Bacteriorhodopsin dynamic structures

Saito H, Kawase Y, Kira A et al (2007) Surface and dynamic structures of bacteriorhodopsin in a 2D crystal, a distorted or dismpted lattice, as revealed by site-directed solid-state 13C NMR. Photochem Photobiol 83 253-262... 

H. Saito, Y. Kawase, A. Kira, K. Yamamoto, M. Tanio, S. Yamaguchi, S. Tuzi, A. Naito, Surfece and dynamic structures of bacteriorhodopsin in 2D crystal, distorted or disrupted lattice, revealed by site-directed soHd-state C NMR, Photochem. Pho-tobiol. 83 (2007) 253-262. 

Notwithstanding this complexity, the need for three-dimensional, structural information at the atomic level of resolution is central and indispensable to biomembrane science. X-ray, and to a lesser extent neutron-diffraction, as the most important sources for such information have, therefore, been widely used in this field (for reviews, see Refs. 1-4). The success of this approach, however, has generally been less spectacular than for instance in the cases of protein or nucleic acid structure. The reasons for this lie in the very nature of biological membranes with few, notable exceptions (such as the purple membrane of halobacterium halobium, which can be viewed essentially as a two-dimensional crystal of bacteriorhodopsin with only little lipid. Refs. 5, 6,25) biological membranes are characterized by highly complex and variable molecular compositions, and by the structural dynamics, fluidity , which is in many cases essential for enzymatic, or other, functions of membranes. As a reflection of this most natural membranes do not crystallize, and a full, three-dimensional atomic structure analysis seems out of reach. 

The essential role of protein structure dynamics as a mechanistic consideration in proton transport has focused attention on amino acids such as proline (3, 9), which can confer localized flexibility within and between helical segments. Except for the unique case of bacteriorhodopsin, which is amenable to spectroscopic examination (10), little is known about the nature of molecular dynamics in transport enzymes. 

In a related work, NMR spectra of [3- C]Ala- and [l- C]Val-labelled bacteriorhodopsin and a variety of its mutants have also been reported. These studies were undertaken in order to clarify contributions of the extracellular Glu residues to the conformation and dynamics of bacteriorhodopsin. Significant dynamic changes were induced for the triple or quadruple mutants, as shown by broadened NMR peaks of [l- C]Val-labelled proteins. These changes were due to acquired global fluctuation motions of the order of 10 -10" s as a result of disorganised trimeric form. It was concluded that the Glu residues at the extracellular surface play an important role in maintaining the native secondary structure of bacteriorhodopsin in the purple membrane. 

Backbone Dynamics and Structures in the Interfacial Domains of Bacteriorhodopsin from Purple Membrane... 

BACKBONE DYNAMICS AND STRUCTURES IN THE INTERFACIAL DOMAINS OF BACTERIORHODOPSIN FROM PURPLE MEMBRANE... 

Optically induced cis-trans isomerization is a key structural dynamic element for many types of photochromic switches as stilbenes and azobenzene derivatives and for photosensor proteins as bacteriorhodopsin, rhodopsin, and photoactive yellow protein. 

S. Tuzi, A. Naito, H. Saito, Local protein structure and dynamics at kinked transmembrane a-helices of [1- C] Pro-labeled bacteriorhodopsin as revealed by site-directed solid-state NMR, J. Mol. Struct. 654 (2003) 205-214. 

Recently, several other reports have appeared where pK calculations for protein structures were performed using structures sampled from molecular dynamics trajectories. One combination of pK calculation and molecular dynamics was described by Sandberg and Edholm, who performed pK calculations for residues in bacteriorhodopsin along a 400 ps molecular dynamics trajectory. Another example, from McCammon s group, is presented in more detail below. 

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