1. Toward direct determination of conformations of protein building units from multidimensional NMR experiments part II: a theoretical case study of formyl-L-valine amide
A Perczel, A G Császár Chemistry. 2001 Mar 2;7(5):1069-83. doi: 10.1002/1521-3765(20010302)7:53.0.co;2-u.
Chemical shielding anisotropy tensors have been determined for all twenty-seven characteristic conformers of For-L-Val-NH2 using the GIAO-RHF formalism with the 6-31 + G* and TZ2P basis sets. The individual chemical shifts and their conformational averages have been compared to their experimental counterparts taken from the BioMagnetic Resonance Bank (BMRB). At the highest level of theory applied, for all nuclei but the amide proton, deviations between statistically averaged theoretical and experimental chemical shifts are as low as 1-3%. Correlated chemical shift plots of selected nuclei, as function of the respective phi, psi, chi1, and chi2 torsional angles, have been generated. On two-dimensional chemical shift-chemical shift plots, for example, 1H(NH)-15N(NH) and 15N(NH)-13Calpha, regions corresponding to major conformational clusters have been identified, providing a basis for the quantitative identification of conformers from NMR shift data. Experimental NMR resonances of nuclei of valine residues have been deduced from 18 selected proteins, resulting in 93 1Halpha-13Calpha chemical shift pairs. These experimental results have been compared to relevant ab initio values revealing remarkable correlation between the two sets of data. Correlations of 1Halpha and 13Calpha values with backbone conformational parameters (phi and psi) have also been found for all pairs (e.g. 1Halpha/phi and 13Calpha/phi) but 1Halpha/psi. Overall, the appealing idea of establishing backbone folding of proteins by employing chemical shift information alone, obtained from selected multiple-pulse NMR experiments (e.g. 2D-HSQC, 2D-HMQC, and 3D-HNCA), has received further support.
2. Conformation and hydrogen bonding of N-formylmethionyl peptides. Parallel beta-sheet in the crystal structure of N-formyl-L-methionyl-L-valine
A Chatterjee, R Parthasarathy Int J Pept Protein Res. 1984 Nov;24(5):447-52.
Crystals of N-formyl-L-methionyl-L-valine (C11H20N2O)4S, M.W. = 276.3) are orthorhombic, space group )2(1)2(1)2(1) with cell constants at 294K of a = 4.851 (1), b = 14.925 (1), c = 19.745 (3) A, V = 1429.8 (1) A3, Z = 4 and observed (Dm) and calculated (Dx) of 1.49 and 1.488 g x cm-3, respectively. The crystal structure was solved using automatic diffractometer data (1260 reflections larger than or equal to 3 sigma) and refined to a final R-value of 0.035. This structure contains a short (2.626 (3) A) intermolecular hydrogen bond between the carboxyl OH and the N-acyl oxygen, a feature common to most N-acylamino acids and N-acylpeptides. The peptide is nearly planar (omega = 174.6 (5)); the values of psi 1, phi 2, psi 1T and psi 2T are, respectively, 131.8 (4) degrees, -139.9 (5) degrees, -39.3 (4) degrees and 142.1 (4) degrees. The methionine side chain is not zig-zag transplanar; the side chain torsion angles are: chi 1(1) = -60.0 (4) degrees, chi 2(1) = 176.0 (4) degrees and chi 3(1) = 71.8 (4) degrees. The two C gamma's for valine have psi 1-values of -64.4 (5) degrees and 173.7 (5) degrees. The formation of the parallel rather than antiparallel beta-sheet structure, the participation of the N-formyl group in the parallel beta-sheet and the use of C-H ... O hydrogen bonds to stabilize the beta-sheet are novel features found in this structure.
3. Cyclosporin H is a potent and selective formyl peptide receptor antagonist. Comparison with N-t-butoxycarbonyl-L-phenylalanyl-L-leucyl-L-phenylalanyl-L- leucyl-L-phenylalanine and cyclosporins A, B, C, D, and E
K Wenzel-Seifert, R Seifert J Immunol. 1993 May 15;150(10):4591-9.
The cyclic undecapeptide, cyclosporin (Cs) H, is a potent inhibitor of FMLP-induced superoxide anion (O2-) formation in human neutrophils. We studied the effects of CsH in comparison with those of N-t-butoxycarbonyl-L-phenylalanyl-L-leucyl-L-phenylalanyl-L-leucyl-L- phenylalanine (BocPLPLP), a well known formyl peptide receptor antagonist, and of other Cs on activation of N6,2'-O-dibutyryl adenosine 3:5'-monophosphate-differentiated HL-60 cells and human erythroleukemia cells (HEL cells). CsH inhibited FMLP binding in HL-60 membranes with a Ki (inhibition constant) of 0.10 microM. CsH inhibited activation by FMLP of high affinity GTPase (the enzymatic activity of alpha-subunits of heterotrimeric regulatory guanine nucleotide-binding proteins) in HL-60 membranes with a Ki of 0.79 microM. CsH inhibited the stimulatory effects of FMLP on cytosolic Ca2+ concentration ([Ca2+]i), O2- formation, and beta-glucuronidase release with Ki values of 0.08, 0.24, and 0.45 microM, respectively. BocPLPLP was 14-fold less potent than CsH in inhibiting FMLP binding and 4- to 6-fold less potent than CsH in inhibiting FMLP-induced GTP hydrolysis, rises in [Ca2+]i, O2- formation, and beta-glucuronidase release. CsA reduced FMLP-induced O2- formation by 20%, but CsB, CsC, CsD, and CsE did not. CsA, CsB, CsC, CsD, and CsE did not affect FMLP-induced rises in [Ca2+]i. BocPLPLP inhibited leukotriene B4-induced rises in [Ca2+]i with a Ki of 0.33 microM, whereas CsH showed no inhibitory effect. CsH and BocPLPLP did not inhibit the rises in [Ca2+]i induced by several other stimuli in HL-60 cells and HEL cells. Our results show that 1) CsH is a more potent formyl peptide receptor antagonist than BocPLPLP; 2) unlike BocPLPLP, CsH is selective; and 3) N-methyl-D-valine which is present at position 11 of the amino acid sequence of CsH but not of other Cs is crucial for FMLP antagonism.
