Search results for "Secondary"
showing 10 items of 1765 documents
Revisiting Secondary Structures in NCA Polymerization: Influences on the Analysis of Protected Polylysines
2014
Two series (degree of polymerization: 20–200) of polylysines with Z and TFA protecting groups were synthesized, and their behavior in a range of analytical methods was investigated. Gel permeation chromatography of the smaller polypeptides reveals a bimodal distribution, which is lost in larger polymers. With the help of GPC, NMR, circular dichroism (CD), and MALDI-TOF, it was demonstrated that the bimodal distribution is not due to terminated chains or other side reactions. Our results indicate that the bimodality is caused by a change in secondary structure of the growing peptide chain that occurs around a degree of polymerization of about 15. This change in secondary structure interferes…
Host–guest inclusion complexes between peracetylated β-cyclodextrin and diphenyl(4-phenylphenyl)phosphine : computational studies
2006
PM3 and molecular dynamic calculations were performed upon the inclusion complexation of peracetylated β-cyclodextrin (Per-Ac-β-CD) with diphenyl(4-phenylphenyl)phosphine (DBP). Results show that the 4-phenylphenyl part of the DBP phosphine fits tightly in the cavity of the Per-Ac-β-CD, leading to the formation of stable inclusion complexes. Complexation energies indicate that the complex formed via the primary side of the Per-Ac-β-CD is more stable than that formed via the secondary side. Electrostatic potential mapping and frontier orbital analysis suggest that van der Waals interaction constitute a major driving force in the complexation of the DBP and Per-Ac-β-CD.
Protein Unfolding:1H-NMR Studies of Paramagnetic Ferricytochrome c-550 from Horse Heart
2005
Electronic transfer protein cytochrome c-550 from horse heart is studied in the unfolded state by means of paramagnetic 1H NMR. The protein contains 104 aminoacid residues and a heme group with low spin FeIII ion in the oxidized form of protein. The global secondary structure is of the α-helix type as occurs in the case of very other cytochromes c investigated such as cyt c-550 from Thiobacillus versutus or cyt c-551 from Pseudomonas aeruginosa. We have studied the coordination characteristic and electronic properties of heme iron horse heart ferricytochrome c-550 at increasing denaturing conditions (up to 3.1 M GuHCl and 288-323 K). The 1H T1 values of the signals were measured and some re…
Impact of O → S Exchange in Ferrocenyl Amides on the Structure and Redox Chemistry
2014
The conformations and redox chemistry of ferrocenyl amides have been investigated in considerable depth in the last few years, while ferrocenyl thioamides have attracted less interest so far, although distinctly different conformations and reactivity patterns are expected. Monoferrocenyl amides Fc-NHC(O)CH3 (1) and 1,1′-CH3O(O)C-Fn-NHC(O)CH3 (2) and diferrocenyl amides Fc-NHC(O)-Fc (5) and Fc-NHC(O)-Fn-NHC(O)CH3 (6) are easily transformed into the corresponding thioamides (3, 4, 7, 8) by treatment with Lawesson’s reagent (2,4-bis(p-methoxyphenyl)-1,3-dithiaphosphetane-2,4-disulfide) (Fc = Fe(C5H4)(C5H5), Fn = Fe(C5H4)2). The thioamide conformations (cis/trans) in 3, 4, 7, and 8 and the hydr…
Conformational stability of oligoferrocene oligoamide foldamers
2016
Abstract Organometallic oligoamides built from three to four ferrocene amino acid units ( H-Fca-OH , 1-amino-1′-ferrocene carboxylic acid) fold into hydrogen bonded secondary structures featuring eight-membered rings by cooperative hydrogen bonds. NMR studies and DFT calculations (CAM-B3LYP, LANL2DZ, IEFPCM (THF)) reveal that the organometallic zigzag foldamer structures are highly resistant toward denaturation by hydrogen bond acceptors such as dimethyl sulfoxide and 2,4-lutidine. Replacing one ferrocene amino acid unit by the organic α -amino acid glycine at the C -terminal end (Fca → Gly) significantly destabilizes the secondary zigzag structure facilitating denaturation by DMSO. Highly …
Conformational studies of hexapeptides containing two dehydroamino acid residues in positions 2 and 5 in peptide chain
2008
Conformational preferences of a group of hexapeptides containing two dehydroamino acid residues in Positions 2 and 5 in peptide chain were investigated by means of spectroscopic methods (NMR and CD) and theoretical calculations. In the case of dimethylsulfoxide (DMSO) solution, only peptide with free N-termini adopted rigid 310-helical conformation, for the rest of examined peptides extended and “zig-zag” conformers were predominant. CD measurements showed that only in chloroform solution the conformational freedom of investigated peptides was restricted. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 691–699, 2008. This article was originally published online as an accepted preprint. The “…
SPM and TOF-SIMS investigation of the physical and chemical modification induced by tip writing of self-assembled monolayers
2003
Abstract The nanoelectrochemical modification of alkyl self-assembled monolayers (SAMs) obtained on hydrogenated silicon surfaces via radical-initiated reactions of 1-octadecene has been investigated. Scanning Probe Microscopy (SPM) showed that the modification of the organic layer occurs by applying either positive or negative biases to the tip at a threshold of about ±5 V. When the bias absolute value was ≤6 V, the height of the monolayer was only faintly modified, whereas a consistent increase in tip/sample friction force was observed, in agreement with the formation of hydrophilic moieties at the organic surface. In addition to the increase of friction, bias absolute values larger than …
Structure-based statistical analysis of transmembrane helices
2012
Recent advances in determination of the high-resolution structure of membrane proteins now enable analysis of the main features of amino acids in transmembrane (TM) segments in comparison with amino acids in water-soluble helices. In this work, we conducted a large-scale analysis of the prevalent locations of amino acids by using a data set of 170 structures of integral membrane proteins obtained from the MPtopo database and 930 structures of water-soluble helical proteins obtained from the protein data bank. Large hydrophobic amino acids (Leu, Val, Ile, and Phe) plus Gly were clearly prevalent in TM helices whereas polar amino acids (Glu, Lys, Asp, Arg, and Gln) were less frequent in this …
Orientation and Dynamics of Peptides in Membranes Calculated from 2H-NMR Data
2009
Solid-state (2)H-NMR is routinely used to determine the alignment of membrane-bound peptides. Here we demonstrate that it can also provide a quantitative measure of the fluctuations around the distinct molecular axes. Using several dynamic models with increasing complexity, we reanalyzed published (2)H-NMR data on two representative alpha-helical peptides: 1), the amphiphilic antimicrobial peptide PGLa, which permeabilizes membranes by going from a monomeric surface-bound to a dimeric tilted state and finally inserting as an oligomeric pore; and 2), the hydrophobic WALP23, which is a typical transmembrane segment, although previous analysis had yielded helix tilt angles much smaller than ex…
Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28-nm resolution. Structural peculiarities in a folded protein conformation.
1996
The Bowman-Birk inhibitor from soybean is a small protein that contains a binary arrangement of trypsin-reactive and chymotrypsin-reactive subdomains. In this report, the crystal structure of this anticarcinogenic protein has been determined to 0.28-nm resolution by molecular replacement from crystals grown at neutral pH. The crystal structure differs from a previously determined NMR structure [Werner, M. H. & Wemmer, D. E. (1992) Biochemistry 31, 999-1010] in the relative orientation of the two enzyme-insertion loops, in some details of the main chain trace, in the presence of favourable contacts in the trypsin-insertion loop, and in the orientation of several amino acid side chains. The p…