Accommodation of hydroxyl groups and their hydrogen bond system in a hydrocarbon matrix

From data of sisingle crystal analysis of 12-D-hydroxyoctadecanoic acid methyl ester principles for the incorporation of hydroxyl groups into a hydrocarbon chain matrix can be deduced. In the crystalline compound infinite hydrogen bond systems are accommodated in an orthorhombic perpendicular (O) chain arrangement. The O hydrocarbon subcell is expanded towards a hexagonal packing pattern, allowing more space and optimal geometry for the hydrogen bond system. The arrangement of the bond system in the O subcell requires that hydrogen bonded carbon chains carry alternatingly hydroxyl roups with opposite configuration. For the enantiomeric compound this requirement is met by a head to tail packing of molecules in a single layer arrangement. The corresponding racemates on the other hand pack head to head in double layers as confirmed by X-ray powder and IR studies. In monolayers both enantiomers and racemates behave identicalyy. The hydrogen bonding of the hydroxyl groups apparently leads to the formation of lipid clusters, in which the geometric conditions for both a close packing of hydrocarbon chains and the formation of an extensive hydrogen bond system do not exist.     

Protein-protein recognition and the association of immunoglobulin constant domains

Four immunoglobulin constant domain interfaces were analysed to determine how the light and heavy chains of the domains recognize each other and secondarily, why the packing of the beta sheets is different from that normally observed in the interior of domains of beta sheet proteins. It was found that two bulky groups in the centre of each of the domain interfaces prevent the alignment of sheet axes by intercalating with residues in the sheet opposite. This intercalation forms the basis of constant domain light chain-heavy chain recognition.     

Production of (+)-globulol needle crystals on the surface mycelium of Quambalaria cyanescens

The structure of unique colorless needle crystals growing from the surface mycelium of the basidiomycete Quambalaria cyanescens and identified as (+)-globulol was followed by mass spectrometry, X-ray diffraction, and polarimetry. The mechanism of (+)-globulol fragmentation is proposed based on collision induced dissociation mass spectrometry. X-Ray analysis revealed that crystal packing is governed by hydrogen bond O-H.....O connecting the molecules into an infinite helix along a 3-fold screw axis propagating along the longest dimension of the needle crystal (c-axis of the unit cell). The X-ray diffraction data correspond well with the proposed structure determined by mass spectrometry.     

Drosophila laminin A chain sequence, interspecies comparison, and domain structure of a major carboxyl portion.

Recent studies ascribed some biological actions of cell adhesion and cell outgrowth to the carboxyl-most 1200 amino acids of vertebrate laminin A chains. Here we report a 6.1-kilobase pair nucleotide cDNA sequence encoding 1951 amino acids and the carboxyl end of a Drosophila laminin A chain. It corresponds to the mouse laminin A domains G, I, II, and III, but may represent a different type of laminin A chain. The arrangement of the cysteine-rich repeats of domain III resembles that of B2 chains. However, it has more amino acid identity with a portion of the mouse laminin A chain domain IIIb than with other laminin repeats. Domains I and II are consistent with an interrupted coiled-coil alpha-helical model of the long arm of laminin but are poorly conserved. The G domain contains five subdomains which are individually related to subdomains of vertebrate laminin A chains. The results indicate that laminin G subdomains should be considered individually, rather than merely as parts of a G-globule. A sequence of hydroxyamino acids contributes to a spacer between two of the subdomains. Stretches of hydroxyamino acids may be indicative of junctions between domains of extracellular Drosophila proteins.     

Evolution of variable and constant domains and joining segments of rearranging immunoglobulins

The rearranging immunoglobulins (Igs) are a family of recognition and defense proteins found in all vertebrate classes. These proteins consist of two types of polypeptide chains; each of these contains a variable (V) domain, a joining (J) segment, and a constant (C) region, which can itself consist of one to four domains. The distinction between light and heavy chains is an ancient one phylogenetically that is reflected in the structures of V, J, and C regions. Despite the early emergence of these genetic elements, conservatism is apparent in the peptide structures encoded by V, J, and C exons. C regions of heavy chains did not evolve as single units; rather the individual domains show their own clustering patterns, which apparently are independent of heavy-chain designation or species. C-region domains of light chains and the T cell receptor beta chain are similar to one another and to the most carboxyl-terminal domain of heavy chains. Comparison of the light chains of sharks, bullfrogs, chickens, and mammals indicated that a phylogenetic distinction can be made between kappa and lambda light chains. V and J segments of the rearranging T cell receptors alpha, gamma, and delta are homologous to the corresponding segments of Igs, but their C regions form a group that is markedly distinct from those of conventional Igs and Tcr beta.     

Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides

The flavin-binding BLUF domain of AppA represents a new class of blue light photoreceptors that are present in a number of bacterial and algal species. The dark state X-ray structure of this domain was determined at 2.3 A resolution. The domain demonstrates a new function for the common ferredoxin-like fold; two long alpha-helices flank the flavin, which is bound with its isoalloxazine ring perpendicular to a five-stranded beta-sheet. The hydrogen bond network and the overall protein topology of the BLUF domain (but not its sequence) bear some resemblance to LOV domains, a subset of PAS domains widely involved in signaling. Nearly all residues conserved in BLUF domains surround the flavin chromophore, many of which are involved in an intricate hydrogen bond network. Photoactivation may induce a rearrangement in this network via reorientation of the Gln63 side chain to form a new hydrogen bond to the flavin O4 position. This shift would also break a hydrogen bond to the Trp104 side chain, which may be critical in induction of global structural change in AppA.     

Locations of disulfide bonds and free cysteines in the heavy and light chains of recombinant human factor VIII (antihemophilic factor A).

The locations of disulfide bonds and free cysteines in the heavy and light chains of recombinant human factor VIII were determined by sequence analysis of fragments produced by chemical and enzymatic digestions. The A1 and A2 domains of the heavy chain and the A3 domain of the light chain contain one free cysteine and two disulfide bonds, whereas the C1 and C2 domains of the light chain have one disulfide bond and no free cysteine. The positions of these disulfide bonds are conserved in factor V and ceruloplasmin except that the second disulfide bond in the A3 domain is missing in both factor V and ceruloplasmin. The positions of the three free cysteines of factor VIII are the same as three of the four cysteines present in ceruloplasmin. However, the positions of the free cysteines in factor VIII and ceruloplasmin are not conserved in factor V.     

Heterotypic complex formation between subunits of microtubule-associated proteins 1A and 1B is due to interaction of conserved domains

The microtubule-associated proteins MAP1A and MAP1B are related but distinct multi-subunit protein complexes that consist of heavy and light chains. The predominant forms of these complexes are homotypic, i.e. they consist of a MAP1A heavy chain associated with MAP1A light chains or a MAP1B heavy chain associated with MAP1B light chains, respectively. In addition, MAP1A and MAP1B can exchange subunits and form heterotypic complexes consisting of a MAP1A heavy chain associated with MAP1B light chains which might play a role in a transition period of neuronal differentiation. Here we extend previous findings by confirming that heterotypic MAP1B heavy chain-MAP1A light chain complexes also exist in the developing murine brain. We show that these complexes form through interaction of homologous domains conserved in heavy and light chains of MAP1A and MAP1B. Likewise, conserved domains of the MAP1A and MAP1B light chains account for formation of light chain heterodimers. By yeast 2-hybrid analysis we located the light chain binding domain on the heavy chain to amino acids 211-508, thereby defining a new functional subdomain.     

Crystal structure of the ENT domain of human EMSY

EMSY is a recently discovered gene encoding a BRCA2-associated protein and is amplified in some sporadic breast and ovarian cancers. The EMSY sequence contains no known domain except for a conserved approximately 100 residue segment at the N terminus. This so-called ENT domain is unique in the human genome, although multiple copies are found in Arabidopsis proteins containing members of the Royal family of chromatin remodelling domains. Here, we report the crystal structure of the ENT domain of EMSY, consisting of a unique arrangement of five alpha-helices that fold into a helical bundle arrangement. The fold shares regions of structural homology with the DNA-binding domain of homeodomain proteins. The ENT domain forms a homodimer via the anti-parallel packing of the extended N-terminal alpha-helix of each molecule. It is stabilized mainly by hydrophobic residues at the dimer interface and has a dissociation constant in the low micromolar range. The dimerisation of EMSY mediated by the ENT domain could provide flexibility for it to bind two or more different substrates simultaneously.     

Analysis of immunoglobulin domain interactions. Evidence for a dominant role of salt bridges

Available crystallographic data for homologous immunoglobulin constant domains were correlated with measured association constants for these domains. High correlation was found between the association constant and both the buried surface area (number of interdomain contacts) and the number of salt bridges formed in the interaction, whereas no correlation with the number of hydrogen bonds between domains was evident. The total free energy of binding, as determined from the association constant, was related to the number of contacts, hydrogen bonds and salt bridges found in the domain:domain interface by the crystallographic studies. These calculations yielded reasonable average energy terms for each interaction category.     

Analysis of interspecies variability of immunoglobulin lambda chains reveals differences in domain tertiary structures.

X-ray crystallography showed the NH₂-proximal (variable, V) and COOH-proximal (constant, C) halves of the λ chain to fold independently into autonomous three-dimensional domains, homologous domains from different chains interacting strongly by non-covalent forces to form domain dimers. In this letter, interspecies homology of five immunoglobulin λ chain primary structures from man, mouse and pig has been evaluated separately for those segments of polypeptide chains that correspond to basic structural elements of a domain fold. The highest degree of phylogenetic conservation has always been found with segments forming the innermost part of domain dimers, though the V-V dimer is known to be packed inside out with respect to the C-C dimer, its inner segments being different from those of the C-C dimer. Differences of interspecies homology between analogous segments from the variable and the constant domain have been revealed which correlate with differences in domain architectures. Two different measures of interspecies homology have been defined (% positions with identical residues; % positions displaying 80% homology) the ratio of which is indicative of packing density and of folding constraints imposed on a particular segment.     

The structure of 2Zn pig insulin crystals at 1.5 A resolution

The paper describes the arrangement of the atoms within rhombohedral crystals of 2Zn pig insulin as seen in electron density maps calculated from X-ray data extending to 1.5 A (1 A = 10(-10) m = 10(-1) nm) at room temperature and refined to R = 0.153. The unit cell contains 2 zinc ions, 6 insulin molecules and about 3 x 283 water molecules. The atoms in the protein molecules appear well defined, 7 of the 102 side chains in the asymmetric unit have been assigned alternative disordered positions. The electron density over the water molecules has been interpreted in terms of 349 sites, 217 weighted 1.0, 126 weighted 0.5, 5 at 0.33 and 1 at 0.25 giving ca. 282 molecules. The positions and contacts of all the residues belonging to the two A and B chains of the asymmetric unit are shown first and then details of their arrangement in the two insulin molecules, 1 and 2, which are different. The formation from these molecules of a compact dimer and the further aggregation of three dimers to form a hexamer around two zinc ions, follows. It appears that in the packing of the hexamers in the crystal there are conflicting influences; too-close contacts between histidine B5 residues in neighbouring hexamers are probably responsible for movements of atoms at the beginning of the A chain of one of the two molecules of the dimer that initiate movements in other parts, particularly near the end of the B chain. At every stage of the building of the protein structure, residues to chains of definite conformation, molecules, dimers, hexamers and crystals, we can trace the effect of the packing of like groups to like, aliphatic groups together, aromatic groups together, hydrogen-bonded structures, positive and negative ions. Between the protein molecules, the water is distributed in cavities and channels that are continuous throughout the crystals. More than half the water molecules appear directly hydrogen bonded to protein atoms. These are generally in contact with other water molecules in chains and rings of increasing disorder, corresponding with their movement through the crystals. Within the established crystal structure we survey next the distribution of hydrogen bonds within the protein molecules and between water and protein and water and water; all but eight of the active atoms in the protein form at least one hydrogen bond.(ABSTRACT TRUNCATED AT 400 WORDS)     

Conformational flexibility and crystallization of tandemly linked type III modules of human fibronectin.

Fibronectin is a large cell adhesion molecule that is composed of several functional domains. The cell-binding domain that binds to cell surface integrins consists of repeated homologous type III modules. In this study, recombinant fragments from the cell-binding domain of human fibronectin that participate in a newly characterized fibronectin-fibronectin interaction with FNIII1 were crystallized. In each case, the crystals had more than one fibronectin fragment in the asymmetric unit. Crystals of FNIII10-11 grew in the space group C2 with a = 117.1 A, b = 38.6 A, c = 80.6 A, beta = 97.2 degrees, and two molecules in the asymmetric unit. These crystals diffracted to 2.5 A resolution. Fragment FNIII8-11 and a shorter fragment, FNIII8-10, crystallized in hexagonal space groups with large unit cells and two to four molecules per asymmetric unit. Even very large crystals of these fragments did not diffract beyond 4 A. The crystal packing for this collection of fibronectin fragments suggests conformational flexibility between linked type III modules. The functional relevance of this flexibility for elongated versus compact models of the cell-binding domain of fibronectin is discussed.     

Structural study of anhydrous tendon chitosan obtained via chitosan/acetic acid complex

The molecular structure and packing arrangement of anhydrous tendon chitosan was determined by the X-ray fibre diffraction method together with the linked-atom least-squares refinement technique. The specimen was prepared from chitosan/acetic acid complex which was obtained by exposing tendon chitosan to acetic acid vapour at room temperature for several days. There is high degree of orientation and crystallinity compared with the specimen obtained by the annealing method. Two chitosan chains are present in an orthorhombic unit cell of dimensions a = 8.26(2), b = 8.50(1), c (fibre axis) = 10.43(2) A and space group P2(1)2(1)2(1). The 2-fold helical chain is stabilised by O3 triple bond O5 hydrogen bond with the gt orientation of O6. There are direct hydrogen bonds (N2 triple bond O6) between adjacent chains along the a-axis, which makes a sheet structure parallel to the ac-plane. On the other hand, no hydrogen bond is found between the sheets.     

Peptidoglycan recognition by Pal, an outer membrane lipoprotein

Peptidoglycan-associated lipoprotein (Pal) is a potential vaccine candidate from Haemophilus influenzae that is highly conserved in Gram-negative bacteria and anchored to the outer membrane through an N-terminal lipid attachment. Pal stabilizes the outer membrane by providing a noncovalent link to the peptidoglycan (PG) layer through a periplasmic domain. Using NMR spectroscopy, we determined the three-dimensional structure of a complex between the periplasmic domain of Pal and a biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-alpha-d-Glu-m-Dap-D-Ala-d-Ala (m-Dap is meso-diaminopimelate). Pal has a binding pocket lined with conserved surface residues that interacts exclusively with the peptide portion of the ligand. The m-Dap residue, which is mainly found in the cell walls of Gram-negative bacteria, is sequestered in this pocket and plays an important role by forming hydrogen bond and hydrophobic contacts to Pal. The structure provides insight into the mode of cell wall recognition for a broad class of Gram-negative membrane proteins, including OmpA and MotB, which have peptidoglycan-binding domains homologous to that of Pal.     

Conformation of the oleate chains in crystals of cholesteryl oleate at 123 K

At 123 K, crystals of cholesteryl cis-9-octadecenoate (cholesteryl oleate, C45H78O2) are monoclinic, space group P2(1) with unit cell dimensions a = 12.356(2), b = 8.980(3), c = 18.382(2) A, beta = 85.49(2) degrees, and have two molecules in the unit cell. The crystal structure including all H atoms has been determined from 3812 independent X-ray reflections with sin theta/lambda less than 0.61 A-1 and refined to give Rw = 0.08. At 123 K, the crystal structure consists of an antiparallel efficient packing of cholesteryl ring systems to form layers that are very similar to those observed in the room temperature structure. The oleate chains that protrude from these layers have a somewhat different packing arrangement from the room temperature structure because they have undergone a conformational change. At 123 K, the oleate chains are well ordered and are almost fully extended except for a kink at the cis double bond. The oleate chains at 123 K are 1.7 A longer than at 295 K due in part to an uncoiling whereby their helical character is lost. On cooling, there is a substantial change in the unit cell beta-angle from obtuse (93.3 degrees) to acute (85.5 degrees) which involves a shearing motion of 2.5 A between adjacent molecular layers. Cell dimension measurements at 10 temperatures in the range 295 K to 123 K show that much of the change occurs in two narrow ranges centered at 262 K and 215 K.     

Synthesis and X-ray crystal structure study of the hydroxyurea and hydantoin derivatives of L-valine.

The novel hydroxyurea 5 derivative of L-valine was prepared by aminolysis of N-(1-benzotriazolecarbonyl)-L-valine cyclohexanemethylamide 4 with hydroxylamine. The corresponding hydantoin derivative 6 was synthesized by base catalyzed cyclization of the amide 4. The exact stereostructure of hydantoin derivative 6 has been determined by X-ray crystal structure analysis. The chiral atom of the hydantoin ring in 6 has S configuration what is in agreement with its configuration in the starting L-valine. The molecules of 6 are joined into infinite chains by N-H...O intermolecular hydrogen bond. The infinite chains are additionally linked by two C-H...O hydrogen bonds, thus forming two-dimensional network. The hydantoin derivative of L-valine 6 and its L-leucine analogue LH have similar packing arrangements, so they are homostructural.     

Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104

Hsp104, a yeast protein-remodeling factor of the AAA+ (ATPases associated with various cellular activities) superfamily, and its homologs in bacteria and plants mediate cell recovery after severe stress by disaggregating denatured proteins through a poorly understood mechanism. Here, we present cryo-electron microscopy maps and domain fitting of Hsp104 hexamers, revealing an unusual arrangement of AAA+ modules with the prominent coiled-coil domain intercalated between the AAA+ domains. This packing results in a greatly expanded cavity, which is capped at either end by N- and C-terminal domains. The fitted structures as well as mutation of conserved coiled-coil arginines suggest that the coiled-coil domain plays a major role in the extraction of proteins from aggregates, providing conserved residues for key functions in ATP hydrolysis and potentially for substrate interaction. The large cavity could enable the uptake of polypeptide loops without a requirement for exposed N or C termini.     

The structure of an entire noncovalent immunoglobulin kappa light-chain dimer (Bence-Jones protein) reveals a weak and unusual constant domains association.

Monoclonal free light chains secreted in immunoproliferative disorders are frequently involved in renal complications, including a specific proximal tubule impairment, Fanconi's syndrome. The latter is characterized in most cases by intracellular crystallization including a light-chain variable-domain fragment which resists lysosomal proteases. Bence-Jones protein (BJP) DEL was isolated from a patient with myeloma-associated Fanconi's syndrome. The crystal structure of this human kappa immunoglobulin light-chain noncovalent dimer was determined using molecular replacement with the structure of molecule REI, as the variable domain, and that of BJP LOC as the constant domain. To our knowledge, DEL is the first complete kappa BJP structure described to date. The R-factor is 20.7% at 2.8 A resolution. The BJP DEL dimer was compared with other light-chain dimers and with Fab fragments with a kappa light chain. Although the domain-folding pattern was similar, the relative positions of the constant domains differed. BJP DEL showed a noncanonical quaternary structural arrangement which may be attributable to the poor CL-CL affinity and lack of an interchain disulfide bridge, combined with the conformational editing effect of the crystal-packing forces. Our results suggest that, in the absence of a disulfide bridge, most BJP CLs are probably mobile in solution. This may explain their high susceptibility to proteases and the absence of naturally occurring crystals for these dimers. Furthermore, these findings of an unusual quaternary structure of an immunoglobulin light-chain association extend our knowledge about the large and highly diverse structures of the immunoglobulin superfamily.