Common Force Field Thermodynamics of Cholesterol
نویسندگان
چکیده
Four different force fields are examined for dynamic characteristics using cholesterol as a case study. The extent to which various types of internal degrees of freedom become thermodynamically relevant is evaluated by means of principal component analysis. More complex degrees of freedom (angle bending, dihedral rotations) show a trend towards force field independence. Moreover, charge assignments for membrane-embedded compounds are revealed to be critical with significant impact on biological reasoning.
منابع مشابه
Ion solvation thermodynamics from simulation with a polarizable force field.
Thermodynamic measurements of the solvation of salts and electrolytes are relatively straightforward, but it is not possible to separate total solvation free energies into distinct cation and anion contributions without reference to an additional extrathermodynamic assumption. The present work attempts to resolve this difficulty using molecular dynamics simulations with the AMOEBA polarizable f...
متن کاملFolding and insertion thermodynamics of the transmembrane WALP peptide.
The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this com...
متن کاملVariational-lagrangian Thermodynamics of Evolution of Collective Chemical Systems
New concepts in thermodynamics are further extended and combined with a principle of virtual dissipation to provide general equations of evolution of collective open chemical systems. A new definition of the chemical potential is introduced, and some new expressions for the affinity are discussed. Application of the principle of virtual dissipation leads very simply to quite general continuum f...
متن کاملModel parameters for simulation of physiological lipids
Coarse grain simulation of proteins in their physiological membrane environment can offer insight across timescales, but requires a comprehensive force field. Parameters are explored for multicomponent bilayers composed of unsaturated lipids DOPC and DOPE, mixed-chain saturation POPC and POPE, and anionic lipids found in bacteria: POPG and cardiolipin. A nonbond representation obtained from mul...
متن کاملThermodynamic approach to phase coexistence in ternary phospholipid-cholesterol mixtures.
We introduce a simple and predictive model for determining the phase stability of ternary phospholipid-cholesterol mixtures. Assuming that competition between the liquid and gel order of the phospholipids is the main driving force behind lipid segregation, we derive a Gibbs free energy of mixing, based on the thermodynamic properties of the lipids main transition. A numerical approach was devis...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
دوره 2013 شماره
صفحات -
تاریخ انتشار 2013