Driven by conditions set by smaller solutes, proteins fold and unfold. Experimentally, these conditions are stated as intensive variables--pH and other chemical potentials--as though small solutes were infinite resources that come at an externally varied free energy cost. Computationally, the finite spaces of simulation allow only fixed numbers of these solutes. By combining the analytic Gibbs ...

An understanding of the various states available to a polypeptide chain is important for a description of the protein folding process. We use a 16-monomer chain on a two-dimensional square lattice to model a protein. This makes it possible to enumerate all self-avoiding conformations from which any equilibrium thermodynamic quantity can be calculated. By varying the external conditions of tempe...

We study the fraction f of nucleotides involved in the formation of a cactuslike secondary structure of random heteropolymer RNA-like molecules. In the low-temperature limit, we study this fraction as a function of the number c of different nucleotide species. We show, that with changing c, the secondary structures of random RNAs undergo a morphological transition: f(c)→1 for c≤c(cr) as the cha...

Lignocellulose, which comprises the cell walls of plants, is the Earth’s most abundant renewable source of convertible biomass. However, in order to access the fermentable sugars of the cellulose and hemicellulose fraction, the extremely recalcitrant lignin heteropolymer must be hydrolyzed and removed—usually by harsh, costly thermochemical pretreatments. Biological processes for depolymerizing...

Rhizobium tropici, a member of the Rhizobiaceae family, has the ability to synthesize and secrete extracellular polysaccharides (EPS). Rhizobial EPS have attracted much attention from the scientific and industrial communities. Rhizobial isolates and R. tropici mutants that produced higher levels of EPS than the wild-type strain SEMIA4080 were used in the present study. The results suggested a h...

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of a heteropolymer. Technically, the most common approach to diversity is randomness, which is usually implemented in two body interactions (charges, polar character,..). On the other hand, the (almost) universa...

We report a numerical study of the design of lattice heteropolymers that can refold when the properties of only a few monomers are changed. If we assume that the effect of an external agent on a heteropolymer is to alter the interactions between its constituent monomers, our simulations provide a description of a simple allosteric transition. We characterize the free energy surfaces of the init...

A novel numerical method for determining the conformational structure of macromolecules is applied to idealized biomacromolecules in solution. The method computes effective inter-residue interaction potentials solely from the corresponding radial distribution functions, such as would be obtained from experimental data. The interaction potentials generate conformational ensembles that reproduce ...

The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is obtained even for sequences with very different thermodynamic properties. Furthermore, the degree of cooperativity in the folding process is examined by stu...

Recent single-molecule force measurements on single-domain proteins have highlighted a three-state folding mechanism where a stabilized intermediate state (I) is observed on the folding trajectory between the stretched state and the native state. Here we investigate on-lattice protein-like heteropolymer models that lead to a three-state mechanism and show that force experiments can be useful to...