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

Direct observation of the glue pairing the halo of the nucleus 11Li

With the help of a unified description of the nuclear structure and of the direct reaction mechanism we show that a recent 1H(11Li,9Li)3H experiment provides, for the first time in nuclear physics, direct evidence of phonon mediated pairing.Comment: 9 pages, 4 figures. Major change

Study of the transition from pairing vibrational to pairing rotational regimes between magic numbers N=50 and N=82, with two-nucleon transfer

Absolute values of two-particle transfer cross sections along the Sn-isotopic chain from closed shell to closed shell (100Sn,132Sn) are calculated taking properly into account nuclear correlations, as well as the successive, simultaneous and non-orthogonality contributions to the differential cross sections. The results are compared with systematic, homogeneous bombarding conditions (p, t) data. The observed agreement, almost within statistical errors and without free parameters, testify to the fact that theory is able to be quantitative in its predictions

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

Structure and reactions of 11Be: many-body basis for single-neutron halo

The exotic nucleus 11Be has been extensively studied and much experimental information is available on the structure of this system. Treating, within the framework of empirically renormalised nuclear field theory in both configuration and 3D-space, the mixing of bound and continuum single-particle states through the coupling to collective particle-hole (p,h) and pairing vibrations of the 10Be core, as well as Pauli principle acting not only between the particles explicitly considered and those participating in the collective states, but also between fermions involved in two-phonon virtual states it is possible, for the first time, to simultaneously and quantitatively account for the energies of the 1/2+,1/2- low-lying states, the centroid and line shape of the 5/2+ resonance, the one-nucleon stripping and pickup absolute differential cross sections involving 11Be as either target or residual nucleus, and the dipole transitions connecting the 1/2+ and 1/2- parity inverted levels as well as the charge radius, thus providing a unified and exhaustive characterisation of the many-body effects which are at the basis of this paradigmatic one-neutron halo system.Comment: Supplemental materials include