Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics

The determination of the intermediate state structures of the bacteriorhodopsin photocycle has lead to an unprecedented level of understanding of the catalytic process exerted by a membrane protein. However, the crystallographic structures of the intermediate states are only relevant if the working cycle is not impaired by the crystal lattice. Therefore, we applied visible and Fourier transform infrared spectroscopy (FTIR) microspectroscopy with microsecond time resolution to compare the photoreaction of a single bacteriorhodopsin crystal to that of bacteriorhodopsin residing in the native purple membrane. The analysis of the FTIR difference spectra of the resolved intermediate states reveals great similarity in structural changes taking place in the crystal and in PM. However, the kinetics of the photocycle are significantly altered in the three-dimensional crystal as compared to PM. Strikingly, the L state decay is accelerated in the crystal, whereas the M decay is delayed. The physical origin of this deviation and the implications for trapping of intermediate states are discussed. As a methodological advance, time-resolved step-scan FTIR spectroscopy on a single protein crystal is demonstrated for the first time which may be used in the future to gauge the functionality of other crystallized proteins with the molecular resolution of vibrational spectroscopy.

Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins

The CTs (cytotoxins) I and II are positively charged three-finger folded proteins from venom of Naja oxiana (the Central Asian cobra). They belong to S- and P-type respectively based on Ser-28 and Pro-30 residues within a putative phospholipid bilayer binding site. Previously, we investigated the interaction of CTII with multilamellar liposomes of dipalmitoylphosphatidylglycerol by wide-line (31)P-NMR spectroscopy. To compare interactions of these proteins with phospholipids, we investigated the interaction of CTI with the multilamellar liposomes of dipalmitoylphosphatidylglycerol analogously. The effect of CTI on the chemical shielding anisotropy and deformation of the liposomes in the magnetic field was determined at different temperatures and lipid/protein ratios. It was found that both the proteins do not affect lipid organization in the gel state. In the liquid crystalline state of the bilayer they disturb lipid packing. To get insight into the interactions of the toxins with membranes, Monte Carlo simulations of CTI and CTII in the presence of the bilayer membrane were performed. It was found that both the toxins penetrate into the bilayer with the tips of all the three loops. However, the free-energy gain on membrane insertion of CTI is smaller (by approximately 7 kcal/mol; 1 kcal identical with 4.184 kJ) when compared with CTII, because of the lower hydrophobicity of the membrane-binding site of CTI. These results clearly demonstrate that the P-type cytotoxins interact with membranes stronger than those of the S-type, although the mode of the membrane insertion is similar for both the types.

Human chemokine receptors CCR5, CCR3 and CCR2B share common polarity motif in the first extracellular loop with other human G-protein coupled receptors implications for HIV-1 coreceptor function

Chemokine receptors (CRs) are 7-helix membrane proteins from the family of G-protein coupled receptors (GPCRs). A few human CRs act as cofactors for macrophage-tropic (M-tropic) human immunodeficiency virus type-1 (HIV-1) entry into cells, while others do not. In this study, we describe an application of molecular modeling techniques to delineate common molecular determinants that might be related to coreceptor activity, and the use of the data to identify other GPCRs as putative cofactors for M-tropic HIV-1 entry. Subsequently, the results were confirmed by an experimental approach. The sequences of extracellular domains (ECDs) of CRs were employed in a compatibility search against a database of environmental profiles derived for proteins with known spatial structure. The best-scoring sequence-profile alignments obtained for each ECD were compared in pairs to check for common patterns in residue environments, and consensus sequence-profile fits for ECDs were also derived. Similar hydrophobicity motifs were found in the first extracellular loops of the CRs CCR5, CCR3, and CCR2B, and are all used by M-tropic HIV-1 for cell entry. In contrast, other CRs did not reveal common motifs. However, the same environmental pattern was also delineated in the first extracellular loop of some human GPCRs showing either high (group 1) or low (group 2) degree of similarity of their polarity patterns with those in HIV-1 coreceptors. To address the question of whether the delineated molecular determinant plays a critical role in the receptor-virus binding, three of the identified GPCRs, bradykinin receptor (BRB2) and G-protein receptor (GPR)-CY6 from group 1, and GPR8 from group 2, were cloned and transfected into HeLa-CD4 cells, which are nonpermissive to M-tropic HIV-1 infection. We demonstrate that, similar to CCR5, the two selected GPCRs from group 1 were capable of mediating M-tropic HIV-1 entry, whereas GPR8 from group 2 did not serve as HIV-1 coreceptor. The potential biological significance of the identified structural motif shared by the human CCR5, CCR3, CCR2B and other GPCRs is discussed.