SynopsisFourier transform ir vibrational circular dichroism (VCD) spectra in the amide I' region of poly(L-lysine) in D,O solutions have confirmed the existence of three distinct conformational states F d an unordered conformational state in this homopolypeptide. Characteristic VCD spectra are presented for the right-handed a-helix, the antiparallel P-sheet, an extended helix conformation previously referred to as the so-called "random coil," and a completely unordered conformation characterized by the absence of any amide I' VCD. VCD for the antiparallel P-sheet in solution and the unordered chain conformation are presented for the first time. Each of the four different VCI) spectra is unique in appearance and lends weight to the view that VCD has the potential to become a sensitive new probe of the secondary structure of proteins in solution.

The sequence-dependent local destabilization in the interior of the collagen triple helix has been evaluated by means of conformational energy computations. Using a model poly(Gly-Pro-Pro) triple helix as the reference state, a method was developed for generating local loops, i.e., internal deformations, and analyzing their conformations. A seven-residue Gly-Pro-Pro- Gly-Pro-Pro-Gly fragment was replaced by the Gly-Pro-Ala-Gly-Ala-Ala-Gly sequence in one, two, or all three of the strands of the loop region. A set of loop conformations was generated in which the ends of the loop were initially fixed in the triple-helical structure. The potential energy of the entire deformed triple helix was then minimized, resulting in a variety of structures that contained deformed loops. The conformations of the triple helices at the two ends of the loops remained essentially unchanged in many of the low-energy conformations. In numerous high-energy conformations, however, the triple-helical segments were also partially or totally disrupted. The minimum-energy conformations of the whole structures were compared in terms of rms deviations of atomic coordinates with respect to the original triple helix, and of the shapes of the loops (using a distance function derived from differential geometry). Three new geometrical parameters-stretch S, kink K, and unwinding U-were defined to describe the changes in the overall orientation of the triple helices at the two ends of the loop. It is shown that, when the number of Pro residues in a short fragment is reduced, the triple helical structure can accomodate internal loops (i.e., distortions) within a 5 kcal/mol cutoff from the essentially unperturbed triple helical structure. For structures with a Gly-Pro-Ala-Gly-Ala-Ala-Gly sequence in all three strands, the probability of finding conformations with internal loops is small, i.e., 0.06. Internal loops affect the overall orientation of these structures, as measured by the helix-distortion parameters S, K, and U.

An alignment of the transmembrane domains of halobacterial retinal proteins (including bacteriorhodopsin) and G-protein coupled receptors (GPCRs) is presented based on the commonality of conserved residues between families. Due to the limited sequence homology displayed by these proteins, an alternative strategy is proposed for sequence alignment that correlates residues within secondary structure elements. The nonsequential alignment developed identifies three proline and two aspartates residues that share common positions and, in the former case, similar functions in the transmembrane domain. The alignment is further applied to model the packing of transmembrane helices 5 and 6 of the beta-adrenergic receptor based on the backbone coordinates of bacteriorhodopsin helices 3 and 2, respectively. Unlike models derived from standard sequential alignments, the approach developed here allows the key structural features conferred by the proline residues to be captured during model building. The structure described is also compared with available site directed mutagenesis results as well as existing GPCR models. In addition to the implications to model building, the commonality observed suggests a potential relationship among the GPCRs and retinal proteins.