Steric hindrance between side chains

The conformation of the whole main chain of a protein is determined by two conformational angles, phi (0) and psi (i(f), for each amino acid. Only certain combinations of these angles are allowed because of steric hindrance between main-chain atoms and side-chain atoms, except for glycine. 

The amplitude and correlation time tc of the libration in the stacked state were estimated by using the diffusion in a cone model. The semiangle of the cone 6c at 20° C were obtained to be 22° and 26° for the TiL component and PBG- d2 and PBLG- d2, respectively. The tc values were obtained to be about 10 12 s at 19°C in both states. The 6C of r1L component is 4° smaller than that of PBLG- d2, showing that the amplitude of the libration in the stacked state is smaller than that in the free state due to the steric hindrance between the adjacent side chains forming the stacking... 

The structural basis of one of the classic examples of such stereospecificity, that of chymotrypsin for L-amino acid derivatives, is immediately obvious on examination of the crystal structure of the enzyme. D-Amino acid derivatives differ from those of L-amino acids by having the H atom and the side chain attached to the chiral carbon interchanged (structure 8.10). The d derivatives cannot bind because of steric hindrance between the side chain and the walls of enzyme around the position normally occupied by the H atom of L derivatives (Chapter 1). 

The results of MM2 calculations also reveal that the 3HB unit, included within the P(4HB)-type lattice, takes a conformation which significantly deviates from a complete planar-zigzag conformation, which is the putative preferred one for the crystalline P(4HB) [64]. This is chosen in order to relax the steric hindrance between the methyl side chains of the 3HB units and the adjacent carbonyl oxygen atoms. Thus, the structural difference between the 3HB and the 4HB units is too large for them to cocrystallize into the same P(3HB)- or P(4HB)-type crystalline lattice. 

Experimental evidence therefore paints a rather clear picture of the thermochromic phenomena in the solid state side chain interaction with each other, and with the main chain, occur and control the geometry of the chain at low and at high temperatures, respectively. The amount of steric hindrance between side chains and between side chain and main chain increases with increasing temperature. This is because the alkyl chains are more and more converted to a small random coil, with the increase in the number of gauche bonds. If polymers with 3-,4-dialkyl substituted thiophenes show high band-gaps, it is because at low temperatures already there is no possibility for the chain to be planar. 

The average dimensions solved in many crystal structures show that almost all peptide bonds are in a trans configuration creating staggered residues due to steric hindrance between nonbonded atoms. One main exception occurs with the amino acid proline. Its cyclic side chain reduces the repulsion between atoms and so favors the trans and cis conformations equally (see Figure 2). 

All in all, affinity and potency of an agonist at a particular mGluR subtype seem to correlate with the nature of its interactions with Lobe I and II and to what extent it is capable of stabilizing the closed ATD. Selectivity, on the other hand, arises from sterical hindrance or ionic repulsion between the distal acidic group of the agonist and side chains of distal residues present in some mGluR subtypes but not in others. The Y74/R57/K74 residue in mGluRl/2/4 appears to be a particular important determinant of selectivity. The side... 

The hemicellulose forms the glue around and between the cellulose bundles. It consists of shorter, branched polymer chains of various C6 and C5 sugars. The C6 sugars consist mainly of glucose together with mannose and galactose. The C5 sugars include xylose and arabinose. The steric hindrance offered by the side-... 

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