Intrahelical side chain-side chain contacts: the consequences of restricted rotameric states and implications for helix engineering and design |
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Authors: | Walther Dirk; Argos Patrick |
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Affiliation: | European Molecular Biology Laboratory, Meyerhofstraße I Postfach 10.2209, 69012 Heidelberg, Germany |
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Abstract: | Intrahelical side chainside chain (scsc) interactionsare assumed to play a crucial role in the formation and stabilityof -helices, yet it was found that only 37.2% of all helicalresidues are involved in such close contacts, assuming a specificminimum contact distance. The majority (58.0%) of these weredetected between residues with amino acid sequence spacing i,i + 4. The low frequency of intrahelical scsc contactswith sequence separations i, i + 1 and ii, i + 3, each observedwith only about one-third of the i, i + 4 counts, can be directlyand generally attributed to the absence of the g- conformationin helices for the dihedral angle X1- However, if it was assumedthat each side chain may maximally make only one scsccontact, as most commonly observed, the percentage of contactingpairs increased relative to the maximum possible pairs for agiven sequence spacing by a factor of {small tilde}4, e.g. from20.9 to 81.7% for i, i + 4 contacts. Stereochemical reasonsare also given for the observation that i, i + 3 contacts arecomposed largely of ion or polar pairs, while hydrophobic residuesdominate the i, i + 4 contacts. No significantly increased densityof intrahelical scsc contacts with increasing helix lengthwas found. Although there were generally fewer intrahelicalcontacts between buried helical residues when more contactswere made to the tertiary protein environment, the number ofintrahelical contacts did not increase with increasing solventexposure of the helices. Implications for helix design and thepacking of helices are discussed. |
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Keywords: | helix stabilization// intrahelical side chain-side chain contacts// secondary structure// side chain rotamers |
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