Download Protein Side Chain Absorptions in the Infrared Finger Print Region

 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
asCOOsCOOsCH3
C=O
NH2
SH
C=O
asCOOsCOOC=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
asCOOsCOOC=O
SD
C=O
asCOOsCOOC=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.