Side-chain interactions bonds

By using an effective, distance-dependent dielectric constant, the ability of bulk water to reduce electrostatic interactions can be mimicked without the presence of explicit solvent molecules. One disadvantage of aU vacuum simulations, corrected for shielding effects or not, is the fact that they cannot account for the ability of water molecules to form hydrogen bonds with charged and polar surface residues of a protein. As a result, adjacent polar side chains interact with each other and not with the solvent, thus introducing additional errors. 

Three welan helices pass through the unit cell, as shown in Fig. 37b. Two of them, I and II, at (2A A0) and ( A2A0), are antiparallel as in gellan. A third helix, III, at (000) is new and parallel to the first. They are equilaterally 12.0 A apart from each other, 2.9 A farther than in 41. The unit cell contains a total of nine pentasaccharides surrounded by ordered guest molecules, which are accounted by six calcium ions and 75 water molecules. The two up and down helices interact via side chains, calcium ions, and/or water molecules. Specifically, helices I and II are linked only by side chain side chain hydrogen bonds... 

Bond, J. P., Deverin, S. P., Inouye, H., el-Agnaf, O. M., Teeter, M. M., and Kirschner, D. A. (2003). Assemblies of Alzheimer s peptides A beta 25—35 and A beta 31-35 Reverse-turn conformation and side-chain interactions revealed by X-ray diffraction./. Struct. Biol. 141, 156-170. 

These achiral poly(A -propargylamides) form helices with an equivalent amount of right- and left-handed screw senses. Addition of chiral alcohols induces predominantly one-handed screw sense in polyl7a and polyl7d. NMR spectroscopic analysis has revealed that the amide side chains interact with optically active alcohols by hydrogen bonding. Terpenes also induce a one-handed helix. In this case, hydrophobic interaction plays an important role for helix induction. 

The Ufson-Roig matrix theory of the helix-coil transition In polyglycine is extended to situations where side-chain interactions (hydrophobic bonds) are present both In the helix and in the random coil. It is shown that the conditional probabilities of the occurrence of any number and size of hydrophobic pockets In the random coil can be adequately described by a 2x2 matrix. This is combined with the Ufson-Roig 3x3 matrix to produce a 4 x 4 matrix which represents all possible combinations of any amount and size sequence of a-helix with random coil containing all possible types of hydrophobic pockets In molecules of any given chain length. The total set of rules is 11) a state h preceded and followed by states h contributes a factor wo to the partition function 12) a state h preceded and followed by states c contributes a factor v to the partition function (3) a state h preceded or followed by one state c contributes a factor v to the partition function 14) a state c contributes a factor u to the partition function IS) a state d preceded by a state other than d contributes a factor s to the partition function 16) a state d preceded by a state d contributes a factor r to the partition function. 

After Ala, residues with long side chains exhibit higher tendencies to form helices due to possible position-dependent, side-chain interactions that are helix stabilizing, such as salt bridges and hydrogen bonding. However, aromatic or ((-branched side chains act as helix breakers in monomeric peptides due to constraints on side-chain rotational entropy when in an a-helical conformation/11,14 201... 

The existence of electrostatic interactions between oppositely charged residues and hydrogen bonding between side chains agrees with the observations in protein helices that (1) helix probability correlates with the frequency of occurrence of oppositely charged residues spaced i, i + 4 apart in proteins 88 and (2) there is a strong tendency for nearby, oppositely charged, side chains to point toward each other. 89 In the case of C-peptide, the side-chain interactions were also evident in the crystal structure of RNase A. 

The simplest j3 structure is the hairpin (Chapter 1, section C3 and Figure 1.12). The /3 hairpin requires the pairing of hydrophobic side chains to stabilize it. The hairpin has to nucleate at its central turn, unlike the helix, which can nucleate at any residue whose >C=0 can form a hydrogen bond with residue i + 4. The formation of j3 structure is inherently slower than the formation of a helixes because of the fewer nucleation sites and the requirements to make side-chain interactions.5 Depending on precise structure, helixes form with half-lives of a few hundred nanoseconds, and /3 structures form with half-lives 10 times longer. 

Interchain Hydrogen-bonding Side-chain interaction Hydration Shell... 

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