Protein internal water

Internal water molecules may be located in the same sites in related proteins. In many proteins, internal waters are an essential part of the three-dimensional structure and their positions are typical for a whole family of proteins. Thus, in the three related plant cysteine proteinases, actinidin, papain, and calotropin Dl, 15 of the 16 internal waters (8 of which are illustrated in Fig. 19.13) are found in... 

Protein Internal Waters in X-ray Data Predicted Waters (total/X-ray) RMS Deviation J (A)... 

In the case of E-IIs, we do not deal with a transport protein as described in Fig. 5. Clearly, the most important difference is that the substrate is chemically modified. Therefore, we do not know whether or not a state Ecyt S is in contact with the internal water phase, if it exists at all. On the other hand, since transport is part of the overall function of E-IIs, translocations as described in Fig. 5 may very well be part of the... 

Water in oil microemulsions with reverse micelles provide an interesting alternative to normal organic solvents in enzyme catalysis with hydrophobic substrates. Reverse micelles are useful microreactors because they can host proteins like enzymes. Catalytic reactions with water insoluble substrates can occur at the large internal water-oil interface inside the microemulsion. The activity and stability of biomolecules can be controlled, mainly by the concentration of water in these media. With the exact knowledge of the phase behaviom" and the corresponding activity of enzymes the application of these media can lead to favomable effects compared to aqueous systems, like hyperactivity or increased stability of the enzymes. 

The water-in-oil-in-water (w/o/w) emulsion method (Figure 11.4) is the predominant method used for encapsulation of biomacromolecules in these microparticles. Protein solution forms the internal water phase of the w/o/w emulsion. Loading efficiency of the microparticles has not been optimal using water or buffer as an internal phase, so water is sometimes substituted with polymeric liquids, such as low molecular weight polyethylene glycol. The primary emulsion is then added to a secondary liquid phase, forming the secondary emulsion. The solvent for the... 

The seven helices of rhodopsin form a "box" around the bound retinal. Tire environment of the retinal is largely hydrophobic. However, there are also buried polar groups, some of which lie in conserved positions in more than 200 G-protein-coupled receptors458 and internal water molecules whose vibrational... 

Both internal structure and overall size and shape of proteins vary enormously. Globular proteins vary considerably in the tightness of packing and the amount of internal water of hydration. However, a density of 1.4 g cm-3 is typical. 

Internal Water Molecules as Integral Part of Protein Structures... 

Internal water is an integral part of a protein structure. Even globular proteins of small size are observed to contain buried water molecules. Examples are pancreatic trypsin inhibitor, with 58 amino acid residues and 4 interior water molecules, lysozyme with 129 residues and 4 waters, and larger proteins like ac-tinidin with 218 residues which may contain 10 to 20 molecules of internal water (Fig. 19.13). These water molecules can be buried deep inside the globular proteins or located in cavities near the surface. In some cases, therefore, the distinction in-ternal/external water can be ambiguous. 

Internal water molecules tend to form clusters. In general, internal water molecules in protein structures are not found isolated but are assembled in clusters. Their hydrogen-bonding scheme could be derived in actinidin (Fig. 19.13), in lysozyme, and in penicillopepsin, based oh the assumption that water molecules act as double donors and acceptors. In some of the protein structures, which have been analyzed in greater detail, an internal water is associated with three acceptor sites indicating three-center bonding as observed in the amino acid zwitterion crystal structures (see Part IB, Chap. 8). 

Hydrogen-bond partners for internal water molecules. In the five proteins lysozyme, carboxypeptidase, cytochrome c, actinidin and penicillopepsin (Table 19.1), the protein groups (numbers in parentheses) which are bonded to internal water molecules are the main-chain C=0 (75), N-H (38), and side-chain atoms... 

The most important side-chains for hydration are Asp and Glu which bind, on average, 2 water molecules per carboxylate group (see Thble 23.4 b). Whereas Asp and Glu are preferentially located at the outside of the globular proteins and therefore in contact with solvent, the other amino acids are more buried in the interior. They hydrogen-bond not only with internal water molecules but also with protein main-chain and side-chain atoms. Consequently their functional groups are less accessible for water molecules, with only 0.34 water molecules bound per hydrogen-bond site on average... 

Because hydration water molecules are more tightly bound if they are located in cavities [see, for instance, the internal water molecules in proteins (Part III, Chap. 19)], water molecules in the deep major groove of A-DNA and in the narrow minor grooves of B- and Z-DNA are better defined and therefore easier to locate from the electron density maps. Presumably these grooves are, however, not more hydrated than the other, shallower grooves, where it is inherently more difficult to define the positions of water molecules. 

A typical globular protein adopts a unique minimum energy conformation that is compact with few or no internal water molecules. Hydrophobic (nonpolar) R groups tend to be on the inside (away from water) and most hydrophilic (polar) R groups tend to be on the outside where they can be solvated by hydrogen bonding with H20. In the case of enzymes (proteins that catalyse specific chemical reactions) there may be special structural features of which the best known are active site depressions or grooves on the surface that bind the chemical substrates of the enzyme-catalysed reaction. 

The intercept on the ordinate in Figure 2-11 is the chloroplast volume theoretically attained in an external solution of infinite osmotic pressure —a l/n° of zero is the same as a n° of infinity. For such an infinite 11°, all of the internal water would be removed = 0), and the volume, which is obtained by extrapolation, is that of the nonaqueous components of the chloroplasts. (Some water is tightly bound to proteins and other substances and presumably remains bound even at the hypothetical infinite osmotic pressure such water is not part of the internal water, Vwn v). Thus the intercept on the ordinate of a F-versus-l/n° plot corresponds to b in the conventional Boyle-Van t Hoff relation (Eq. 2.15). This intercept (indicated by an arrow in Fig. 2-11) equals 17 pm3 for chloroplasts both in the light and in the... 

Internal water plays a role in the structure of proteins. It is difficult to detect and measure these waters by means of X-rays and therefore statistical thermodynamic... 

Helms V. Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules. Chem. Phys. Chem. 2007 8 23-33. 

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