Josef Kapitán

Residual structure in disordered peptides and unfolded proteins from multivariate analysis and ab initio simulation of Raman optical activity data

Vibrational Raman optical activity (ROA), measured as a small difference in the intensity of Raman scattering from chiral molecules in right‐ and left‐circularly polarized incident light, or as the intensity of a small circularly polarized component in the scattered light, is a powerful probe of the aqueous solution structure of proteins. The large number of structure‐sensitive bands in protein ROA spectra makes multivariate analysis techniques such as nonlinear mapping (NLM) especially favorable for determining structural relationships between different proteins. We have previously used NLM to map a large dataset of peptide, protein, and virus ROA spectra into a readily visualizable two‐dimensional space in which points close to or distant from each other, respectively, represent similar or dissimilar structures. As well as folded proteins, our dataset contains ROA spectra from many natively unfolded proteins, proteins containing both folded and unfolded domains, denatured partially structured molten globule and reduced protein states, together with folded proteins containing little or no α‐helix or β‐sheet. In this article, the relative positions of these systems in the NLM plot are used to obtain information about any residual structure that they may contain. The striking differences between the structural propensities of proteins that are unfolded in their native states and those that are unfolded due to denaturation may be responsible for their often very different behavior, especially with regard to aggregation. An ab initio simulation of the Raman and ROA spectra of an alanine oligopeptide in the poly(L‐proline) II‐helical conformation confirms previous suggestions that this conformation is a significant structural element in disordered peptides and natively unfolded proteins. The use of ROA to identify and characterize proteins containing significant amounts of unfolded structure will, inter alia, be valuable in structural genomics/proteomics since unfolded sequences often inhibit crystallization. Proteins 2008.

Vibrational Raman optical activity of 1-phenylethanol and 1-phenylethylamine: revisiting old friends.

The samples used for the first observations of vibrational Raman optical activity (ROA) in 1972, namely both enantiomers of 1-phenylethanol and 1-phenylethylamine, have been revisited using a modern commercial ROA instrument together with state-of-the-art ab initio calculations. The simulated ROA spectra reveal for the first time the vibrational origins of the first reported ROA signals, which comprised similar couplets in the alcohol and amine in the spectral range approximately 280-400 cm(-1). The results demonstrate how easy and routine ROA measurements have become, and how current ab initio quantum-chemical calculations are capable of simulating experimental ROA spectra quite closely provided sufficient averaging over accessible conformations is included. Assignment of absolute configuration is, inter alia, completely secure from results of this quality. Anharmonic corrections provided small improvements in the simulated Raman and ROA spectra. The importance of conformational averaging emphasized by this and previous related work provides the underlying theoretical background to ROA studies of dynamic aspects of chiral molecular and biomolecular structure and behavior.

Vibrational Analysis of an Industrial Fe-Based Fischer–Tropsch Catalyst Employing Inelastic Neutron Scattering†

Inelastic neutron scattering (INS) has been used to obtain the vibrational spectrum of a technical-grade iron-based Fischer–Tropsch catalyst that has been taken from an industrial large-scale unit operation. Whereas previous reports on iron Fischer–Tropsch catalysts highlight the presence of retained carbonaceous species, the INS spectra reveal the additional presence of partially hydrogenated aromatic molecules.

Poly(L-proline) II Helix Propensities in Poly(L-lysine) Dendrigraft Generations from Vibrational Raman Optical Activity

Vibrational Raman optical activity (ROA), measured as small circularly polarized components in Raman scattering from chiral molecules, was applied to study the backbone conformations of the first five generations of poly(L-lysine) dendrigrafts (DGLs) in water. Generation 1 was found to support predominantly the poly(L-proline) II (PPII) conformation, the amount of which steadily decreased with increasing generation, with a concomitant increase in other backbone conformations. This behavior may be due to increasing crowding of the lysine side chains, together with suppression of backbone hydration, with increasing branching. In contrast, the ROA spectra of a series of linear poly(L-lysine)s in water show little change with increasing molecular weight. Our results may have implications for the nonimmunogenic properties of DGLs.

Enantiomerically pure quaternary ammonium salts with a chiral alkyl chain N(CH3)(n-C3H7)2(sec-C4H9)I: Synthesis and physical studies†‡

A pair of enantiomerically pure quaternary ammonium salts with a chiral side chain, methyl-(R)-(1-methylpropyl)di(n-propyl)ammonium iodide 1 and methyl-(S)-(1-methylpropyl)di(n-propyl)ammonium iodide 2, and the related racemate, methyl-(rac)-(1-methylpropyl)di(n-propyl)ammonium iodide 3, were synthesized through a reductive alkylation procedure, starting from enantiomerically pure and, also, racemic forms of (rac)-(1-methylpropyl)amine. A spectroscopic chiroptical signature in solution was provided by the Raman optical activity spectra of compounds 1 and 2. The crystallographic structures of 1, 2, and 3 were examined by single crystal X-ray diffraction. 1 crystallizes in the tetragonal space group P4(3)2(1)2 (no. 96), a = b = 12.826 (2) A, c = 17.730 (2) A, V = 2916.9 (5) A(3), Z = 8, Flack coefficient 0.04 (2). 2 crystallizes in the tetragonal space group P4(1)2(1)2 (no. 92), a = b = 12.842 (1) A, c = 17.749 (2) A, V = 2927.0 (5) A(3), Z = 8, Flack coefficient 0.05 (2). The crystal structures and space groups for 1 and 2 are enantiomorphs and the crystallographic investigation confirmed the absolute configuration of the stereocenter in both compounds. 3 crystallizes in the monoclinic space group P2(1)/n(no. 14), a = 8.178 (1) A, b = 14.309 (2) A, c = 12.328 (2) A, beta = 96.811 (6) degrees, V = 1432.4 (2) A(3), Z = 4.

Identification of a human estrogen receptor α-derived antiestrogenic peptide that adopts a polyproline II conformation

Polyproline II (PPII) helix is an extended secondary structure present in a number of proteins. PPII‐containing sequences mediate specific protein–protein interactions with partners containing appropriate cognate domains called PPII‐recognizing domains (PRDs) and are involved in the activation of intracellular signaling pathways. Thus, the identification of PPII structures in proteins is of great interest, not only to explore molecular and physiological mechanisms, but also to elaborate new potential drugs. By revisiting X‐ray crystal structures of liganded α‐type human estrogen receptor (ERα), we have identified an 11‐residue PPII‐helical sequence (D321AEPPILYSEY331) in the ligand‐binding domain of the receptor. The data recorded by far‐ultraviolet circular dichroism (far‐UV CD), vibrational Raman optical activity (ROA) and differential scanning calorimetry (DSC) show that the corresponding peptide (Ac‐DAEPPILYSEY‐NH2) is particularly well structured in PPII, with the same proportion of PPII as observed from X‐ray structures (∼85%). In addition, studies carried out on ERα‐negative Evsa‐T breast cancer cells transiently co‐transfected with a pcDNA3‐ERα plasmid and a Vit‐tk‐Luc reporter gene revealed that the peptide antagonizes the estradiol‐induced transcription providing perspectives for researching new molecules with antagonistic properties. Copyright