Multicanonical study of coarse-grained off-lattice models for folding heteropolymers

Abstract

We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions of selected sequences with 20 monomers. Another aspect of the investigation was the comparison with the purely hydrophobic homopolymer and the study of general conformational properties induced by the "disorder" in the sequence of a heteropolymer. Furthermore, we applied an optimization algorithm to sequences with up to 55 monomers and compared the global-energy minimum found with lowest-energy states identified within the multicanonical simulation. This was used to find out how reliable the multicanonical method samples the free-energy landscape, in particular for low temperatures.

Re‐examination of structure optimization of off‐lattice protein AB models by conformational space annealing

“…The new lowest energy is shown in bold case. Table 2 shows the lowest energies of our model1 in three dimensions, along with the results by nPERMis, ELP, 8 our previous work, and STA. 9 Recent three methods report identical results for S 13 , S 21 , and S 34 .…”

“…Although putative groundstate conformations have been reported, they are continually being updated, [4][5][6][7][8][9] and thus it is not clear if they correspond to true ground-state conformations.…”

Structural properties of small semiconductor-binding synthetic peptides

“…For such systems, reduced all-atom models [15] or models at a higher coarse-grained level [16,17] could be, depending on the particular question, much more promising. Coarse-grained lattice and off-lattice models allow for systematic thermodynamic studies and, at least partly, sequence analyses of heteropolymers with up to 100 monomers [18,19,20].…”

Thermodynamics and kinetics of a Gō proteinlike heteropolymer model with two-state folding characteristics

“…In particular, for such systems it is known from model studies of realistic amino acid sequences that knowledge-based Gō type models reveal kinetic aspects of folding and unfolding processes reasonably well [11,16]. For performing kinetic studies of S in the simplified hydrophobic-polar approach as well, we use the (putative) global-energy minimum, identified in energylandscape paving (ELP) minimizations [27] of the AB model [28], as input for the definition of a hydrophobicpolar GōL model. The (putative) native conformation R (0) is shown in Fig.…”