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The application of the multicanonical simulation method to small proteins and peptides seems to be feasible and should be undertaken. In this work, the three-dimensional structures of five common tetrapeptide sequences (QPGQ, QSGQ, YPTS, SPQQ and QPGY, in one letter code) in the repetitive central domain of HMW glutenin subunits are investigated by using the multicanonical simulation procedure. Ramachandran plots were prepared and analyzed to predict the relative occurrence probabilities of β-turn and γ-turn structures and helical states. Structural predictions of the five tetrapeptide sequences indicated the presence of high level of β-turns and considerable level of γ-turns. It was also possible to distinguish different type of turns and their occurrence probabilities.

The three-dimensional structures of two hexapeptide repeat motifs (PGQGQQ and SGQGQQ, in one letter code) in the repetitive central domain of HMW glutenin subunits are investigated by using the multicanonical simulation procedure. Ramachandran plots were prepared and analyzed to predict the relative occurrence probabilities of β-turn and γ-turn structures and helical state. Structural predictions of PGQGQQ repeat motif indicated the presence of high level of β-turns and considerable level of γ-turns. Simulations of the repeat motifs in the repetitive central domain of HMW glutenin subunits indicated that these structures take important part in the three-dimensional structures of repeat motifs.

We propose a hybrid algorithm, which combines the features of the energy landscape paving (ELP) and Monte Carlo Minimization (MCM) methods. We have tested its performance in studying the low-energy conformations of the heptapeptide deltorphin.

A combination of replica exchange Monte Carlo sampling techniques and energy landscape paving approach is presented. This hybrid algorithm combines the features of the energy landscape paving (ELP) and replica exchange methods (REM). I have tested its performance in studying the low-energy conformations of the benchmark peptide Met-enkephalin.

Molecular dynamics simulation is performed to investigate self-insertion behaviors of peptides into single-walled carbon nanotubes (SWCNTs) in water environment. Peptides of different hydrophobicities and varied lengths are tested to show that the propensities of peptides to self-insert into SWCNTs differ drastically. Our results indicate that there exists a potential well for the system of SWCNT and peptide that is able to self-insert into the nanotube. Further investigations of energy components demonstrate that electrostatic interactions, combined with van der Waals interactions, play dominant roles in the self-insertion of peptides into nanotubes. In addition, we also observe a significant correlation between the propensity of a peptide to insert into nanotube and its hydrophobicity. Such results provide valuable information on the potential applications of carbon nanotubes in the fields of drug delivery, drug design and protein control, etc.

Bionomics Acquires Melbourne-based Iliad Chemicals.

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Mesoporous silica composites filling densely peptide assemblies (Proteosilica) were newly synthesized as transparent films. Spiropyran guest was co-doped in the films and photo-isomerization between spiropyran form and merocyanine form was repeated by alternate irradiation of visible and UV lights. Circular dichroism (CD) active spectra were observed only for the spiropyran form in the Proteosilica with hexagonal geometry. However, the CD active behavior was absent for the spiropyran in lamellar Proteosilica. Difference in peptide assembling structures would affect chiral sensitivity of the doped spiropyran guest.

The present article reviews the self-assembly of oligopeptides to form nanostructures, both in solution and in solid state. The solution structures of the peptides were examined using circular dichroism and dynamic light scattering. The solid state assembly was examined by adsorbing the peptides onto a mica surface and analyzing it using atomic force microscopy. The role of pH and salt concentration on the peptide self-assembly was also examined. Nanostructures within a size range of 3–10 nm were obtained under different conditions.

Computation of accurate hydrogen bonding energies in peptides is of great importance in understanding the conformational stabilities of peptides. In this paper, the intramolecular 8- and 12-membered ring N–H…O=C hydrogen bonding energies in β-peptide structures were evaluated. The optimal structures of the β-peptide conformers were obtained using MP2/6-31G(d) method. The MP2/6-311++G(d,p) calculations were then carried out to evaluate the single-point energies. The results show that the intramolecular 8-membered ring N–H…O=C hydrogen bonding energies in the five β-dipeptide structures β-di, β-di-R1, β-di-R2, β-di-R3, and β-di-R4 are -5.50, -5.40, -7.28, -4.94, and -6.84 kcal/mol with BSSE correction, respectively; the intramolecular 12-membered ring N–H…O=C hydrogen bonding energies in the nine β-tripeptide structures β-tri, β-tri-R1, β-tri-R2, β-tri-R3, β-tri-R4, β-tri-R1', β-tri-R2', β-tri-R3' and β-tri-R4' are -10.23, -10.32, -9.53, -10.30, -10.32, -10.55, -10.09, -10.51, and -9.60 kcal/mol with BSSE correction, respectively. Our calculation results further indicate that for the intramolecular 8-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "a–a" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "e–e", while for the intramolecular 12-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "e–e" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "a–a". The method is also applied to estimate the individual intermolecular hydrogen bonding energies in the dimers of amino-acetaldehyde, 2-amino-acetamide, 2-oxo-acetamide, and oxalamide, each dimer having two identical intermolecular hydrogen bonds. According to our method, the individual intermolecular hydrogen bonding energies in the four dimers are calculated to be -1.71, -1.50, -4.67, and -3.22 kcal/mol at the MP2/6-311++G(d,p) level, which are in good agreement with the values of -1.84, -1.72, -4.93, and -3.26 kcal/mol predicted by the supermolecular method.

Two new zinc(II)porphyrin oligopeptide conjugates (zinc(II)-5,10,15,20-bis[4-(peptide)- phenyl]porphyrin (5) and -tetrakis[3,5-di(peptide)phenyl]porphyrin (9; peptide = -CH₂(CO)Gly-Phe-Ala-CNH₂) were prepared using the click chemistry with azides and ethynyl-containing precursors. The spectroscopic signature (S₀→S₁ and transient T₁→T_n absorption, excitation and emission spectra) are typical for zinc(II)porphyrin and shows no perturbation upon anchoring the oligopeptides, whereas some small decreases in the photophysical parameters (𝜏_F and Φ_F), and larger decrease in T₁ lifetimes are noted, which are attributable to the known "loose bolt" effect. The structure for 9 in solution was addressed qualitatively using computer modeling and the comparison of the bimolecular fluorescence quenching rate constants between 5 and 9 using C₆₀ as a photooxidative agent. While 5 exhibits a totally accessible zinc(II)porphyrin unit for a C₆₀ approach, 9 shows a slower quenching rate constant meaning some steric hindrance must be present.

This paper proposes a new paradigm for the biophysical concept of measuring the affinity of molecular complexes, based on a matrix representation of biological interactions and subsequent numerical analysis of the stability of this matrix. Our numerical criterion of stability (lg(cond($W$))) correlates well with experimental values such as $K_d$ and IC${}_{50}$ as well as with experimental data of aggregation kinetics in studies of amyloid peptides. The main goal of this work is to reduce the cost of biochemical experiments by obtaining preliminary information on the interaction of chemical compounds. The paper also presents our numerical calculations in comparison with a large amount of experimental data on the examples of binding of small chemical molecules gefitinib, erlotinib, imatinib, naquatinib, and CO-1686 with proteins, protein–peptide interactions of the Bcl-2 protein family, antibody–antigen CD20–rituximab, and aggregation of amyloid peptides. The description of the software package that implements the presented algorithm is given on the website: https://binomlabs.com/.

With the demonstration of direct electron transfer between the redox active prosthetic group, flavin adenine dinucleotide (FAD), of glucose oxidase (GOx) and single-walled carbon nanotubes (SWCNT), there has been growing interest in the fabrication of CNT-enzyme supramolecular constructs that control the placement of SWCNTs within the tunneling distance of co-factors for enhanced electron transfer efficiency in generation-3 biosensors and advanced biofuel cells. These conjugate systems raise a series of questions such as: which peptide sequences within the enzymes have high affinity for the SWCNTs? And, are these high affinity sequences likely to be in the vicinity of the redox-active co-factor to allow for direct electron transfer? Phage display has recently been used to identify specific peptide sequences that have high affinity for SWCNTs. Molecular dynamics simulations were performed to study the interactions of five discrete peptides with (16,0) SWCNT in explicit water as well as with graphene. From the progression of the radius of gyration, R_g, the peptides studied were concertedly adsorbed to both the SWCNT and graphene. Peptide properties calculated using individual amino acid values, such as hydrophobicity indices, did not correlate with the observed adsorption behavior as quantified by R_g, indicating that the adsorption behavior of the peptide was not based on the individual amino acid residues. However, the R_g values, reflective of the physicochemical embrace of the surface (SWCNT or graphene) had a strong positive correlation with the solubility parameter, indicating concerted, cooperative interaction of peptide segments with the materials. The end residues appear to dominate the progression of adsorption regardless of character. Sequences identified by phage display share some homology with key enzymes (GOx, lactate oxidase and laccase) used in biosensors and enzyme-based biofuel cells. These analogous sequences appear to be buried deep within the shell of fully folded proteins and as such are expected to be close to the redox-active prosthetic group.

Engineering the molecular assembly at biomolecular interface is one of the prevailing techniques in synthetic biology to derive novel supramolecular structures. In this study, we have biofunctionalized polyoxometalates with peptide-based cationic polymer. Surface functionalization of polyoxometalates (POMs) results in derivation of self-assembled polymer–POM nanocomposites with novel antifungal activity. Electron rich POM triggers the morphological alteration in molecularly enriched $\beta$-sheet peptide polymer promoting the evolution of nanorods. Due to the inherited biocidal properties of the cationic polymer and the POM, the nanorods exhibit enhanced antifungal activity highlighting the significance of combinatorial systems in advanced drug therapeutics.

Mesoporous silica composites filling densely peptide assemblies (Proteosilica) were newly synthesized as transparent films. Spiropyran guest was co-doped in the films and photoisomerization between spiropyran form and merocyanine form was repeated by alternate irradiation of visible and UV lights. Circular dichroism (CD) active spectra were observed only for the spiropyran form in the Proteosilica with hexagonal geometry. However, the CD active behavior was absent for the spiropyran in lamellar Proteosilica. Difference in peptide assembling structures would affect chiral sensitivity of the doped spiropyran guest.

The present article reviews the self-assembly of oligopeptides to form nanostructures, both in solution and in solid state. The solution structures of the peptides were examined using circular dichroism and dynamic light scattering. The solid state assembly was examined by adsorbing the peptides onto a mica surface and analyzing it using atomic force microscopy. The role of pH and salt concentration on the peptide self-assembly was also examined. Nanostructures within a size range of 3–10 nm were obtained under different conditions.