Arg–Cys and Arg–cysteamine adsorbed on gold and the G-protein–adsorbate interaction

The dipeptide, Arg–Cys, and the related molecule, Arg–cysteamine, are adsorbed to gold surfaces and the monolayers are characterized. Chemical binding and electronic structure of the monolayers are obtained by X-ray photoelectron spectroscopy (XPS). Strong molecular binding of the adsorbates to gold surface through the sulfur atom is attained. Orientation of the adsorbates on gold is studied using infrared reflection absorption spectroscopy (IRAS). Arg–Cys is interpreted to be adsorbed on gold in a compact configuration. The Arg–cysteamine molecule is adsorbed on gold with the main molecular axis perpendicular to the surface. Interaction of G-protein with the adsorbates was studied using the surface plasmon resonance (SPR) technique. It is believed that arginine has a major role in G-protein recognition since the G-protein-coupled receptor (GPCR) ₂A has an arginine-rich region in the G-protein-binding part of the third intracellular loop.     

Reactivity of Tyr–Leu and Leu–Tyr dipeptides: identification of oxidation products by liquid chromatography–tandem mass spectrometry

The exposure of peptides and proteins to reactive hydroxyl radicals results in covalent modifications of amino acid side‐chains and protein backbone. In this study we have investigated the oxidation the isomeric peptides tyrosine–leucine (YL) and leucine–tyrosine (LY), by the hydroxyl radical formed under Fenton reaction (Fe²⁺/H₂O₂). Through mass spectrometry (MS), high‐performance liquid chromatography (HPLC‐MS) and electrospray tandem mass spectrometry (HPLC‐MSⁿ) measurements, we have identified and characterized the oxidation products of these two dipeptides. This approach allowed observing and identifying a wide variety of oxidation products, including isomeric forms of the oxidized dipeptides. We detected oxidation products with 1, 2, 3 and 4 oxygen atoms for both peptides; however, oxidation products with 5 oxygen atoms were only present in LY. LY dipeptide oxidation leads to more isomers with 1 and 2 oxygen atoms than YL (3 vs 5 and 4 vs 5, respectively). Formation of the peroxy group occurred preferentially in the C‐terminal residue. We have also detected oxidation products with double bonds or keto groups, dimers (YL–YL and LY–LY) and other products as a result of cross‐linking. Both amino acids in the dipeptides were oxidized although the peptides showed different oxidation products. Also, amino acid residues have shown different oxidation products depending on the relative position on the dipeptide. Results suggest that amino acids in the C‐terminal position are more prone to oxidation. Copyright © 2009 John Wiley & Sons, Ltd.     

Conformational study on telaprevir by HPLC–DAD–MS and theoretical calculation

Telaprevir is a potent, selective, peptidomimetic inhibitor of the hepatitis C virus (HCV) NS3‐4A serine protease. it is used for the treatment of HCV infection in combination with peginterferon alfa and ribavirin. In the present work, the E–Z isomerization process of telaprevir in solution was revealed by online HPLC–DAD (diode array detector)–MS, variable‐temperature and variable‐gradient experiments. The molecular geometry information of the two isomers was established by molecular mechanics calculations, and good correlation between the two isomers' UV–vis spectra and their molecular geometry information was also discovered. In addition, it was revealed by molecular docking that the two isomers have different affinities to HCV NS3?4A protease, and the Z isomer, the minor form of telaprevir in solution, is the more effective inhibitor of HCV NS3?4A protease. The investigation can provide more structure information about telaprevir in solution and in the binding process of HCV NS3?4A protease.     

N‐Z‐Pro–d‐Leu using synchrotron radiation data from a very small crystal

The crystal structure of the neuroactive artificial dipeptide N‐­benzyl­oxy­carbonylprolyl‐d ‐leucine, C₁₉H₂₆N₂O₅, was solved using synchrotron radiation data collected on a very small crystal (20 × 20 × 380 μm). The mol­ecules form hydrogen‐bonded 2₁ helices. The acid carbonyl group does not participate in strong hydrogen bonds. This is interpreted as a consequence of close‐packing requirements.     

Conformational changes and excitation energy transfer in myosin–auramine O system

In the myosin–auramine O system 10 or 11 binding sites of auramine O on the rod-like part of myosin were discovered. The myosin fluorescence decreases with an increase in auramine O concentration. This is evidence of the excitation energy transfer from tryptophanyls situated near the binding sites to auramine O. The effective distance of energy transfer is 35 Å. It is suggested that the light meromyosin has binding sites with periodicities of 77-86 Å. Every binding site has a negative charge and hydrophobic locus.     

Perturbative calculation of the Hartree–Fock interaction energy using orthogonalized orbitals

A many‐body perturbation theory based on the partitioning of the dimer Hamiltonian, formulated in an orthogonalized basis set, is used for the calculation of interaction energies at the Hartree–Fock (HF) level. Numerical results for the (HF)₂ and (H₂O)₂ systems in selected geometries are presented. The interaction‐energy components are compared with the results obtained from the standard supermolecular approach and the intermolecular perturbation theory based on the biorthogonal basis set. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 81–88, 1999     

Energetic switch of the proline effect in collision‐induced dissociation of singly and doubly protonated peptide Ala‐Ala‐Arg‐Pro‐Ala‐Ala

Suppression of the selective cleavage at N‐terminal of proline is observed in the peptide cleavage by proteolytic enzyme trypsin and in the fragment ion mass spectra of peptides containing Arg‐Pro sequence. An insight into the fragmentation mechanism of the influence of arginine residue on the proline effect can help in prediction of mass spectra and in protein structure analysis. In this work, collision‐induced dissociation spectra of singly and doubly charged peptide AARPAA were studied by ESI MS/MS and theoretical calculation methods. The proline effect was evaluated by comparing the experimental ratio of fragments originated from cleavage of different amide bonds. The results revealed that the backbone amide bond cleavage was selected by the energy barrier height of the fragmentation pathway although the strong proton affinity of the Arg side chain affected the stereostructure of the peptide and the dissociation mechanism. The thermodynamic stability of the fragment ions played a secondary role in the abundance ratio of fragments generated via different pathways. Fragmentation studies of protonated peptide AACitPAA supported the energy‐dependent hypothesis. The results provide an explanation to the long‐term arguments between the steric conflict and the proton mobility mechanisms of proline effect.     

Multicanonical Monte Carlo calculation of the free‐energy map of the base–amino acid interaction

The specific interactions between base pairs and amino acids were studied by the multicanonical Monte Carlo method. We sampled numerous interaction configurations and side‐chain conformations of the amino acid by the multicanonical algorithm, and calculated the free energies of the interactions between an amino acid at given C_α positions and a fixed base pair. The contour maps of free energy derived from this calculation represent the preferred C_α position of the amino acid around the base, and these maps of various combinations of bases and amino acids can be used to quantify the specificity of intrinsic base–amino acid interactions. Similarly, enthalpy and entropy maps will provide further details of the specific interactions. We have also calculated the free‐energy map of the orientations of the C_α C_β bond vector, which indicates the preferential orientation of the amino acid against the base. We compared the results obtained by the multicanonical method with those of the exhaustive sampling and canonical Monte Carlo methods. The free‐energy map of the base–amino acid interaction obtained by the multicanonical simulation method was nearly identical to the accurate result derived from the exhaustive sampling method. This indicates that a single multicanonical Monte Carlo simulation can produce an accurate free‐energy map. Multicanonical Monte Carlo sampling produced free‐energy maps that were more accurate than those produced by canonical Monte Carlo sampling. Thus, the multicanonical Monte Carlo method can serve as a powerful tool for estimating the free‐energy landscape of base–amino acid interactions and for elucidating the mechanism by which amino acids of proteins recognize particular DNA base pairs. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 954–962, 2000     

Conformational structure of the tetrapeptide Boc–Aib–Leu–Leu–Aib–OMe–the central fragment of the nonapeptide antibiotic leucinostatin A

The conformational structure of the tetrapeptide Boc–Aib–Leu–Leu–Aib–OMe has been investigated by the PCILO method. The computational results show the formation of two closed β-turns, both of which are of type III, and the peptide backbone folds into a right-handed 3₁₀-helical conformation stabilized by two intramolecular 4 → 1 hydrogen bonds. The helix thus formed generates a pore of ～3 Å along helix axis with hydrophobic amino acid side chains located on the outside of the helix, and this tendency of leucine side chains may enable leucinostatin A to fit into the membrane bilayer. The pore thus formed is cation-selective, and through this pore, the cation can pass only in a single file.     

Conformational energy contribution to the heat of solution in polymer–solvent systems. Part I. Theory

The conformational energy contribution (ΔU_conf) to the heat of solution in polymer-solvent systems is presented and discussed in connection with chain conformational properties. In particular, ΔU_conf has been discussed in terms of various possible mechanisms of coil deformation.     

First‐principles calculation of OH−/OH adsorption on gold nanoparticles

The OH^? and OH adsorption structures on Au₅₅ and Au₁₃ nanoparticles surfaces are analyzed using density functional theory. The most stable OH^? adsorption site of Au₅₅ and Au₁₃ nanoparticles is found to be the vertex top site followed by the (111)‐(100) edge bridge site. On the contrary, the stability order of OH adsorption is opposite to that of OH^?. The adsorption of OH^? is calculated to be weaker than that of OH, which shows different charge transfer and interactions with gold surface. Coadsorption on nanoparticles is studied to find that multiple OH^? species prefer the most stable sites of single OH^? adsorption. The hydrogen bonding between adsorbed OH^? on gold surface is a key factor in stabilizing the adsorbates on the Au surface. © 2015 Wiley Periodicals, Inc.     

Conformational energy contribution to the heat of solution in polymer–solvent systems. Part II. Experimental results

Heats of solution (ΔH_exp) in solvents of increasing thermodynamic power have been measured for four polymers: polystyrene (PS), poly(vinyl acetate) (PVAc), polyisobutylene (PIB) and polydimethylsiloxane (PDMS). After subtraction from ΔH_exp of an interaction term (calculated by the Hildebrand treatment based on solubility parameters) and the excess volume term, the quantity remaining is interpreted as the conformational energy contribution (ΔU_conf) to the heat of solution. ΔU_conf appears to correlate well with some basic conformational properties of the chain, such as the sign of the temperature coefficient of unperturbed dimensions derived from solution properties, and shows a monotonic behavior with α, the expansion coefficient of the polymer coil in the final solution. Numerical values of ΔU_conf, at least for those cases in which polymer solubility parameters are known with some certainty, are much larger than those evaluated from rubber elasticity experiments (through the experimentally accessible value of the energy component of the force of retraction im simple elongation).     

cyclo(‐Cha–Oxz–d‐Val–Thz–Ile–Oxz–d‐Val–Thz‐) N,N‐di­methyl­acetamide dihydrate: a square form of cyclo­hexyl­alanine‐incorporated ascidiacycl­amide having the strongest cytotoxicity

The title compound, 1‐cyclo­hexyl­methyl‐1‐de(1‐methyl­propyl)­asci­dia­cycl­amide N,N‐di­methyl­acet­amide di­hy­drate, C₃₉H₅₆N₈O₆S₂·C₄H₉NO·2H₂O, a cyclo­hexyl­alanine‐incorporated ascidiacycl­amide analogue ([Cha]ASC), shows a square form similar to natural ASC. On the other hand, CD (circular dichroism) spectra showed [Cha]ASC to have a folded structure in solution, making it the second known analogue to show a discrepancy between its crystal and solution structures. Moreover, the cytotoxicity of [Cha]ASC (ED₅₀ = 5.6 µg ml⁻¹) was approximately two times stronger than that of natural ASC or a related phenyl­alanine‐incorporated analogue, viz. cyclo(‐Phe–Oxz–d ‐Val–Thz–Ile–Oxz–d ‐Val–Thz‐) ([Phe]ASC), and was confirmed to be associated with the square form. However, [Phe]ASC was previously shown to be folded in the crystal structure, which suggests that the difference between the aromatic and aliphatic rings affects the molecular folding of the ASC mol­ecule.     

Electrostatic energy calculations by a Finite-difference method: Rapid calculation of charge–solvent interaction energies

Finite-difference Poisson–Boltzmann (FDPB) methods allow a fast and accurate calculations of the reaction field (charge–solvent) energies for molecular systems. Unfortunately, the energy in the FDPB calculations includes the self-energies and the finite-difference approximation to the Coulombic energies as well as the reaction field energy. A second finite-difference calculation, in a uniform dielectric, is therefore necesssary to eliminate these contributions. In this article we describe a rapid and accurate method to calculate the self energy and finite-difference Coulombic energies in a uniform dielectric thus eliminating the need for a second finite-difference calculation. The computational savings for this method range from a factor of 4 for a typical protein to a factor of 10³ for small molecules. © 1992 by John Wiley & Sons, Inc.     

Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase

The controversial 'near attack conformation'(NAC) effect in the important model enzyme chorismate mutase is calculated to be 3.8-4.6 kcal mol(-1) by QM/MM free energy perturbation molecular dynamics methods, showing that the NAC effect by itself does not account for catalysis in this enzyme.     

Ab initio calculation for inner reorganization energy of gas-phase electron transfer in organic molecule–ion systems

A series of electron transfer (ET) reactions between some organic molecules have been investigated through ab initio calculations. Biphenyl (Bp) and 9,9^′-dimethylfluorene anion radicals are chosen as the donor, whereas several organic molecules with different redox abilities are chosen as the acceptor. The inner reorganization energy and the endothermicity of the ET reactions in those molecule–ion systems have been estimated through the HFSCF and complete active space multiconfiguration SCF calculations. Double-well potentials for the gas-phase ET reactions have been constructed using the linear reaction coordinate, and the results show that the quinone-containing ET reactions are in Marcus' inverted region. It has been found that the inner reorganization energies are different for various donor-acceptor couples, unlike the experimentally fitted ones. The contribution from the inter-ring torsional motion in Bp to the inner reorganization energy has been evaluated from the energy difference of the biphenyl-acceptor and the dimethylfluorine-acceptor systems. Comparisons with the experimentally observed results have been made.     

Conformational Properties of Arenicins: From the Bulk to the Air–Water Interface

The structures of two antimicrobial peptides (arenicin Ar‐1 and its linear derivative C/S‐Ar‐1) are studied in different solutions and at the air–water interface using spectroscopic methods such as circular dichroism (CD) and infrared reflection absorption spectroscopy (IRRAS) as well as grazing incidence X‐ray diffraction (GIXD) and specular X‐ray reflectivity (XR). Both peptides exhibit similar structures in solution. In the buffer used for most of the experiments the main secondary structure elements are 22 % β‐turn, 38 % β‐sheet and 38 % random coil. The amphiphilic peptides are surface‐active and form a Gibbs monolayer at the air–buffer interface. The surface activity is drastically increased by increasing the ionic strength of the subphase. The β‐sheet layer is quite stable and can be compressed to higher surface pressures. This adsorption layer is very crystalline. Bragg peaks corresponding to an interstrand distance of 4.78 Å and to an end‐to‐end distance have been observed. This end‐to‐end distance can be connected with the observed differences in the layer thickness leading to the assumption that the peptides form a hairpin which is bended depending on the interactions with the counterions.