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PubMed1993

Peptide mimics for structural features in proteins. Crystal structures of three heptapeptide helices with a C-terminal 6-->1 hydrogen bond.

The crystal structure determination of three heptapeptides containing alpha-aminoisobutyryl (Aib) residues as a means of helix stabilization provides a high-resolution characterization of 6-->1 hydrogen-bonded conformations, reminiscent of helix-terminating structural features in proteins. The crystal parameters for the three peptides, Boc-Val-Aib-X-Aib-Ala-Aib-Y-OMe, where X and Y are Phe, Leu (I), Leu, Phe (II) and Leu, Leu (III) are: (I) space group P1, Z = 1, a = 9.903 A, b = 10.709 A, c = 11.969 A, alpha = 102.94 degrees, beta = 103.41 degrees, gamma = 92.72 degrees, R = 4.55%; (II) space group P21, Z = 2, a = 10.052 A, b = 17.653 A, c = 13.510 A, beta = 108.45 degrees, R = 4.49%; (III) space group P1, Z = 2 (two independent molecules IIIa and IIIb in the asymmetric unit), a = 10.833 A, b = 13.850 A, c = 16.928 A, alpha = 99.77 degrees, beta = 105.90 degrees, gamma = 90.64 degrees, R = 8.54%. In all cases the helices form 3(10)/alpha-helical (or 3(10)helical) structures, with helical columns formed by head-to-tail hydrogen bonding. The helices assemble in an all-parallel motif in crystals I and III and in an antiparallel motif in II. In the four crystallographically characterized molecules, I, II, IIIa and IIIb, Aib(6) adopts a left-handed helical (hL) conformation with positive phi, psi values, resulting in 6-->1 hydrogen-bond formation between Aib(2) CO and Leu(7)/Phe(7) NH groups. In addition a 4-->1 hydrogen bond is seen between Aib(3) CO and Aib(6) NH groups. This pattern of hydrogen bonding is often observed at the C-terminus of helices proteins, with the terminal pi-type turn being formed by four residues adopting the hRhRhRhL conformation.

Amino Acid Sequence↗
PubMed1983

Conformation and structure of acidic dipeptides. Crystal structures of L-alanyl-L-aspartic acid and alpha-L-glutamyl-L-aspartic acid.

The crystal structures of the dipeptides L-alanyl-L-aspartic acid, C7H12N2O5, and alpha-L-glutamyl-L-aspartic acid, C9H14N2O7, have been determined from three-dimensional X-ray diffractometer data. Alanylaspartic acid crystallizes in the orthorhombic space group P2(1)2(1)2(1) with four formula units in a cell of dimensions a = 13.389(5), b = 14.467(3), c = 4.781(1) A. Glutamylaspartic acid also crystallizes in space group P2(1)2(1)2(1) with four formula units in a cell of dimensions a = 13.709(5), b = 16.126(7), c = 4.939(5) A. Both structures were solved by direct methods and refined by full-matrix least squares methods; the final value of the weighted R-factors (on F) were 0.040 based on 790 independent intensities with I greater than or equal to 2 sigma (I) for Ala-Asp and 0.033 based on 1105 intensities with I greater than or equal to 2 sigma (I) for Glu-Asp. Each dipeptide occurs as a zwitterion with the amino terminus protonated and the main chain carboxyl group deprotonated. The conformation of the peptide linkage is trans in both molecules, the omega torsion angle being - 175.9 degrees in Ala-Asp and 174.3 degrees in Glu-Asp. There is considerable intermolecular, but not intramolecular, hydrogen bonding in the crystals. The conformations and structures of Ala-Asp and Glu-Asp are compared to those of other structurally characterized acidic dipeptides.

Dipeptides↗
PubMed1998

Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure.

The solution structure of the 64 amino acid Fe4S4 ferredoxin I from Desulfovibrio africanus has been determined using two-dimensional 1H NMR spectroscopy. Sequence-specific assignments were obtained for 59 amino acid residues and the structure determined with the program DIANA on the basis of 549 nuclear Overhauser enhancement (NOE) upper distance limits, and four dihedral angle and 52 distance constraints for the Fe4S4 cluster. The NMR structure was refined using the simulated annealing and energy minimisation protocols of the program X-PLOR to yield a final family of 19 structures selected on the basis of good covalent geometry and minimal restraint violations. The r.m.s.d. values to the average structure for this family are 0.49(+/-0.07) A and 0.94(+/-0.09) A for the backbone and heavy-atoms of residues 3 to 62, respectively. The NMR structure has been compared to the previously reported X-ray structures for the two molecules within the asymmetric unit of the crystal, which have a network of seven hydrogen bonds between them. This intermolecular interface, involving residues 38, 40 to 43 and 46, has the same conformation in the solution structures showing that the crystal packing does not perturb the structure. There are three regions in which the NMR and X-ray structures differ: around the cluster, a turn involving residues 8 to 10, and a loop involving residues 29 to 32. In the family of solution structures the backbone of the loop region incorporating residues 29 to 32 is well-defined whilst in both of the X-ray molecules it is ill-defined. The small differences between the X-ray and NMR structures for the cluster environment and the turn between residues 8 to 10 probably reflects a lack of NMR constraints. The observation of relatively rapid amide NH hydrogen exchange of NH groups close to the cluster, together with rapid flipping for Phe25, which is also close to the cluster, indicates that the cluster environment is more dynamic than the corresponding regions of related Fe/S proteins.

Amino Acid Sequence↗
PubMedDate not supplied

Structural features of B-DNA dodecamer crystal structures: influence of crystal packing versus base sequence.

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral two-fold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon = g-, xi = t) BII conformation at the 10th position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures.

Base Sequence↗
PubMed2002

New software for searching the Cambridge Structural Database and visualizing crystal structures.

Two new programs have been developed for searching the Cambridge Structural Database (CSD) and visualizing database entries: ConQuest and Mercury. The former is a new search interface to the CSD, the latter is a high-performance crystal-structure visualizer with extensive facilities for exploring networks of intermolecular contacts. Particular emphasis has been placed on making the programs as intuitive as possible. Both ConQuest and Mercury run under Windows and various types of Unix, including Linux.

Journal Article↗
PubMed2006

Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis.

Non-canonical base pairs contribute immensely to the structural and functional variability of RNA, which calls for a detailed characterization of their spatial conformation. Intra-base pair parameters, namely propeller, buckle, open-angle, stagger, shear and stretch describe structure of base pairs indicating planarity and proximity of association between the two bases. In order to study the conformational specificities of non-canonical base pairs occurring in RNA crystal structures, we have upgraded NUPARM software to calculate these intra-base pair parameters using a new base pairing edge specific axis system. Analysis of base pairs and base triples with the new edge specific axis system indicate the presence of specific structural signatures for different classes of non-canonical pairs and triples. Differentiating features could be identified for pairs in cis or trans orientation, as well as those involving sugar edges or C-H-mediated hydrogen bonds. It was seen that propeller for all types of base pairs in cis orientation are generally negative, while those for trans base pairs do not have any preference. Formation of a base triple is seen to reduce propeller of the associated base pair along with reduction of overall flexibility of the pairs. We noticed that base pairs involving sugar edge are generally more non-planar, with large propeller or buckle values, presumably to avoid steric clash between the bulky sugar moieties. These specific conformational signatures often provide an insight into their role in the structural and functional context of RNA.

Base Pairing↗
PubMed2006

Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis.

Non-canonical base pairs, mostly present in the RNA, often play a prominent role towards maintaining their structural diversity. Higher order structures like base triples are also important in defining and stabilizing the tertiary folded structure of RNA. We have developed a new program BPFIND to analyze different types of canonical and non-canonical base pairs and base triples involving at least two direct hydrogen bonds formed between polar atoms of the bases or sugar O2' only. We considered 104 possible types of base pairs, out of which examples of 87 base pair types are found to occur in the available RNA crystal structures. Analysis indicates that approximately 32.7% base pairs in the functional RNA structures are non-canonical, which include different types of GA and GU Wobble base pairs apart from a wide range of base pair possibilities. We further noticed that more than 10.4% of these base pairs are involved in triplet formation, most of which play important role in maintaining long-range tertiary contacts in the three-dimensional folded structure of RNA. Apart from detection, the program also gives a quantitative estimate of the conformational deformation of detected base pairs in comparison to an ideal planar base pair. This helps us to gain insight into the extent of their structural variations and thus assists in understanding their specific role towards structural and functional diversity.

Algorithms↗
PubMed1977

Molecular structure of thyroxine analogues. Crystal structure of 3,5,3'-triiodothyroacetic and 3,5,3',5'-tetraoiodothyroacetic acid N-diethanolamine (1:1) complexes.

Crystallographic data demonstrated that conformations of thyroid hormones and their derivatives in which the phenyl rings are either skewed (phi,phi'; +/-90,0 degrees) or twist-skewed (phi,phi'; +/-108, +/-28 degrees) are energetically favored. Acetic acid metabolites are consistently observed in the skewed conformation whereas their parent hormones are observed in the twist-skewed conformation. These preferences are manifestations of long-range conformational transmission and together with plasma protein binding data may indicate a site-specific preference for the skewed vs. twist-skewed conformation. These findings result in part from the crystal structure determinations of the N-diethanolamine (1:1) complexes of the active thyroxine metabolites 3,5,3'-triiodothyroacetic acid (T3AA) and 3,5,3'5'-tetraiodothyroacetic acid (T4AA) which are reported here. The conformation of the 3'-iodine in the hypocholestermic agent T3AA is distal, the biologically preferred conformation, and the overall conformation of T3AA is transoid, while that of T4AA is cisoid.

Chemical Phenomena↗
PubMed2006

Propagating structural perturbation inside bacteriorhodopsin: crystal structures of the M state and the D96A and T46V mutants.

The X-ray diffraction structure of the non-illuminated D96A bacteriorhodopsin mutant reveals structural changes as far away as 15 A from residue 96, at the retinal, Trp-182, Ala-215, and waters 501, 402, and 401. The Asp-to-Ala side-chain replacement breaks its hydrogen bond with Thr-46, and the resulting separation of the cytoplasmic ends of helices B and C is communicated to the retinal region through a chain of covalent and hydrogen bonds. The unexpected long-range consequences of the D96A mutation include breaking the hydrogen bond between O of Ala-215 and water 501 and the formation of a new hydrogen bond between water molecules 401 and 402 in the extracellular region. Because in the T46V mutant a new water molecule appears at Asp-96 and its hydrogen-bond to Ile-45 replaces Thr-46 as its link to helix B, the separation of helices B and C is smaller than that in D96A, and there are no atomic displacements elsewhere in the protein. Propagation of conformational changes along the chain between the retinal and Thr-46 had been observed earlier in the crystal structures of the D96N and E204Q mutants but in the trapped M state. Consistent with the perturbation of the retinal region in D96A, little change of the Thr-46 region occurs between the non-illuminated and M states of this mutant. It appears that a local perturbation can propagate along a track in both directions between the retinal and the Asp-96/Thr-46 pair, either from photoisomerization of the retinal in the wild-type protein in one case or from the D96A mutation in the other.

Amino Acid Substitution↗
PubMed2002

Analysis of voids in crystal structures: the methods of 'dual' crystal chemistry.

The theoretical basics of the analysis of voids in crystal structures by means of Voronoi-Dirichlet polyhedra (VDP) and of the graph theory are stated. Topological relations are considered between VDPs and atomic domains in a crystal field. These relations allow the separation of two non-intersecting topological subspaces in a crystal structure, whose connectednesses are defined by two finite 'reduced' graphs. The first, 'direct', subspace includes the atoms (VDP centres) and the network of interatomic bonds (VDP faces), the second, 'dual', one comprises the void centres (VDP vertices) and the system of channels (VDP edges) between them. Computer methods of geometrical-topological analysis of the 'dual' subspace are developed and implemented within the program package TOPOS. They are designed for automatically restoring the system of channels, visualizing and sizing voids and void conglomerates, dimensional analysis of continuous void systems, and comparative topological analysis of 'dual' subspaces for various substances. The methods of analysis of 'dual' and 'direct' subspaces are noted to differ from each other only in some details that allows the term 'dual' crystal chemistry to be introduced. The efficiency of the methods is shown with the analysis of compounds of different chemical nature: simple substances, ionic structures, superionic conductors, zeolites, clathrates, organic supramolecular complexes.

Journal Article↗
PubMed1990

Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex.

The structure of a complex of bacteriophage lambda Cro protein with a 17-base-pair operator has been determined at 3.9-A resolution. Isomorphous derivatives obtained by the synthesis of site-specific iodinated DNA oligomers were of critical importance in solving the structure. The crystal structure contains three independent Cro-operator complexes that have very similar, although not necessarily identical, conformations. In the complex, the protein dimer undergoes a large conformational change relative to the crystal structure of the free protein. One monomer rotates by about 40 degrees relative to the other, this being accomplished primarily by a twisting of the two beta-sheet strands that connect one monomer with the other. In the complex, the DNA is bent by about 40 degrees into the shape of a boomerang but maintains essentially Watson-Crick B-form. In contrast to other known protein-DNA complexes, the DNA is not stacked end-to-end. The structure confirms the general features of the model previously proposed for the interaction of Cro with DNA.

Amino Acid Sequence↗
PubMed2006

Characterization and crystal structure of cadmium(II) halide complexes with amino acids and their derivatives: VII. Crystal structures of aquadibromo(3-aminopropanoic acid)cadmium(II), dichloro(4-aminobutanoic acid)cadmium(II), diaquabis(aminohexanoic acid)cadmium(II) tetrachlorocadmium(II), and dibromo(azetidine-3-carboxylic acid)cadmium(II).

Seven cadmium complexes: [CdX2(Hapro)(H2O)n] (X: Cl(1), Br(2)), [CdX2(Hgaba)] (X: Cl(3), Br(4)), [Cd(Hahex)2(H2O)2][CdCl4] (5), and [CdX2(Haze-3)](H2O)n (X: Cl(6), Br(7)) have been prepared and investigated by means of IR and FT Raman spectra. The crystal and molecular structures of 2, 3, 5 and 7 were determined by a single-crystal X-ray diffraction method. In complex 2, the cadmium atom is in a distorted octahedral geometry, ligated by two carboxyl oxygen atoms of Hapro, a water molecule, and three bromine atoms; one is terminal and each of the other two is bridging two cadmium atoms to make a polymer. The structure of 3 consists of one-dimensional polymers bridged by two chlorine atoms and a carboxyl group. The carboxyl oxygen atoms of Hgaba coordinate forkedly to two cadmium atoms. The cadmium atom of [Cd(Hahex)2(H2O)2]2+ in complex 5 is in a distorted octahedral geometry, ligated by four carboxyl oxygen atoms of two molecules of Hahex and by two water molecules. [Cd(Hahex)2(H2O)2]2+ exists between two layers which are formed of infinite [CdCl4]2- chains. The carboxyl oxygen atoms of Hahex coordinate to the same cadmium atom. In complex 7, the cadmium atom is ligated by two carboxyl oxygen atoms and four bridging bromine atoms to make a polymer.

Amino Acids↗
PubMed2005

Oxidative DNA cleavage mediated by a new copper (II) terpyridine complex: crystal structure and DNA binding studies.

The copper (II) complex [Cu(Itpy)(2)](ClO(4))(2) (1), (Itpy=imidazole terpyridine) has been synthesized and structurally characterized. Crystal structure of the complex shows the complex to be a monomeric copper (II) species with two Itpy ligands coordinated to the metal ion to give a six coordinate complex. The complex has a distorted octahedral geometry with axial elongation. Variable temperature crystal structure data shows dynamic nature of the Jahn-Teller distortion. The complex is an avid DNA binder with a binding constant of 4.26+/-0.20x10(3)M(-1). Observed changes in the viscosity and circular dichroic spectrum of calf thymus DNA solution in the presence of complex 1 suggests intercalative binding of complex 1 to DNA. The complex cleaves supercoiled pBR322 DNA oxidatively in the presence of hydrogen peroxide.

Animals↗
PubMed1998

Synthesis and Crystal Structure of a New Type of Ionic Technetium(V) Dioxo Phosphine Complexes, [Tc(O)(2)(PR(3))(3)](+). Reactions with Pyridine and Crystal Structures of trans,cis,cis-[Tc(O)(2)(PR(3))(2)(py)(2)](+) Compounds.

New ionic technetium complexes of the type [TcO(2)(PR(3))(3)](+) have been synthesized from the reaction of [TcO(4)](-) with the phosphine in methanol. The crystal structures of two crystallographic forms of [TcO(2)(PEt(3))(3)](BPh(4)) were determined. The first form is monoclinic, space group P2(1)/n with a = 14.353(3) Å, b = 11.731(2) Å, c = 26.478(6) Å, beta = 101.22(1) degrees, and Z = 4. The second form is also monoclinic, space group P2(1)/c with a = 10.043(3) Å, b = 21.122(4), c = 20.994(5) Å, beta = 97.43(2) degrees, and Z = 4. [TcO(2)(PPr(3))(3)](BPh(4)) belongs to the monoclinic C2/c space group with a = 34.097(7) Å, b = 16.944(4) Å, c = 19.033(4) Å, beta = 102.99(1) degrees, and Z = 8. The geometry around the Tc atom is a trigonal bipyramid with the two oxo ligands in the trigonal plane. The Tc-O bond distances are between 1.707(4) and 1.726(3) Å, while the Tc-P bonds vary from 2.507(2) to 2.528(2) Å for the axial ligands and between 2.395(1) and 2.403(1) Å for the equatorial bond. The O-Tc-O angles are in the range 141.5(2)-143.4(2) degrees. The reaction of these complexes with pyridine produced trans,cis, cis-[Tc(O)(2)(PR(3))(2)(py)(2)](+) (py = pyridine). [Tc(O)(2)(PMe(3))(2)(py)(2)](BPh(4)) is monoclinic, space group P2(1)/c with a = 30.346(8) Å, b = 12.865(4) Å, c = 21.464(9) Å, beta = 110.35(2) degrees, and Z = 8, while [Tc(O)(2)(PEt(3))(2)(py)(2)](BPh(4)) is monoclinic, space group P2(1)/c with a = 10.594(6) Å, b = 19.921(7) Å, c = 21.306(10) Å, beta = 95.31(5) degrees, and Z = 4. The geometry around the Tc atom is a distorted octahedron with the oxo ligands located in trans positions to each other, while the phosphine and the pyridine ligands are cis to each other.

Journal Article↗
PubMed2003

Syntheses, reactivity, and crystal structures of molybdenum complexes with pyridine-2-thionate (pyS)-containing ligands: crystal structures of [Mo(eta(3)-C(3)H(5))(CO)(2)](2)(mu-eta(1),eta(2)-pyS)(2), exo-[Mo(eta(3)-C(3)H(5))(CO)(eta(2)-pyS)(eta(2)-dppe)], [Mo(CO)(3)(eta(1)-SC(5)H(4)NH)(eta(2)-dppm)], and [Mo(CO)(eta(2)-pyS)(2)(eta(2)-dppm)].

The doubly bridged pyridine-2-thionate (pyS) dimolybdenum complex [Mo(eta(3)-C(3)H(5))(CO)(2)](2)(mu-eta(1),eta(2)-pyS)(2) (1) is accessible by the reaction of [Mo(eta(3)-C(3)H(5))(CO)(2)(CH(3)CN)(2)Br] with pySK in methanol at room temperature. Complex 1 reacts with piperidine in acetonitrile to give the complex [Mo(eta(3)-C(3)H(5))(CO)(2)(eta(2)-pyS)(C(5)H(10)NH)] (2). Treatment of 1 with 1,10-phenanthroline (phen) results in the formation of complex [Mo(eta(3)-C(3)H(5))(CO)(2)(eta(1)-pyS)(phen)] (3), in which the pyS ligand is coordinated to Mo through the sulfur atom. Four conformational isomers, endo,exo-complexes [Mo(eta(3)-C(3)H(5))(CO)(eta(2)-pyS)(eta(2)-diphos)] (diphos = dppm, 4a-4d; dppe, 5a-5d), are accessible by the reactions of 1 with dppm and dppe in refluxing acetonitrile. Homonuclear shift-correlated 2-D (31)P((1)H)-(31)P((1)H) NMR experiments of the mixtures 4a-4d have been employed to elucidate the four stereoisomers. The reaction of 4 and pySK or [Mo(CO)(3)(eta(1)-SC(5)H(4)NH)(eta(2)-dppm)] (6) and O(2) affords allyl-displaced seven-coordinate bis(pyridine-2-thionate) complex [Mo(CO)(eta(2)-pyS)(2)(eta(2)-dppm)] (7). All of the complexes are identified by spectroscopic methods, and complexes 1, 5d, 6, and 7 are determined by single-crystal X-ray diffraction. Complexes 1 and 5d crystallize in the orthorhombic space groups Pbcn and Pbca with Z = 4 and 8, respectively, whereas 6 belongs to the monoclinic space group C2/c with Z = 8 and 7 belongs to the triclinic space group Ponemacr; with Z = 2. The cell dimensions are as follows: for 1, a = 8.3128(1) A, b = 16.1704(2) A, c = 16.6140(2) A; for 5d, a = 17.8309(10) A, b = 17.3324(10) A, c = 20.3716(11) A; for 6, a = 18.618(4) A, b = 16.062(2) A, c = 27.456(6) A, beta = 96.31(3) degrees; for 7, a = 9.1660(2) A, b = 12.0854(3) A, c = 15.9478(4) A, alpha = 78.4811(10) degrees, beta = 80.3894(10) degrees, gamma = 68.7089(11) degrees.

Journal Article↗
PubMed1989

Platelet activating factor antagonist design. 3. X-ray crystal structure and intermolecular crystal lattice interactions of methyl trans-4-acetoxymethyl-4,5-dihydro-2,5-bis(3,4-methylenedioxyphenyl)- 3-furancarboxylate.

C23H20O9, Mr = 440.41, monoclinic, P21/c, a = 11.433 (1), b = 7.808 (2), c = 23.313 (3) A, beta = 99.67 (1) degree, V = 2052 A3, Z = 4, Dx = 1.43 g cm-3, lambda(MoK alpha) = 0.71073 A, mu = 0.69 cm-1, F(000) = 920, T = 293 K, final R = 0.048 for 1645 observed [Fo greater than or equal to 5 sigma(Fo)] reflections. The observed structure reveals a trans relationship for the 4-acetoxymethyl and 5-aryl substituents. The 4,5-dihydrofuran ring system adopts an envelope conformation. There is no crystallographically imposed symmetry. Several intermolecular van der Waals interactions occur in the cell lattice of this compound.

Chemical Phenomena↗
PubMed2004

Can the low-resolution structures of photointermediates of bacteriorhodopsin explain their crystal structures?

To understand the molecular mechanism of light-driven proton pumps, the structures of the photointermediates of bacteriorhodopsin have been intensively investigated. Low-resolution diffraction techniques have demonstrated substantial conformational changes at the helix level in the M and N intermediates, between which there are noticeable differences. The intermediate structures at atomic resolution have also been solved by x-ray crystallography. Although the crystal structures have demonstrated local structural changes, such as hydrogen bond network rearrangements including water molecules, the large conformational changes at the helix level are not necessarily observed. Furthermore, the two reported crystal structures of an intermediate accumulated using a common method were distinct. To reconcile these apparent discrepancies, low-resolution projection maps were calculated from the crystal structures and compared to the low-resolution intermediate structures obtained using native membranes. The crystal structures can be categorized into three groups, which qualitatively correspond to the low-resolution structures of the M1-type, M2-type, and N-type determined in the native membrane. Based on these results, we conclude that at least three types of intermediate structures play a role during the photocycle.

Bacteriorhodopsins↗