Interaction hydrophobic-hydrophilic, protein

To address the difficulty imposed by the limitations on sampling and the time scales accessible to computer simulations of atomic-level models, mimimal models of proteins have been developed. These models are meant to preserve the most fundamental interactions that are believed to contribute to the thermodynamic and kinetic properties of proteins (see Protein Modeling). These include solvophobic interactions (hydrophobic/hydrophilic partitioning), backbone hydrogen bonding, and structural constraints (imposed by backbone dihedral angles summarized in the Ramachandran potential energy surface). ... 

Deactivation generally refers to a change in the physical structure of the enzyme, often caused by an increase in temperature. Some of the amino acids in a protein chain are hydrophobic. Others are hydrophilic. Proteins in solution fold into elaborate but characteristic shapes to increase like-to-like interactions... 

The ProteinChip System from Ciphergen Biosystems uses patented SELDI (Surface-Enhanced Laser Desorption/Ionization) ProteinChip technology to rapidly perform the separation, detection, and analysis of proteins at the femtomole level directly from biological samples. ProteinChip Systems use ProteinChip Arrays which contain chemically (cationic, anionic, hydrophobic, hydrophilic, etc.) or biochemically (antibody, receptor, DNA, etc.) treated surfaces for specific interaction with proteins of interest. Selected washes create on-chip, high-resolution protein maps. This protein mass profile, or reten-tate map of the proteins bound to each of the ProteinChip Array surfaces, is quantitatively detected in minutes by the ProteinChip Reader. 

Adsorbents for biomacromolecules such as proteins have special properties. First, they need to have large pore sizes. A ratio of pore radius to molecule radius larger than 5 is desirable to prevent excessive diffusional hindrance (see Intraparticle Mass Transfer in this section). Thus, for typical proteins, pore radii need to be in excess of 10-15 nm. Second, functional groups for interactions with the protein are usually attached to the adsorbent backbone via a spacer arm to provide accessibility. Third, adsorbents based on hydrophilic structures are preferred to limit nonspecific interactions with the adsorbent backbone and prevent global unfolding or denaturation of the protein. Thus, if hydrophobic supports are used, their surfaces are usually rendered hydrophilic by incorporating hydrophilic coatings such as dextran or polyvinyl alcohol. Finally, materials stable in sodium hydroxide solutions (used for clean-in-place) are... 

Common bean protein and procyanidin interactions can be hydrophilic or hydrophobic, depending on the sites on the protein available for interaction. Thermal processing can denature the protein and change the type of interaction possible. Once bean protein is denatured, hydrophobic interactions between the protein and procyanidin are likely. Since the strength of hydrophobic interactions increases with increased in temperature, the interaction between protein and procyanidin will be enhanced during thermal processing. Removal of procyanidin will be easiest prior to thermal processing. 

Figure 9.15 Enzymes in aqueous (light-coloured) and hydrophobic (shaded) phases. (A) A protein in the periplasm (PP) of a cell (OM = outer membrane, CM = cytoplasmic membrane) (B) membrane-bound protein in a lipid bilayer (C) hydrophilic protein in an inverted micelle (D) interaction between enzyme and substrates in aqueous micelles (E) graph of catalytic activity as a function of micelle concentration.

This chapter aims to summarize our efforts to investigate the effects of fluorinated amino acid substitutes on the interactions with natural protein environments. In addition to a rather specific example concerning the interactions of small peptides with a proteolytic enzyme, we present a simple polypeptide model that aids for a systematic investigation of the interaction pattern of amino acids that differ in side chain length as well as fluorine content within both a hydrophobic and hydrophilic protein environment. Amino acid side chain fluoiination highly affects polypeptide folding due to steric effects, polarization, and fluorous interactions. 

The a-helical coiled coil-based screening system already provided a wide variety of information about the interactions of fluorinated amino acids within hydrophobic and hydrophilic protein environments. Investigations on the thermal stability as well as the replicase activity have both emphasized the orthogonal properties of fluorinated aliphatic amino acid side chains. The term orthogonal in this context has been chosen by us to demonstrate that they are in fact hydrophobic... 

Hydrophobic dehydration results from bonding of the protein s hydrophobic patches to the hydrophobic regions on the adsorbent. The enthalpic part of this interaction is small the entropy change is positive. Hydrophobic dehydration is relatively unimportant for hydrophilic surfaces and/or rigid hydrophilic proteins. 

The now classic studies by Norde and Lyklema and their detailed thermodynamic analysis (Sect. 4.2) have established that the interaction between a protein and a surface increases with increasing hydrophobicity of the surface and increases with increasing hydrophobicity of the protein. Desorption from hydrophobic surface usually does not occur whereas proteins can often be removed from hydrophilic surfaces by exposure to extreme pH, high ionic strength, or by extensive rinsing 61). ... 

Hydrophobic interaction chromatography relies on hydrophobic interactions between apolar amino acid residues in the proteins and a resin containing hydrophobic groups, such as /7-octyl or phenyl groups. After the protein mixture is applied to the column, an elution buffer with decreasing ionic strength is used. Hydrophilic proteins will elute first, whereas hydrophobic proteins elute last. 

Flavonoids and other polyphenols can interact with lipids and proteins. The interactions with proteins could be both unspecific or specific, meanwhile the interactions with lipids seems to be rather unspecific, based essentially on physical adsorption. This physical adsorption would mostly depend on the hydrophobic/hydrophilic characteristics of the flavonoid molecule, the number of hydroxyl substituents, and the polymerization degree [Erlejman et al., 2004 Verstraeten et al., 2005, 2003, 2004]. 

Protein chains generally contain hydrophobic, hydrophilic and/or charged amino acid residues, which can be regarded as amphiphilic copolymers in a broad definition. The coordinate and cooperative interactions, such as... 

The conclusion that was drawn for the stabilization of protein structure in aqueous solvent systems was as follows the type of protein, the hydrophilic or hydrophobic character and thus the subsequent interaction of the protein with, (i) water and, (ii) the additives themselves, all play an important part of the stabilization process. 

Fig. 8. Schematic representation of protein-mediated cell adhesion on biomaterial surfaces. Biomaterial surface properties (such as hydrophilicity/hydrophobicity, topography, energy, and charge) affect subsequent interactions of adsorbed proteins these interactions include but are not limited to adsorbed protein type, concentration, and conformation. Changes in protein-surface interactions may alter accessibility of adhesive domains (such as the peptide sequence arginine-glycine-aspartic acid) to cells (such as osteoblasts, fibroblasts, or endothelial cells) and thus modulate cellular adhesion. (Adapted and redrawn from Schakenraad, 1996.)...

A typical structure of a water-soluble globular protein consists of hydrophilic amino acid residues outside and hydrophobic ones inside. The hydrophobic environments support various electrostatic interactions within the protein, which plays a crucial role in the enzymatic reaction. Therefore, a simple model complex involving such electrostatic interactions must have hydrophobic environments around the active site such that they are not much influenced by an external effect of solvent. It follows that the models must to some extent be examined in a nonpolar solvent in order to mimic the behavior of native ones. 

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