Lattice models of peptide aggregation: evaluation of conformational search algorithms

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.     

Intercalation assembly of kojic acid into Zn-Ti layered double hydroxide with antibacterial and whitening performances

The inhibitor of melanin and the bacteriostatic agent kojic acid was inserted into Zn-Ti layered double hydroxide (LDH) by anion-exchange reaction. The structure, slow release, antibacterial and skin whitening activity were studied.     

Solid-phase synthesis of metal-complex containing peptides

We report the synthesis of Fmoc protected single amino acid chelates (SAAC) and their metal complexes. The modified amino acids are suitable for solid-phase peptide synthesis. The use of 4-hydroxymethylbenzoic acid AM (HMBA-AM) resin allows the nucleophilic cleavage of the peptide-metal complexes from the resin without decomplexation.     

磷酰化肽链中电子转移的ESR研究

当前生命科学正以前所未有的速度向前发展，从对核酸的深入研究开始过渡到对蛋白质结构与功能的注意，尤其是近年来基因调控研究的重大进展是发现非组蛋白具有高度的磷酸化的特性［1］，研究证明，核内蛋白磷酸化和去磷酸化则是基因表达调控的重要方式之一［2，3］，它是酶活性调节、基因表达调控、细胞转化恶变的关键环节；同时在解决肿瘤的发生和治疗、病毒的感染和诊治、辐射损伤、抗衰老等实际问题上有突出意义，如1992年Krebus和Fisher因为在蛋白的可逆磷酸化方面的突出贡献而获得诺贝尔生理和医学奖．而电子转移是一切化学变化的基础…     

多肽合成中羧基活化方法的一些新进展

本文简要叙述了多肽合成中的羧基活化问题。重点讨论了作者近年来在此领域所进行的工作,如含氮杂环作为活化羧基的离去基团和几个新的含磷多肽试剂。     

Conformational changes of the amyloid beta-peptide (1-40) adsorbed on solid surfaces

The conformational change of the 39-43 residues of the amyloid beta-peptide (Abeta) toward a beta-sheet enriched state promotes self-aggregation of the peptide molecules and constitutes the major peptide component of the amyloid plaques in Alzheimer patients. The crucial question behind the self-aggregation of Abeta is related to the different pathways the peptide may take after cleavage from the amyloid precursor proteins at cellular membranes. This work is aiming at determining the conformation of the Abeta (1-40) adsorbed on hydrophobic Teflon and hydrophilic silica particles, as model sorbent surfaces mimicking the apolar transmembrane environment and the polar, charged membrane surface, respectively. The mechanism by which the Abeta interacts with solid surfaces strongly depends on the hydrophobic/hydrophilic character of the particles. Hydrophobic and electrostatic interactions contribute differently in each case, causing a completely different conformational change of the adsorbed molecules on the two surfaces. When hydrophobic interactions between the peptide and the sorbent prevail, the adsorbed Abeta (1-40) mainly adopts an alpha-helix conformation due to H-bonding in the apolar part of the peptide that is oriented towards the surface. On the other hand, when the peptide adsorbs by electrostatic interactions beta-sheet formation is promoted due to intermolecular association between the apolar parts of the adsorbed peptide. Irrespective of the characteristics of the solid sorbent, crowding the surface results in intermolecular association between adsorbed molecules leading to a strong aggregation tendency of the Abeta (1-40). [Diagram: see text] CD spectra of Abeta (1-40) at pH 7: A) in solution ([Abeta]=0.2 mg.ml(-1)) freshly prepared (line) and after overnight incubation (symbols);B) on Teflon (Gamma=0.5 mg.m(-2)).     

Synthesis and antimicrobial activity of a perfluoroalkyl-containing quaternary ammonium salt

A novel perfluoroalkyl-containing quaternary ammonium salt 5 was designed and synthesized. Consequently, the antimicrobial activities of compound 5 were measured with Escherichia coli 8099 as a Gram-negative strain and Staphylococcus aureus ATCC 6538 as a Gram-positive strain. Both the minimum inhibitory concentration (MIC, the lowest concentration of compound 5 that inhibits microbial growth) values of quaternary ammonium salt 5 against Escherichia coli 8099 and Staphylococcus aureus ATCC 6538 were 7.8 μg/ml.     

Synthesis,characterization and antimicrobial studies on 13-membered-N6-macrocyclic transition metal complexes containing trimethoprim

Asymmetrical macrocyclic complexes of Mn^II, Co^II, Ni^II, Cu^II and Zn^II have been synthesized by the template process using bis(benzil)ethylenediamine as precursor. Bis(benzil)ethylenediamine reacts with transition metal chlorides and trimethoprim in a 1:1:1 molar ratio in methanol to give several solid metal complexes of the general composition [M(L)X₂] (M = Mn^II, Co^II, Ni^II, Cu^II and Zn^II, L = ligand and X = Cl^?). They were characterized by physicochemical and spectroscopic techniques. Based on analytical, spectral and magnetic moments, all the complexes are identified as distorted octahedral structures. All the complexes are of the [M(L)X₂] type. The shifts of the ν(CN) (azomethine) stretches have been monitored. To find out the donor sites of the ligands, the activity data show that the metal complexes are more potent than the parent ligand. The [M(L)X₂] complexes showed a broad spectrum of antimicrobial activity in vitro against both gram-positive and gram-negative human pathogenic bacterial isolates and the antimicrobial spectrum enhanced only with a combination of metal chlorides and trimethoprim complex. From the results it is imperative that the synthesized macrocyclic [M(L)X₂] complexes exhibit potent broad spectrum antibacterial activity.     

Structure elucidation and 3D solution conformation of the antibiotic enduracidin determined by NMR spectroscopy and molecular dynamics

Enduracidin and ramoplanin belong to the large family of cyclodepsipeptide antibiotics, highly effective against Gram-positive bacteria. The primary and 3D solution structure of ramoplanin is already well known, and the primary structure of enduracidin has been determined by a combination of chemical and NMR spectroscopic methods. Both antibiotics share a similar peptide core of 17 amino acids and differ mainly in the length of the acyl chain and the presence of two D-mannose moieties in ramoplanin. Based on the high sequence homology with ramoplanin, the structure in solution of enduracidin is modeled as a cyclic peptide. The tertiary structure thus obtained was refined through molecular dynamics (MD) simulation, in which the interatomic NOE-derived distance restraints were imposed. MD simulations yielded a family of representative 3D structures (RMSD = 0.89), which highlighted a backbone geometry similar to that of ramoplanin in its beta-hairpin arrangement. In contrast, enduracidin displays a different arrangement of the side-chain and of the residues forming the hydrophobic core.     

New Cu(II) complexes with polydentate chelating Schiff base ligands: Synthesis, structures, characterisations and biochemical activity studies

We have reported herein the synthesis of three new Cu(II) complexes of tri- and tetradentate Schiff base ligands containing N₃ or N₄ donor set along with terminal NNN⁻ or SCN⁻ ligands: [L¹Cu(NCS)]ClO₄ (1), [L²Cu(NCS)₂] (2) and [L³Cu(NNN)]ClO₄ (3) [L¹ = NC₅H₄C(CH₃)=N(CH₂)₃N=C(CH₃)C₅H₄N, L²= Me₂N–(CH₂)₃–N=C(CH₃)C₅H₄N and L³ = NC₅H₄CH=N–(CH₂)₄–N=CHC₅H₄N]. The complexes have been systematically characterised by elemental, spectroscopic and electrochemical techniques. Antimicrobial activities of the Schiff base ligands and their metal complexes have been studied using the disc diffusion method on the strains of Candida tropicalis and Bacillus megaterium. Structures of all the complexes have been unequivocally established from single crystal X-ray diffraction analyses that show the monomeric units containing a five-coordinated copper center in highly distorted square pyramidal geometry with thiocyanate or azide anion coordinated as terminal ligand. The complexes 1 and 3 crystallise in monoclinic (P2₁/c) and 2 in triclinic (P-1) space group, respectively.