Showing papers by "Mark Gerstein published in 1993"

Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.

Abstract: Structural changes are central to the mechanism of light-driven proton transport by bacteriorhodopsin, a seven-helix membrane protein. The main intermediate formed upon light absorption is M, which occurs between the proton release and uptake steps of the photocycle. To investigate the structure of the M intermediate, we have carried out electron diffraction studies with two-dimensional crystals of wild-type bacteriorhodopsin and the Asp96-->Gly mutant. The M intermediate was trapped by rapidly freezing the crystals in liquid ethane following illumination with a xenon flash lamp at 5 and 25 degrees C. Here, we present 3.5 A resolution Fourier projection maps of the differences between the M intermediate and the ground state of bacteriorhodopsin. The most prominent structural changes are observed in the vicinity of helices F and G and are localized to the cytoplasmic half of the membrane.

An NMR study on the DNA-binding SPKK motif and a model for its interaction with DNA

Abstract: The solution structure of one and two repeats of the 'SPKK' DNA-binding motif is reported on the basis of NMR measurements. In dimethylsulphoxide (DMSO) the major population (approximately 90%) of peptides, SPRKSPRK(S2) and GSPKKSPRK(S2b), adopts a conformation, which has two trans prolines. The two 'SP(R/K)K' units in these peptides are equivalent and each adopts a turn structure exchanging with an extended structure. This is suggested by an NOE connectivity of the beta-turn type, between the backbone amide protons of residues (i+2) and (i+3) and NOE connectivities of the Asx(sigma)-turn type, between protons of the ith Ser and the backbone amide proton on residue (i+2). This suggests that each SP(R/K)K unit has a structural intermediate between (or a combination of) a beta-turn and an Asx(sigma)-turn. In 90-10% DMSO/H2O at 4 degrees C the two units of S2 are connected more tightly by folding into a short 3(10) helix, broken at the second proline. For another peptide, Thr-Pro-Arg-Lys(T1), the major population (75%) in 100% DMSO comprises a beta-turn in rapid exchange with an extended structure. We did not observe an NOE connectivity of the Asx(sigma) type with the T1 peptide. A possible structure of the SPKK motif in the complex with DNA is discussed.

Simulation of water around a model protein helix. 1. Two-dimensional projections of solvent structure

Abstract: The water structure around a model α-helix in solution is investigated by molecular simulation. A marked contrast is seen between the hydration of the α and β carbons on one side of the helix axis and of the carbonyl oxygen on the other side. Three well-defined peaks in the oxygen density, loosely corresponding to three layers of water, are found around the two hydrophobic atoms. In contrast, around the hydrophilic carbonyl oxygen the first two peaks merge into a single large peak. Analysis of the water orientation shows that on average the water dipoles are parallel to the surface of the helix

Simulation of water around a model protein helix. 2. The relative contributions of packing, hydrophobicity, and hydrogen bonding

Abstract: In the preceding paper, the structure of water around a model protein a-helix (made from polyalanine) was investigated using two-dimensional projections of the molccular distribution function. Here an attempt is made to assess the relative importance of pacting, protein-water hydrogen bonding, and water-water hydrogen bonding in creating this water structure. To isolate the effect of protein-water hydrogen bonding, simulations with the helix charges «switched» on and off were compared. Likewise, these «normal» water simulations were compared to ones done with the water charges switched off to assess the relative contributions of packing and hydrogen bonding