Simulation of conformational changes occurring when a protein interacts with its receptor

In order to simulate the conformational changes occurring when a protein interacts with its receptor, we firstly evaluated the structural differences between the experimental unbound and bound conformations for selected proteins and created theoretical complexes by replacing, in each experimental complex, the protein-bound with the protein-unbound chain. The theoretical models were then subjected to additional modeling refinements to improve the side chain geometry. Comparing the theoretical and experimental complexes in term of structural and energetic factors is resulted that the refined theoretical complexes became more similar to the experimental ones. We applied the same procedure within an homology modeling experiment, using as templates the experimental structures of human interleukin-1beta (IL-1beta) unbound and bound with its receptor, to build models of the homologous proteins from mouse and trout in unbound and bound conformations and to simulate the interaction with the related receptors. Our results suggest that homology modeling techniques are sensitive to differences between bound and unbound conformations, and that modeling with accuracy the side chains in the complex improves the interaction and molecular recognition. Moreover, our refinement procedure could be used in protein-protein interaction studies and, also, applied in conjunction with rigid-body docking when is not available the protein-bound conformation.     

PreSSAPro: a software for the prediction of secondary structure by amino acid properties

PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha–beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the different structural classes. The comparison of these predictions represents a novel tool to evaluate what sequence regions can assume different secondary structures depending on the structural class assignment, in the perspective of identifying proteins able to fold in different conformations. The service is available at the URL http://bioinformatica.isa.cnr.it/PRESSAPRO/.     

Conformational diseases and structure-toxicity relationships: lessons from prion-derived peptides

The physiological form of the prion protein is normally expressed in mammalian cell and is highly conserved among species, although its role in cellular function remains elusive. Available evidence suggests that this protein is essential for neuronal integrity in the brain, possibly with a role in copper metabolism and cellular response to oxidative stress. In prion diseases, the benign cellular form of the protein is converted into an insoluble, protease-resistant abnormal scrapie form. This conversion parallels a conformational change of the polypeptide from a predominantly alpha-helical to a highly beta-sheet secondary structure. The scrapie form accumulates in the central nervous system of affected individuals, and its protease-resistant core aggregates into amyloid fibrils outside the cell. The pathogenesis and molecular basis of the nerve cell loss that accompanies this process are not understood. Limited structural information is available on aggregate formation by this protein as the possible cause of these diseases and on its toxicity. A large amount of structure-activity studies is based on the prion fragment approach, but the resulting information is often difficult to untangle. This overview focuses on the most relevant structural and functional aspects of the prion-induced conformational disease linked to peptides derived from the unstructured N-terminal and globular C-terminal domains.     

Self‐Assembly of Decoupled Borazines on Metal Surfaces: The Role of the Peripheral Groups

Two borazine derivatives have been synthesised to investigate their self‐assembly behaviour on Au(111) and Cu(111) surfaces by scanning tunnelling microscopy (STM) and theoretical simulations. Both borazines form extended 2D networks upon adsorption on both substrates at room temperature. Whereas the more compact triphenyl borazine 1 arranges into close‐packed ordered molecular islands with an extremely low density of defects on both substrates, the tris(phenyl‐4‐phenylethynyl) derivative 2 assembles into porous molecular networks due to its longer lateral substituents. For both species, the steric hindrance between the phenyl and mesityl substituents results in an effective decoupling of the central borazine core from the surface. For borazine 1 , this is enough to weaken the molecule–substrate interaction, so that the assemblies are only driven by attractive van der Waals intermolecular forces. For the longer and more flexible borazine 2 , a stronger molecule–substrate interaction becomes possible through its peripheral substituents on the more reactive copper surface.     

A Brush‐Gel/Metal‐Nanoparticle Hybrid Film as an Efficient Supported Catalyst in Glass Microreactors

A polymer‐brush‐based material was applied for the formation and in situ immobilization of silver and palladium nanoparticles, as a catalytic coating on the inner wall of glass microreactors. The brush film was grown directly on the microchannel interior by means of atom‐transfer radical polymerization (ATRP), which allows control over the polymer film thickness and therefore permits the tuning of the number of nanoparticles formed on the channel walls. The wide applicability of the catalytic devices is demonstrated for the reduction of 4‐nitrophenol and for the Heck reaction.     

Coordination and reactivity of white phosphorus and tetraphosphorus trisulphide in the presence of the fragment CpFe(dppe) [dppe = 1,2-bis(diphenylphosphino)ethane]

The reaction of [CpFe(dppe)Cl] (1) [dppe = 1,2-bis(diphenylphosphino)ethane] with one equivalent of P₄ or P₄S₃ in the presence of a chloride scavenger, TlPF₆ or AgOTf (OTf = triflate, OSO₂CF₃), affords the complexes [CpFe(dppe)(η¹-P₄)]PF₆ (2) and [CpFe(dppe)(η¹-P_basal-P₄S₃)]OTf (3) which contain the tetrahedral P₄ and the mixed P₄S₃ cage molecule η¹-bound to the metal. Both P₄ and P₄S₃ yield furthermore the dimetal compounds [{CpFe(dppe)}₂(μ,η^1:1-P₄)](PF₆)₂ (4) and [{CpFe(dppe)}₂(μ,η^1:1-P_apical-P_basal-P₄S₃)](OTf)₂ (5), which contain the tetrahedral P₄ or the mixed-cage P₄S₃ molecule tethering two ruthenium fragments via two phosphorus atoms. All the compounds have been characterized by elemental analyses and NMR measurements. The crystal structure of 4 has been determined by X-ray diffraction methods. The complexes readily react with excess water under mild reaction conditions and the outcoming products have been identified.     

Enzymatic approach to enantiomerically pure 5-alken-2,4-diols and 4-hydroxy-5-alken-2-ones: application to the synthesis of chiral synthons

Enantiomerically pure 1,3-diols 1-3 were obtained by a chemoenzymatic approach (lipase PS from Burkholderia cepacia). These diols were converted into useful chiral synthons, which could be considered homologues of glyceraldehyde and glyceric acid acetonides. Applications of these synthons to the de novo synthesis of sugars and preparation of conagenin carboxylic moiety were shown. Hydroxy ketone 4 was chosen as a model system for another synthetic evolution: it was obtained in enantiomerically pure form by enzymatic resolution and converted into chiral tetrahydropyranes, such as the stereoisomers of the commercial fragrance Gyrane.     

A geometric approach for Hermite subdivision

We present a non-stationary, non-uniform scheme for two-point Hermite subdivision. The novelty of this approach relies on a geometric interpretation of the subdivision steps—related to generalized Bernstein bases—which permits to overcome the usually unavoidable analytical difficulties. The main advantages consist in extra smoothness conditions, which in turn produce highly regular limit curves, and in an elegant structure of the subdivision—described by three de Casteljau type matrices. As a by-product, the scheme is inherently shape preserving.     

Two‐Dimensional Ketone‐Driven Metal–Organic Coordination on Cu(111)

Two‐dimensional metal–organic nanostructures based on the binding of ketone groups and metal atoms were fabricated by depositing pyrene‐4,5,9,10‐tetraone (PTO) molecules on a Cu(111) surface. The strongly electronegative ketone moieties bind to either copper adatoms from the substrate or codeposited iron atoms. In the former case, scanning tunnelling microscopy images reveal the development of an extended metal–organic supramolecular structure. Each copper adatom coordinates to two ketone ligands of two neighbouring PTO molecules, forming chains that are linked together into large islands through secondary van der Waals interactions. Deposition of iron atoms leads to a transformation of this assembly resulting from the substitution of the metal centres. Density functional theory calculations reveal that the driving force for the metal substitution is primarily determined by the strength of the ketone–metal bond, which is higher for Fe than for Cu. This second class of nanostructures displays a structural dependence on the rate of iron deposition.