Alternative hydrogen bond implementations produce opposite effects on collapse cooperativity of lattice homopolypeptide models

@article{citeulike:2153217, abstract = {We use complete enumeration of self-avoiding chains of up to N=26 monomers in two-dimensional lattices to investigate the effect of alternative implementations of backbone hydrogen bonds on the cooperativity of homopolypeptide collapse. Following a recent study on protein folding models, we use the square lattice with z=3 local conformations per monomer and lattice extensions containing diagonal steps which result in z=5 or z=7 and assume that only a subset of zh\<z local conformations is compatible with hydrogen bond formation. As previously observed in heteropolymeric folding, a significant increase in cooperativity, as measured by 2 values, results from the coupling between hydrogen bonds and hydrophobic interactions, in such a way that hydrophobic contacts are favorable only when contacting monomers are involved in hydrogen bond formation. For some z/zh combinations the energy distribution is bimodal at the collapse transition temperature. The situation can be regarded as if all hydrophobic contacts actually decrease the energy by the same amount, 2h, with the addition of an energetic increase, 2=h, as a penalty for each contacting monomer not satisfying the hydrogen bond condition. Cooperativity is little affected and might even decrease, however, when hydrogen bonds produce a decrease in energy by the same amount, 1=h, for each bonding monomer. For the more general situation when the hydrogen bond effect is not equal, in modulus, to the hydrophobic interaction, i.e., 2h or 1h, we observe a pronounced increase in 2 for small 2, with a maximum around 2/h1.5, followed by a gradual decrease to a limiting value at large 2. The opposite behavior is observed when 1 is varied. The observed qualitative difference is shown to arise from opposite effects on the convexity of the total density of states of the system when subdensities corresponding to different numbers of hydrogen bonds are differently favored as opposed to the case when subdensities corresponding to different numbers of contacting monomers not forming hydrogen bonds are differently unfavored. Potential implications for the cooperativity of protein folding and protein unspecific collapse are discussed.}, author = {Fleury, Gustavo M. N. and Barbosa, Marco A. A. and Ant\^onio}, citeulike-article-id = {2153217}, doi = {http://dx.doi.org/10.1103/PhysRevE.76.051914}, journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)}, keywords = {hbproject, hydrophobicity, proteins, secondary-structures}, number = {5}, posted-at = {2007-12-20 21:58:00}, priority = {2}, publisher = {APS}, title = {Alternative hydrogen bond implementations produce opposite effects on collapse cooperativity of lattice homopolypeptide models}, url = {http://dx.doi.org/10.1103/PhysRevE.76.051914}, volume = {76}, year = {2007} }

TY - JOUR ID - citeulike:2153217 L3 - citeulike-article-id:2153217 TI - Alternative hydrogen bond implementations produce opposite effects on collapse cooperativity of lattice homopolypeptide models JF - Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) VL - 76 IS - 5 PB - APS N2 - We use complete enumeration of self-avoiding chains of up to N=26 monomers in two-dimensional lattices to investigate the effect of alternative implementations of backbone hydrogen bonds on the cooperativity of homopolypeptide collapse. Following a recent study on protein folding models, we use the square lattice with z=3 local conformations per monomer and lattice extensions containing diagonal steps which result in z=5 or z=7 and assume that only a subset of zh<z local conformations is compatible with hydrogen bond formation. As previously observed in heteropolymeric folding, a significant increase in cooperativity, as measured by 2 values, results from the coupling between hydrogen bonds and hydrophobic interactions, in such a way that hydrophobic contacts are favorable only when contacting monomers are involved in hydrogen bond formation. For some z/zh combinations the energy distribution is bimodal at the collapse transition temperature. The situation can be regarded as if all hydrophobic contacts actually decrease the energy by the same amount, 2h, with the addition of an energetic increase, 2=h, as a penalty for each contacting monomer not satisfying the hydrogen bond condition. Cooperativity is little affected and might even decrease, however, when hydrogen bonds produce a decrease in energy by the same amount, 1=h, for each bonding monomer. For the more general situation when the hydrogen bond effect is not equal, in modulus, to the hydrophobic interaction, i.e., 2h or 1h, we observe a pronounced increase in 2 for small 2, with a maximum around 2/h1.5, followed by a gradual decrease to a limiting value at large 2. The opposite behavior is observed when 1 is varied. The observed qualitative difference is shown to arise from opposite effects on the convexity of the total density of states of the system when subdensities corresponding to different numbers of hydrogen bonds are differently favored as opposed to the case when subdensities corresponding to different numbers of contacting monomers not forming hydrogen bonds are differently unfavored. Potential implications for the cooperativity of protein folding and protein unspecific collapse are discussed. KW - hbproject KW - hydrophobicity KW - proteins KW - secondary-structures AU - Fleury, Gustavo AU - Barbosa, Marco AU - Ant\^onio PY - 2007/// UR - http://dx.doi.org/10.1103/PhysRevE.76.051914 ER -