Protein Structure
Carboxypeptidase A
Alpha Chymotrypsin
Ribonuclease A
Receptor Sites
Double-Helix B-DNA


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As polypeptides emerge from ribosomes, segments which are shielded from hydration by their R groups, either hydrogen bond internally to produce coils or with other strands to form beta sheets.41 Sometimes strands containing hydrogen-bonding order-disrupting peptides will make an abrupt beta turn or a broad coil turn as illustrated in the protein structures shown below.

Depending on aminoacid sequences, polypeptides spontaneously form coils, beta-sheets, beta truns and loops to form proteins.

Amazing as it may seem, proteins as complex as carboxypeptidase A, on heating in simulated cellular medium, unwrap to yield a single strand of polypeptide which, on cooling, reassembles to give the original three-dimensional structure. However, wrapping is not simple. Even though all the information required to form the final stable structure is resident in the peptide sequence,44,46 the strands sometimes wrap into non-functional forms.  Once again, nature has provided a solution in the form of “chaperone proteins” which bind to the polypeptides, permit them to rehydrate, unwrap and rewrap into functional, low-energy forms.45 On the lower side of the alpha-chymotrypsin structure, it should be noted that there are two open ends of the chain.  Several peptides have been removed enzymatically to activate the protein.43 At times, long polypeptide chains are cleaved enzymatically to form smaller functional units.

Since each peptide in a sequence assists in defining whether a polypeptide strand will be in a coil, a sheet, a beta turn or a broad coil46 and how the strands will fold and fit together, we will begin our analysis with a brief look at three different classes of amino acids.


In this first group, all of the amino acids have aliphatic or aromatic side chains – all of them increase the order of water around them and produce covalent hydrogen-bonding of the amide groups on the upper and lower surfaces of the polypeptide chains. (See www.proteinhydration.com.)

Amino acids with hydrophobic side chains induce order in adjacent water and drive polypeptides into coils.

To reduce hydration order, chains rotate around alpha carbons to form coils or, if ordered only on one side, to form beta sheets. Tyrosine is a particularly important peptide because the phenolic oxygen on its ring often aids in the assembly and function of proteins. Often, tyrosines are on the outside surfaces of proteins hydrogen bonding with surface water while most of the amino acids shown above end up dehydrated on inside of finished proteins.

Amino acids in the second group all have polar side chains which can hydrogen-bond with surface water but they also have hydrogens on their alpha carbons which tend to order hydrogen bonding adjacent to their peptide groups.  Once again, this causes them to form coils and sheets but, in contrast to those in the first group, they often end up on the outer surfaces of proteins disrupting surface hydration order and increasing water solubility.

Amino acids with charged groups in side chains often are in beta-sheets.

Acids, like glutamic and aspartic, and amines, like lysine and arginine, cluster water around them and disrupt the formation of coordinated cubic surface patterning. However, by forming transient linear elements between them, they play a critical role in directing assembly and final function.  Amide peptides, like glutamine and asparagine, disrupt covalent hydrogen bonding by bonding at multiple angles; they usually are on the outside surfaces of water-soluble proteins increasing solubility.30 As you shall see, threonines play a unique internal role in protein assembly.

Glycine, serine and proline readily hydrate, break coils and linear elements of polypepties and form beta turns.

Glycine and serine are so small that they readily hydrate; often they break coils and sheets to form beta turns or random coils. However, serine, with its hydroxyl group positioned properly on surfaces, often fits into a cubic hydration patterning to direct assembly and function.  Proline, with no hydrogen on its nitrogen to hydrogen bond with other peptides in polypeptide chains, usually breaks coils and sheets and causes chains to change direction.

Transient Linear Hydration Analysis

In the pages which follow, a standard cubic matrix with hydrogen bond length of 2.76 angstroms (4.5A for the trimer) will be used in the analyses. 9,10,20

The cubic lattice with a distance of 2.76 Angstroms between water molecules is used in TLH Analyses of proteins.

Although X-ray crystallographic coordinates of proteins will be used to define positions of atoms in the proteins, it must be remembered that in aqueous solution, surface groups and polypeptide chains are not ridged - they have a number of degrees of freedom. Furthermore, positions of protons and water molecules in a cubic water matrix, like those of electrons around atoms, can be defined only by wavefunction probabilities – they can be identified only in theory. Thus, in performing Transient Linear Hydration Analyses, the following rules are followed.

1)       Analyses are performed on portions of proteins in low-entropy crystalline conformations realizing that we really do not know what conformations polypeptide chains adopt as they assemble in water but accepting that it is better to accept stable conformational forms than invent forms which conform to preconceived notions of symmetry and structure.

2)       Water molecules which hydrogen bond to oxygen and nitrogen atoms on a molecule long enough to achieve thermodynamic stability are considered part of the molecule.

3)       Transient linear and planar ordering is reinforced by non-hydrogen-bonding lipid groups and by oxygen, nitrogen and sulfur atoms on surfaces which hydrogen-bond into transient linear surface elements in similar positions and at similar angles to those in cubic patterning. The degree of covalent hydration structuring on surfaces depends on the proportion of ordering to disordering groups.

4)       Surface oxygen, nitrogen and sulfur atoms which do not fit into the spatial positions of water molecules in the quantized cubic matrix around a polypeptide or those which fit, but hydrogen bond at different angles, disrupt the formation of coordinated covalent hydrogen bonding and increase water solubility.

5)        Charged oxygen, nitrogen and sulfur atoms on surfaces cluster water molecules around them to transfer charge outward through transient linear dielectric covalent elements to oppositely-charged atoms or ions to delocalize charge.

6)       Linear polypeptides which induce the formation of covalent linear elements of hydration on both upper and lower surfaces rapidly form coils to reduce order in surface hydration.

7)       Linear polypeptides which induce the formation of covalent linear hydration on one side and more dynamic hydrogen-bonding on the opposite side tend to retain linear forms and move spontaneously toward each other to form beta sheets or toward complimentary ordering surfaces of coils to form linear segment/coil complexes.

8)       Cations, like sodium and calcium, which bind water molecules spherically around them, disrupt covalent surface hydration if present in high concentrations but radiate protonic charge through covalent linear elements of hydration to reduce charge potential at normal physiological concentrations.

9)       As molecules and ions approach each other and their quantized hydration environments intersect, they are drawn into unique thermodynamically-stable associations to perform covalent hydration-ordered functions.

With these basic principles of TLH Analysis in place, we are now prepared to examine how they can be used to interpret the assembly and function of four proteins, the structural properties of a number of receptor binding sites and the stabilization of the spatial structure of double-helix B-DNA.

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