Proteins internal water presence

It may be noted that present calculations of protein structure and function neglect the presence of so much internal water. In calculations, a quantity called the dielectric constant, required in electrostatic calculations of the energy of interaction between charges, is utilized. The value of the dielectric constant of bulk water is about 80, and commonly the assumption is made that the value shifts at the surface of the protein from 80 to 5 or less within the protein. The presence of the waters of Thales raises concern about such assumptions. Similarly, in Chapter 5, particularly in Figure 5.30, the experimental values could only be approximated by electrostatic calculations when a value of 5 or less was used, whereas direct measurement of the dielectric constant for the model protein system required that the value within the model protein motor be no less than 65. These points provide substantial support for the consilient mechanism. 

Plastocyanin (PC) mediates electron transfer from the cytochrome f (cyt f) component of the cytochrome b6/f complex to the Photosystem I reaction center during photosynthetic electron transport. At the preceeding International Congress on Photosynthesis, predictions were made regarding regions on cyt f which might be likely candidates for the PC interaction site (1). To further examine this hypothesis, we have further characterized a covalently linked PC-cyt f adduct. This adduct was prepared by incubation of the two proteins in the presence of EDC, a water soluble carbodiimide, and has been demonstrated to have a 1 1 stoichiometry (2). 

Well different is, instead, the situation observed when the exploration was extended well inside the protein irreversible denaturation region. Two Lorentzians, appear just after the crossing of the border of the ID —> D phases, that is, where both the external protein hydration water and the internal one are detectable. When proteins unfold in an open polymeric structure, the internal water (also considering the effective high T) can easily break the HBs that link it to the protein residuals and can diffuse and interact with the external one. This reason explains the presence of two proton water NMR signals inside the phase D. One contribution for continuity is related with the protein hydration water whereas the second component with the internal water one. Both the components will survive in the measured spectra upto the end of the cooling phase. After the denaturation these two water forms are present in the system and can interact with each other or with the open biopolymer, in a complete different physical scenario if compared with the folded protein native state. 

The presence of water molecules near the Qb site suggests that water plays an important role in proton transfer. The positions of these waters are not established with certainty by the computational analysis. However, a strong indication of their existence is the presence in the X-ray structure of significant voids near Qb that are bordered by polar groups in the protein. Because the distances between protonatable amino acid groups are, in some cases, significantly larger than the distances for proton transfer, internal water molecules are likely to play an important role as proton donors and acceptors. 

The nature of the amino acid residues is of prime importance in the development and maintenance of protein structure. Polypeptide chains composed of simple aliphatic amino acids tend to form helices more readily than do those involving many different amino acids. Sections of a polypeptide chain which are mainly non-polar and hydrophobic tend to be buried in the interior of the molecule away from the interface with water, whereas the polar amino acid residues usually lie on the exterior of a globular protein. The folded polypeptide chain is further stabilized by the presence of disulphide bonds, which are produced by the oxidation of two cysteine residues. Such covalent bonds are extremely important in maintaining protein structure, both internally in the globular proteins and externally in the bonding between adjacent chains in the fibrous proteins. 

Any sample of matter is able to produce electrical noise by the stochastic displacement of internal electrons or ions. We can also observe that in biological systems we are in the presence of water, biomolecules, and ions in perpetual fluctuation. All fundamental biomolecules such as nucleic acids, proteins, and lipids are surrounded by water and ions. 

Breathing is enabled by lung surfactant, a mixture of proteins and lipids that forms a surface-active layer and reduces surface tension at the air-water interface in lungs. Surfactant protein B (SP-B) is an essential component of lung surfactant. Researchers probed the mechanism underlying the important functional contributions made by the N-terminal 7-residues of SP-B, a region sometimes called the insertion sequence . These studies employed a construct of SP-B, SP-B (1-25,63-78), also called Super Mini-B, which is a 41-residue peptide with internal disulfide bonds comprising the N-terminal 7-residue insertion sequence and the N- and C-terminal helixes of SP-B. CD, solution NMR, and SS NMR were used to study the structure of SP-B (1-25,63-78) and its interactions with phospholipid bilayers. Comparison of results for SP-B (8-25,63-78) and SP-B (1-25,63-78) demonstrates that the presence of the 7-residue insertion sequence induces substantial disorder near the center of the lipid bilayer. ... 

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