 50 1590 500 1515 150 1255 cm-1 (D2O) 290 1713 570 1648 1849 280 1706 550 1640 1163 1409 1618 200 1455 1382 - cm-1 (D20) > pKs high pH 820 1584 1404 830 1567 1407 1439 350 1630 650 1499 - Mode pKs (pH) asCN3D5+ sCN3D5+ C=O asCOOsCOOC=O SD C=O asCOOsCOOC=O ND2 CN C=C (D2+) C=C (D) CD3, CN (-) asND3+ sND3+ CC, C=C CD, CC, CN ND, CC, CD CC, CD CC CC, CD CC, CD CO, CC 11.6 - 12.6 4.0 - 4.8 9.0-9.5 4.4 - 4.6 6.0-7.0 10.4-11.1 9.8 - 10.4 Figure 1. (Top) Atomic structures of predominant side chains in the amide finger region. (Bottom) Stick plots of side chain absorption from Table 1 in the amide finger print region as a function of solvent and pH. Major changes occur due to the protonation state of ASP, GLU and HIS. Isotopic sensitivity of the vibrational absorption is seen in TRP, ARG, GLU and ASP.