Model hydrophobic-polar

Homology modelling is not an exact technique. Especially, when the extent of sequence homology (exact matches and matches between amino acid residues of similar property, e.g. hydrophobic, polar, acidic, basic) is low, then more attention will be paid to structural rather than sequence similarities and to prediction of structure for unmatched sequences. In such cases, and always when there is no crystal structure of a member of the family to provide a template, then total reliance has to be placed on the experience of the investigator or in one of the many computer programs now available. The principal methods have been reviewed by Sternberg (1986) and Blundell et al. (1987a). 

The interactions between the amino acids and the solvent (electrostatic, hydrophilic, hydrophobic, S-S) determine the globular conformation. We can give some naive picture of the folded state in terms of a liquid-hydrocarbon model where the hydrophobic core stabilizes globular proteins. The hydrophilic (polar and charged) amino acids are exposed to the solvent and the hydrophobic (polar) amino acids are less exposed to the solvent and buried in the interior of the protein. 

To obtain reliable QSRR, appropriate input data and stringent statistical analysis must be conducted. An important point to be emphasized here is that when QSRR are built from MEKC data, a physicochemical model for the solute-micelle interaction must be established before any statistical processing takes place. Therefore, considering that the intermolecular interactions responsible for solute retention are hydrophobic, polar, and specific in character, only the descriptors able to account for these interactions must be preselected. 

The interactions of drugs with their biological counterparts are determined by intermolecular forces, i.e. by hydrophobic, polar, electrostatic, and steric interactions. Quantitative structure-activity relationships (QSAR) derive models which describe the structural dependence of biological activities either by physicochemical parameters (Hansch analysis), by indicator variables encoding different structural features (Free Wilson analysis), or by three-dimensional molecular property profiles of the compounds (comparative molecular field analysis, CoMFA). 

These three unique binding sites represent the second example of nonequivalence in the reovirus core structure. While site iii is partially similar to site ii, sites i and ii are entirely different both in terms of the secondary structure and the pattern of charged/hydrophobic/polar residues that the XI surface presents to g2. a2-i lies over the middle of a XI-A molecule, and a2-ii bridges from the middle of a Xl-B across to the carboxy-terminal part of a Xl-B from another decamer. a2-iii lies on the XI shell directly on an icosahedral 2-fold axis in one of two equally-likely, two-fold related orientations. Consequently, a2-iii has not been built into the 3.6A electron density maps, and instead a a2-ii model has been docked onto that site. It is clear, however, that the various versions of a2 differ only at the interface with the XI surface. The differences between a2-i and ii are subtle, and the most drastic change is an unravelled helix (residues 39-46) in cj2-ii with respect to a2-i. 

It is important to clarify that the PDMS surface employed for adsorption studies in this work serves only as a model hydrophobic, non-polar siu-face. While all of the thermoplastics investigated in this study also display hydrophobic surface characteristics, the magnitude is notably different for each material, as demonstrated by water contact angle measurements (see Table I). Eor instance, PA-6,6 is well known for its net hydrophobic, yet slightly polar smface characteristics due to amide bonds. A detailed characterisation of the adsorption behaviom of the lubricant additives onto each... 

The cohesion between the hydrophobic part of the interfacial adsorption layer and the adjacent nonpolar phase can be modeled nsing the cohesion between model hydrophobic snrfaces in the same liqnid. In snch a simnlation, the hydrophobic solid snrfaces represent the hydrophobic tails of the snrfactant molecnles. This approach allows one to overcome the difficnlties associated with the mutual solubility of the components (see Chapter 1). For the solid/liqnid/solid interface, the main parameter characterizing the interactions is the free energy of interaction, F (or Aoj), which can be established experimentally nsing Derjagnin s theorem, that is, p = %RF, where p is the cohesive force in a direct contact between two spherical particles immersed in a liqnid medinm. Snitable model systems include spherical molecularly smooth glass beads with a radius R 1-1.5 mm and hydrophobized surfaces of different natures, namely, HS and HL, immersed into the hydrocarbon and fluorocarbon liquids, HL and FL. Only dispersion forces are present in such systems, which makes the quantitative description of their interaction well defined and not complicated by the presence of various polar components. 

Figure S. (See Chapter 2.) (a) The ground-state conformation of the two-dimensional model sequence with M = 23 beads and four covalent (S) sites. The red, green, and black circles represent, respectively, the hydrophobic (//), polar (P), and S sites.

Florihydration entropies of hydrophobic, polar, and ionic solutes in the framework of the langevin dipoles solvation model. Journal of Physical... 

Since lattice models suffer from undesired effects of the underlying lattice symmetries, simple hydrophobic-polar off-lattice models were introduced. One such model is the AB model, where, for historical reasons, A symbolizes hydrophobic and B polar regions of the protein, whose conformations are modeled by polymer chains in continuum space governed by effective bending energy and van der Waals interactions [14]. These models allow for the analysis of different mutated sequences with respect to their folding... 

Coarse-graining peptides in a "united atom"approach. Each amino acid is contracted to a single "C "interaction point. The effective distance between adjacent, bonded interaction sites is about 3.8 A. In the coarse-grained hydrophobic-polar models considered here, the interaction sites have no steric extension. The excluded volume is modeled via type-specific Lennard-Jones pair potentiais. in hydrophobic-polar (HP) peptide models, only hydrophobic (H) and polar (P) amino acid residues are distinguished. 

Here, we follow a different approach. We also study a Go-like model, but it is based on a minimalistic coarse-grained hydrophobic-polar representation of the heteropolymer [200]. 

But what if surface fluctuations are non-negligible In this case, the canonical temperature can be a badly defined control parameter for studies of nucleation transitions with phase separation. This becomes apparent in the following microcanonical folding analysis of the hydrophobic-polar heteropolymer sequence 20.6, whose canonical thermodynamic and kinetic properties have been investigated in detail in the previous section, by employing the AB model. 

Secondary-structure phases of a hydrophobic-polar heteropolymer model... 

These phenomena can also be expected to occur in the aggregation process of polymers. To this end, we will now investigate the aggregation behavior of a mesoscopic hydrophobic-polar heteropolymer model for aggregation [254, 255], which is based on the simple AB model [14] that we have already discussed in the context of tertiary folding behavior of proteins from a generic, coarse-grained point of view. 

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