Reading the three-dimensional structure of a protein from its amino acid sequence

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of a protein whose sequence is known. This situation is not particularly satisfactory, in keeping with the fact that while linear sequencing of the amino acids specifying a protein is relatively simple to carry out, the determination of the folded-native-conformation can only be done by an elaborate X-ray diffraction analysis performed on crystals of the protein or, if the protein is very small, by nuclear magnetic resonance techniques. Using insight obtained from lattice model simulations of the folding of small proteins (fewer than 100 residues), in particular of the fact that this phenomenon is essentially controlled by conserved contacts among strongly interacting amino acids, which also stabilize local elementary structures formed early in the folding process and leading to the (post-critical) folding core when they assemble together, we have worked out a successful strategy for reading the three-dimensional structure of a notional protein from its amino acid sequence.Comment: misprints eliminated and small mistakes correcte

Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding

The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations that build out the transition state is particularly cumbersome, mainly because of the large computational cost of generating a statistically-sound set of folding trajectories. Here we show that a biasing algorithm, based on the physics of the ratchet-and-pawl, can be used to identify efficiently the transition state. The basic idea is that the algorithmic ratchet exerts a force on the protein when it is climbing the free-energy barrier, while it is inactive when it is descending. The transition state can be identified as the point of the trajectory where the ratchet changes regime. Besides discussing this strategy in general terms, we test it within a protein model whose transition state can be studied independently by plain molecular dynamics simulations. Finally, we show its power in explicit-solvent simulations, obtaining and characterizing a set of transition--state conformations for ACBP and CI2

Statistical Analysis of Native Contact Formation in the Folding of Designed Model Proteins

The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable native bonds built by some of the most strongly interacting amino acids of the protein, b) non-local bonds formed late in the folding process, in coincidence with the folding nucleus, and involving essentially the same strongly interacting amino acids already participating in the fast bonds, c) the rest of the native bonds whose behaviour is subordinated, to a large extent, to that of the local- and non-local native contacts

Hiking in the energy landscape in sequence space: a bumpy road to good folders

With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space of sequences. Residues which play a key role in the foldability of the chain and in the stability of the native state are highly conserved, even among the chains belonging to different clusters. If, according to the interaction matrix, some strong attractive interactions are almost degenerate (i.e. they can be realized by more than one type of aminoacid contacts) sequence clusters group into a few super-clusters. Sequences belonging to different super-clusters are dissimilar, displaying very small ($\approx 10$) similarity, and residues in key-sites are, as a rule, not conserved. Similar behavior is observed in the analysis of real protein sequences.Comment: 17 pages 5 figures Corrected typos added auxiliary informatio

Defect chemistry of Ti and Fe impurities and aggregates in Al2O3

We report a theoretical evaluation of the properties of iron and titanium impurities in sapphire (corundum structured α-Al2O3). Calculations using analytical force fields have been performed on the defect structure with the metals present in isolated, co-doped and tri-cluster configurations. Crystal field parameters have been calculated with good agreement to available experimental data. When titanium and iron are present in neighbouring face and edge-sharing orientations, the overlap of the d-orbitals facilitates an intervalence charge transfer (FeIII/TiIII → FeII/TiIV) with an associated optical excitation energy of 1.85 eV and 1.76 eV in the respective configurations. Electronic structure calculations based on density functional theory confirm that FeIII/TiIII is the ground-state configuration for the nearest-neighbour pairs, in contrast to the often considered FeII/TiIV pair. Homonuclear intervalence charge transfer energies between both FeIII/FeII and TiIV/TiIII species have also been calculated, with the energy lying in the infra-red region. Investigation of multiple tri-clusters of iron and titanium identified one stable configuration, TiIII–(TiIV/FeII), with the energy of electron transfer remaining unchanged

Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers

One of the main problems of drug design is that of optimizing the drug--target interaction. In the case in which the target is a viral protein displaying a high mutation rate, a second problem arises, namely the eventual development of resistance. We wish to suggest a scheme for the design of non--conventional drugs which do not face any of these problems and apply it to the case of HIV--1 protease. It is based on the knowledge that the folding of single--domain proteins, like e.g. each of the monomers forming the HIV--1--PR homodimer, is controlled by local elementary structures (LES), stabilized by local contacts among hydrophobic, strongly interacting and highly conserved amino acids which play a central role in the folding process. Because LES have evolved over myriads of generations to recognize and strongly interact with each other so as to make the protein fold fast as well as to avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding--inhibitor drugs suggest themselves: short peptides (or eventually their mimetic molecules), displaying the same amino acid sequence of that of LES (p--LES). Aside from being specific and efficient, these inhibitors are expected not to induce resistance: in fact, mutations which successfully avoid their action imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations within the framework of a simple although not oversimplified model, which is able to reproduce the main thermodynamic as well as dynamic properties of monoglobular proteins, we first identify the LES of the HIV--1--PR and then show that the corresponding p--LES peptides act as effective inhibitors of the folding of the protease which do not create resistance