597 research outputs found
Hydrophobicity and Unique Folding of Selected Polymers
In suitable environments, proteins, nucleic acids and certain synthetic
polymers fold into unique conformations. This work shows that it is possible to
construct lattice models of foldable heteropolymers by expressing the energy
only in terms of individual properties of monomers, such as the exposure to the
solvent and the steric factor.Comment: 5 pages, RevTe
Recovery of Protein Structure from Contact Maps
We present an efficient algorithm to recover the three dimensional structure
of a protein from its contact map representation. First we show that when a
physically realizable map is used as target, our method generates a structure
whose contact map is essentially similar to the target. Furthermore, the
reconstructed and original structures are similar up to the resolution of the
contact map representation. Next we use non-physical target maps, obtained by
corrupting a physical one; in this case our method essentially recovers the
underlying physical map and structure. Hence our algorithm will help to fold
proteins, using dynamics in the space of contact maps. Finally we investigate
the manner in which the quality of the recovered structure degrades when the
number of contacts is reduced.Comment: 27 pages, RevTex, 12 figures include
Structurally constrained protein evolution: results from a lattice simulation
We simulate the evolution of a protein-like sequence subject to point
mutations, imposing conservation of the ground state, thermodynamic stability
and fast folding. Our model is aimed at describing neutral evolution of natural
proteins. We use a cubic lattice model of the protein structure and test the
neutrality conditions by extensive Monte Carlo simulations. We observe that
sequence space is traversed by neutral networks, i.e. sets of sequences with
the same fold connected by point mutations. Typical pairs of sequences on a
neutral network are nearly as different as randomly chosen sequences. The
fraction of neutral neighbors has strong sequence to sequence variations, which
influence the rate of neutral evolution. In this paper we study the
thermodynamic stability of different protein sequences. We relate the high
variability of the fraction of neutral mutations to the complex energy
landscape within a neutral network, arguing that valleys in this landscape are
associated to high values of the neutral mutation rate. We find that when a
point mutation produces a sequence with a new ground state, this is likely to
have a low stability. Thus we tentatively conjecture that neutral networks of
different structures are typically well separated in sequence space. This
results indicates that changing significantly a protein structure through a
biologically acceptable chain of point mutations is a rare, although possible,
event.Comment: added reference, to appear on European Physical Journal
Folding Lennard-Jones proteins by a contact potential
We studied the possibility to approximate a Lennard Jones interaction by a
pairwise contact potential. First we used a Lennard-Jones potential to design
off-lattice, protein-like heteropolymer sequences, whose lowest energy (native)
conformations were then identified by Molecular Dynamics. Then we turned to
investigate whether one can find a pairwise contact potential, whose ground
states are the contact maps associated with these native conformations. We show
that such a requirement cannot be satisfied exactly - i.e. no such contact
parameters exist. Nevertheless, we found that one can find contact energy
parameters for which an energy minimization procedure, acting in the space of
contact maps, yields maps whose corresponding structures are close to the
native ones. Finally we show that when these structures are used as the initial
point of a Molecular Dynamics energy minimization process, the correct native
folds are recovered with high probability.Comment: submitted to "Proteins: Structure, Function, and Genetics
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Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3.
We present an analysis of the results obtained at CASD-NMR round 3 by the CHESHIRE and the YAPP methods. To determine protein structures, the CHESHIRE method uses solely information provided by NMR chemical shifts, while the YAPP method uses an automated assignment of NOESY spectra. Of the ten targets of CASD-NMR round 3, nine CHESHIRE predictions and eight YAPP ones were submitted. The eight YAPP predictions ranged from 0.7 to 1.9 Å Cα accuracy, with an average of 1.3 Å. The nine CHESHIRE predictions ranged from 0.8 to 2.6 Å Cα accuracy for the ordered regions of the proteins, with an average of 1.6 Å. Taken together, these results illustrate how the NOESY based YAPP method and the chemical shift based CHESHIRE method can provide structures of comparable quality.This is the author accepted manuscript. The final version is available at http://link.springer.com/article/10.1007%2Fs10858-015-9940-9
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