Discrimination between the Two Closely Related Species of the Operational Group Based on Whole-Cell Fatty Acid Profiling.

(1) Background: and are closely related members of the "operational group ", a taxonomical unit above species level within the " species complex". They have similar morphological, physiological, biochemical, phenotypic, and phylogenetic characteristics. Thus, separating these two taxa from each another has proven to be difficult to implement and could not be pushed easily into the line of routine analyses.

Studying the helical conformations of aspereline peptides.

Asperelines are short-sequence peptaibol molecules, and these peptides composed of 10 residues were isolated from the Trichoderma asperellum. In our study, a detailed structural characterization was performed on the asperelines by means of molecular dynamics methods. For the aspereline peptides, the occurrence of various secondary structural elements (i.

Diversity Profile and Dynamics of Peptaibols Produced by Green Mould Trichoderma Species in Interactions with Their Hosts Agaricus bisporus and Pleurotus ostreatus.

Certain Trichoderma species are causing serious losses in mushroom production worldwide. Trichoderma aggressivum and Trichoderma pleuroti are among the major causal agents of the green mould diseases affecting Agaricus bisporus and Pleurotus ostreatus, respectively. The genus Trichoderma is well-known for the production of bioactive secondary metabolites, including peptaibols, which are short, linear peptides containing unusual amino acid residues and being synthesised via non-ribosomal peptide synthetases (NRPSs).

Characterizing the structural and folding properties of long-sequence hypomurocin B peptides and their analogs.

We studied the folding processes of long-sequence hypomurocin (HM) peptides and their analogs by means of molecular dynamics methods, focusing on the formation of various helical structures and intramolecular H-bonds. The evolution of different helical conformations, such as the 310 -, α-, and left-handed α-helices, was examined, taking into account the entire sequence and each amino acid of peptides. The results indicated that the HM peptides and their analogs possessed a propensity to adopt helical conformations, and they showed a preference for the 310 -helical structure over the α-helical one.

Studying the structural and folding features of long-sequence trichobrachin peptides.

In this theoretical study, the folding processes of long-sequence trichobrachin peptides (i.e., TB IIb peptides) were investigated by molecular dynamics methods.

In silico conformational analysis of the short-sequence hypomurocin a peptides.

In this theoretical study, a conformational analysis was performed on short-sequence hypomurocin A peptides, in order to identify their characteristic structural properties. For each hypomurocin A molecule, not only the backbone conformations, but also the side-chain conformations were examined. The results indicated that certain tetrapeptide units could be characterized by types I and III β-turn structures, and considering the helical conformations, it could be concluded that the hypomurocin A peptides showed a preference for the 310-helical structure over the α-helical structure.

On the Hofmeister effect: fluctuations at the protein-water interface and the surface tension.

We performed molecular dynamics simulations on the tryptophane-cage miniprotein using a nonpolarizable force field, in order to model the effect of concentrated water solutions of neutral salts on protein conformation, which is a manifestation of Hofmeister effects. From the equilibrium values and the fluctuations of the solvent accessible surface area of the miniprotein, the salt-induced changes of the mean value of protein-water interfacial tension were determined. At 300 K, the chaotropic ClO4(-) and NO3(-) decreased the interfacial tension according to their position in the Hofmeister series (by approximately 5 and 2.

Characteristic structural features of indolicidin: effects of the cis-trans isomerism on its conformation.

Indolicidin is an antimicrobial peptide showing a broad spectrum of antibacterial and antifungal activities, and according to the cis-trans isomerism of three Xaa-Pro peptide bonds, eight different stereoisomers could be distinguished for this peptide. As the cis-trans isomerism about the Xaa-Pro peptide bonds was not considered in previous studies, the structural features of distinct stereoisomeric forms were not characterized in detail, so far. In this theoretical study, the influences of cis-trans isomerism on the conformation of indolicidin were investigated, as well as the typical structural properties of each stereoisomer were determined, focusing on the secondary structures and intramolecular interactions.

Structural characterization of the short peptaibols trichobrachins by molecular-dynamics methods.

A structural characterization was carried out by molecular-dynamics methods for eight trichobrachin peptides, to identify the conformational features of these short peptaibols. For all peptides, the backbone and side-chain conformations were investigated, different secondary structures, such as type-I and -III β-turns as well as β-bend ribbon spirals, were determined in certain tetrapeptide units of the molecules, and the preferred rotamers of the side chains of amino acids were identified. Furthermore, the end-to-end and residueresidue distances were examined, as well as the fluctuations of backbone atoms were studied.

Effects of missense mutation on structure and function of photoreceptor.

Phytochromes (PHYs) are photoreceptors of the red (R ~660 nm) and far-red (FR ~730 nm) light, and they control a wide range of responses affecting crucial aspects of plant life. There are five genes PHYA-PHYE encoding for phytochromes of different but overlapping function. One of these, PHYA has the unique function controlling specific responses in high irradiance far-red, as well as in very weak light.

Conformational similarities and dissimilarities between the stereoisomeric forms of endomorphin-2.

In this study, taking into account both the l-d and cis-trans isomerisms, a comprehensive structural characterization and a comparative conformational analysis were performed on the 32 stereoisomeric forms of opioid tetrapeptide, endomorphin-2. For all stereoisomers, the Φ-Ψ and χ conformational spaces were explored, in the course of which the conformational distributions, as well as the rotamer states of aromatic side chains were characterized in detail. Furthermore, the typical β- and γ-turn structures, as well as the characteristic intramolecular interactions (i.

Exploring and characterizing the folding processes of Lys- and Arg-containing Ala-based peptides: a molecular dynamics study.

In this study, molecular dynamics simulations were carried out on Lys- and Arg-containing Ala-based peptides (i.e. Ace-(AAAAK)(n)A-NH(2) and Ace-(AAAAR)(n)A-NH(2), where n=1-4), in order to explore and characterize their folding processes.

Comprehensive structural characterization of the cyclic disulphide-bridged nonapeptides, Arg- and Lys-conopressins.

Arg-conopressin-S and Lys-conopressin-G are cyclic disulphide-bridged nonapeptides isolated from the venom of cone snails. We performed a comprehensive conformational analysis for the cis and trans isomers of these conopeptides, in order to identify their characteristic structural and conformational features. In the course of our theoretical study, the Phi-Psi and chi(1) conformational spaces were explored in detail and the conformational distributions were compared to each other.

Studying the structural properties of polyalanine and polyglutamine peptides.

Poly-(Ala) and poly-(Gln) peptides have important biological effects, and can cause various human illnesses and neurodegenerative diseases. Conformational analysis of these homo-oligopeptides (HOPs) was carried out by simulated annealing in order to identify their structural properties regarding secondary structures and intramolecular H-bonding patterns. Poly-(Ala) and poly-(Gln) peptides composed of 7, 10, 14 or 20 amino acids were modelled in both charged and terminally blocked forms.

Complex kinetics of the electron transfer between the photoactive redox label TUPS and the heme of cytochrome c.

The photoinduced covalent redox label 8-thiouredopyrene-1,3,6-trisulfonate (TUPS) has been attached to two lysine residues (K8 and K39) at opposite sides of horse heart cytochrome c, as well as to cysteines, at the same positions, introduced by site-directed mutagenesis. Electron transfer between TUPS and the heme of cytochrome c deviates from the expected monoexponential kinetic behavior. Neither the overall rate nor the individual exponential components of electron transfer, as followed by kinetic absorption spectroscopy, correlate with the length of the covalent link connecting the dye with the protein.

Aromatic-aromatic and proline-aromatic interactions in endomorphin-1 and endomorphin-2.

We investigated the aromatic-aromatic and proline-aromatic interactions in endomorphin-1 and endomorphin-2, and different types of these interactions were observed. For all the interacting pairs, the preferred geometric orientations were identified. We examined these interactions in the preferred secondary structures, which are different types of beta-turns and gamma-turns.

Comparative study of SP[6-11] and its analogs using simulated annealing.

In this study we compared the steric structures of the bioactive part of substance P (SP[6-11]) and its analogs (NY3460 and pHOPA-SP5). The molecular dynamics-simulated annealing method was used to explore the conformational space, and the structural differences and similarities of these molecules were identified. For the three peptides, the conformational distributions were represented in Ramachandran density plots.

Conformational analysis of endomorphin-2 by molecular dynamics methods.

Endomorphin-2 (EM2, H-Tyr-Pro-Phe-Phe-NH(2)) is a highly potent and selective mu-opioid receptor agonist. A conformational analysis of EM2 was carried out by simulated annealing (SA) and molecular dynamics (MD) methods. Molecular modeling was conducted on both neutral (N-terminal NH(2)) and charged (N-terminal NH(3) (+)) molecules.