Adhesion mechanism of human beta(2)-glycoprotein I to phospholipids based on its crystal structure

Human beta(2)-glycoprotein I is a heavily glycosylated five-domain plasma membrane-adhesion protein, which has been implicated in blood coagulation and clearance of apoptotic bodies from the circulation. It is also the key antigen in the autoimmune disease anti-phospholipid syndrome. The crystal structure of beta(2)-glycoprotein I isolated from human plasma reveals an elongated fish-hook-like arrangement of the globular short consensus repeat domains. Half of the C-terminal fifth domain deviates strongly from the standard fold, as observed in domains one to four. This aberrant half forms a specific phospholipid-binding site. A large patch of 14 positively charged residues provides electrostatic interactions with anionic phospholipid headgroups and an exposed membrane-insertion loop yields specificity for lipid layers. The observed spatial arrangement of the five domains suggests a functional partitioning of protein adhesion and membrane adhesion over the N- and C-terminal domains, respectively, separated by glycosylated bridging domains. Coordinates are in the Protein Data Bank (accession No. 1QUB).

Bactericidal antibody recognition of meningococcal PorA by induced fit. Comparison of liganded and unliganded Fab structures

MN12H2 is a bactericidal antibody directed against outer membrane protein PorA epitope P1.16 of Neisseria meningitidis. Binding of MN12H2 to PorA at the meningococcal surface activates the classical complement pathway resulting in bacterial lysis. We have determined the crystal structure of the unliganded MN12H2 Fab fragment in two different crystal forms and compared it with the structure of the Fab in complex with a P1.16-derived peptide. The unliganded Fabs have elbow bend angles of 155 degrees and 159 degrees, whereas the liganded Fab has a more closed elbow bend of 143 degrees. Substantial differences in quaternary and tertiary structure of the antigen binding site are observed between the unliganded and liganded MN12H2 Fab structures that can be attributed to peptide binding. The variable light and heavy chain interface of the liganded Fab is twisted by a 5 degrees rotation along an axis approximately perpendicular to the plane of the interface. Hypervariable loops H1, H2, and framework loop FR-H3 follow this rotation. The hypervariable loop H3 undergoes conformational changes but remains closely linked to hypervariable loop L1. In contrast with the binding site expansion seen in other Fab-peptide structures, the MN12H2 binding site is narrowed upon peptide binding due to the formation of a "false floor" mediated by arginine residue 101 of the light chain. These results indicate that PorA epitope P1.16 of N. meningitidis is recognized by the complement-activating antibody MN12H2 through induced fit, allowing the formation of a highly complementary immune complex.

Static Laue diffraction studies on acetylcholinesterase

Acetylcholinesterase (AChE) is one of nature's fastest enzymes, despite the fact that its three-dimensional structure reveals its active site to be deeply sequestered within the molecule. This raises questions with respect to traffic of substrate to, and products from, the active site, which may be investigated by time-resolved crystallography. In order to address one aspect of the feasibility of performing time-resolved studies on AChE, a data set has been collected using the Laue technique on a trigonal crystal of Torpedo californica AChE soaked with the reversible inhibitor edrophonium, using a total X-ray exposure time of 24 ms. Electron-density maps obtained from the Laue data, which are of surprisingly good quality compared with similar maps from monochromatic data, show essentially the same features. They clearly reveal the bound ligand, as well as a structural change in the conformation of the active-site Ser200 induced upon binding.

Hypothetical Crystal Structures of Benzene at 0 and 30 kbar

Possible crystal structures of benzene were generated without any prior crystallographic information, using a systematic grid search method. Only structures with one molecule in the asymmetric unit were considered. 31 space groups were investigated, and the resulting structures were clustered and checked for stability upon removal of the space-group symmetry. In the enthalpy range ∼10 kJ mol−1 30 structures were found at zero pressure and 20 structures at a pressure of 30 kbar. Their pressure-dependent rankings and interconversions are discussed. The results are compared to previous, less complete, investigations. A possible structure for the high-pressure phase benzene (II), on which only limited powder diffraction data have been published, is suggested.

Water molecules hydrogen bonding to aromatic acceptors of amino acids: the structure of Tyr-Tyr-Phe dihydrate and a crystallographic database study on peptides

The crystal structure of Tyr-Tyr-Phe dihydrate contains a hydrogen bond formed between a water molecule and the Phe side chain. The geometry is centered with a distance of 3.26 A between the water O atom and the aromatic centroid. In a database study on hydrated peptides, four related examples are found which exhibit a wide variability of hydrogen-bond geometries. The intermolecular surroundings of the water molecules are inspected, showing that they are typically involved in complex networks of conventional and non-conventional hydrogen bonds. Possible relevance for protein hydration is given.

Structure and serotonin 5-HT2C receptor activity of ortho- and meta-substituted phenylpiperazines

The structural characteristics of ortho- and meta-substituted phenylpiperazines have been investigated in order to understand their actions at the serotonin 5-HT2C receptor. The crystal structures of the 4-methylated analogues of two phenylpiperazines that are already known as 5-HT2C ligands, 1-(1-naphthyl)-4-methylpiperazine (1NMP) and 1-[(3-trifluoromethyl)phenyl]-4-methylpiperazine (TFMPMP), and those of two novel 5-HT2C ligands, 1-(2-methoxyphenyl)piperazine (oMPP) and 1-(3-methoxyphenyl)piperazine (mMPP), are determined. Molecular mechanics calculations are performed to calculate the energy profiles of six phenylpiperazines for rotation about the central phenyl-nitrogen bond. The activities of several phenylpiperazines, in combination with their crystal structures and conformational characteristics, lead to the hypothesis that the conformation for which the piperazine ring and the phenyl ring are approximately co-planar should be the 5-HT2C receptor 'activating' conformation. This hypothesis is then used to predict the activities of the two novel 5-HT2C ligands oMPP and mMPP. oMPP is predicted to be an antagonist at this receptor, whereas mMPP is predicted to be an agonist. As this prediction was confirmed by in vitro and in vivo tests, the proposed conformation is very likely to be responsible for the activation of the 5-HT2C receptor.

C-terminal domain of transcription cofactor PC4 reveals dimeric ssDNA binding site

The crystal structure of human replication and transcription cofactor PC4CTD reveals a dimer with two single-stranded (ss)DNA binding channels running in opposite directions to each other. This arrangement suggests a role in establishment or maintenance of melted DNA at promoters or origins of replication.

Crystal structure of the A3 domain of human von Willebrand factor: implications for collagen binding

BACKGROUND

Bleeding from a damaged blood vessel is stopped by the formation of a platelet plug. The multimeric plasma glycoprotein, von Willebrand factor (vWF), plays an essential role in this process by anchoring blood platelets to the damaged vessel wall under conditions of high shear stress. This factor mediates platelet adhesion by binding both to collagen of the damaged blood vessel and to glycoprotein Ib on the platelet membrane. The A3 domain of vWF allows it to bind to collagen types I and III present in the perivascular connective tissue of the damaged vessel wall. To gain insight into the mechanism of collagen binding by vWF, we have determined the crystal structure of the human vWF A3 domain.

RESULTS

The crystal structure of the 20 kDa A3 domain of human vWF (residues 920-1111), determined by the method of multiwavelength anomalous dispersion at 1.8 A resolution, exhibits a common dinucleotide-binding fold. The putative collagen-binding site of the A3 domain is rather smooth and shows a markedly high concentration of negatively charged residues. This region encompasses a potential metal-binding site containing the motif DXSXS, which is required for ligand interaction in the homologous I-type domains of integrins CR3 and LFA-1. Although vWF A3 has considerable sequence and structural similarity with CR3 and LFA-1 in this region, one loop of A3 adopts a conformation which is incompatible with ion binding.

CONCLUSIONS

The structure of the A3 domain suggests that adhesion to collagen is primarily achieved through interactions between negatively charged residues on A3 and positively charged residues on collagen. The absence of a pronounced binding groove precludes a large van der Waals surface interaction between A3 and collagen and is consistent with the low affinity for collagen of a single A3 domain and the requirement for multimeric vWF for tight association with collagen. The absence of bound metal ions upon soaking the crystal in MgCl2 and vWF A3's conformational incompatibility for metal binding is consistent with the absence of a functional role for metal ion binding in A3, which contrasts the metal ion activation required for ligand binding by the homologous integrin I type domains.

Bactericidal antibody recognition of a PorA epitope of Neisseria meningitidis: crystal structure of a Fab fragment in complex with a fluorescein-conjugated peptide

Class 1 outer membrane protein PorA of Neisseria meningitidis is a vaccine candidate against bacterial meningitis. Antibodies against PorA are able to induce complement-mediated bacterial killing and thereby play an important role in protection against meningococcal disease. Bactericidal antibodies are all directed against variable regions VR1 and VR2 of the PorA sequence, corresponding to loops 1 and 4 of a two-dimensional topology model of the porin with eight extracellular loops. We have determined the crystal structure to 2.6 A resolution of the Fab fragment of bactericidal antibody MN12H2 against meningococcal PorA in complex with a linear fluorescein-conjugated peptide TKDTNNNL derived from the VR2 sequence of sero-subtype P1.7,16 (residues 180-187) from meningococcal strain H44/76. The peptide folds deeply into the binding cavity of the Fab molecule in a type I beta-turn, with the minimal P1.16 epitope DTNNN virtually completely buried. The structure reveals H-bonds and van der Waals interactions with all minimal epitope residues and one essential salt bridge between Asp-182 of the peptide and His-31 of the MN12H2 light chain. The key components of the recognition of PorA epitope P1.16 by bactericidal antibody MN12H2 correspond well with available thermodynamic data from binding studies. Furthermore, they indicate the structural basis of an increased endemic incidence of infection by group B meningococci in England and Wales since 1981 associated with the occurrence of an Neisseria meningitidis escape mutant (strain-MC58). The observed three-dimensional conformation of the peptide provides a rationale for the development of a synthetic peptide vaccine against meningococcal disease.

The crystal and molecular structures of cellulose I and II

The paper describes molecular dynamics (MD) simulations on the crystal structures of the Ibeta and II phases of cellulose. Structural proposals for each of these were made in the 1970s on the basis of X-ray diffraction data. However, due to the limited resolution of these data some controversies remained and details on hydrogen bonding could not be directly obtained. In contrast to structure factor amplitudes in X-ray diffraction, energies, as obtained from MD simulations, are very sensitive to the positions of the hydroxyl hydrogen atoms. Therefore the latter technique is very suitable for obtaining such structural details. MD simulations of the Ibeta phase clearly shows preference for one of the two possible models in which the chains are packed in a parallel orientation. Only the parallel-down mode (in the definition of Gardner and Blackwell (1974) J Biopolym 13: 1975-2001) presents a stable structure. The hydrogen bonding consists of two intramolecular hydrogen bonds parallel to the glycosidic linkage for both chains, and two intralayer hydrogen bonds. The layers are packed hydrophobically. All hydroxymethyl group are positioned in the tg conformation. For the cellulose II form it was found that, in contrast to what seemed to emerge from the X-ray fibre diffraction data, both independent chains had the gt conformation. This idea already existed because of elastic moduli calculations and 13C-solid state NMR data. Recently, the structure of cellotetraose was determined. There appear to be a striking similarity between the structure obtained from the MD simulations and this cellotetraose structure in terms of packing of the two independent molecules, the hydrogen bonding network and the conformations of the hydroxymethyl group, which were also gt for both molecules. The structure forms a 3D hydrogen bonded network, and the contribution from electrostatics to the packing is more pronounced than in case of the Ibeta structure. In contrast to what is expected, in view of the irreversible transition of the cellulose I to II form, the energies of the Ibeta form is found to be lower than that of II by 1 kcal mol(-1) per cellobiose.

Possible ligand-receptor interactions for NK1 antagonists as observed in their crystal structures

Crystal structures of nine non-peptide tachykinin NK1 antagonists have been analysed for the intermolecular interactions of their pharmacophoric groups with neighbouring molecules in the crystals. Experimental data on interaction geometries of these antagonists with their environment can be of help in understanding the mechanism of binding to the human NK1 receptor. Several interaction geometries have been identified that are consistent with both structure-activity relationships and reported receptor interactions for the compounds analysed. In addition, an interaction site for the side-chain of Gln-165 in the human NK1 receptor that is probably involved in donating a hydrogen bond to the benzylamino nitrogen or benzylether oxygen of the quinuclidine and piperidine antagonists is explicitly postulated. Also, a superposition based on pharmacophoric elements in the crystal structure conformations of two prototypic NK1 antagonists, CP-96,345 (1) and CP-99,994 (4), suggests how both compounds might interact with the human NK1 receptor in a similar manner.

Towards Automatic Indexing of the Laue Diffraction Pattern

A method is presented for the semi-automatic indexing of the Laue diffraction pattern. The method is based on the recognition of conics in the Laue pattern by a plane-search algorithm in reciprocal space, after which possible cells are constructed in direct space and relative cell parameters and crystal orientation are obtained. These cells, scaled to an arbitrary volume, are refined, reduced and grouped in order of frequency of occurrence. Usually, the cell that occurs most frequently is the correct one. Other cells found have one or more axes doubled. Such cells are easily discriminated by comparison of the corresponding simulated Laue pattern with the measured one. The method is tested with different data sets of an organic and an organometallic compound collected with an image plate using white radiation of a molybdenum sealed tube. For each pattern, the correct cell was found. Further refinement of the relative cell parameters by matching of the calculated and observed positions of the Lane spots showed good agreement with the relative cell parameters obtained from monochromatic data. To scale the cells, additional information is needed. This paper demonstrates the use of the Mo emission line Kβ 1 to determine the cell volume within 1.2%.

Effect of endurance training on muscle activation and force sensation

One of the consequences of endurance training is a reduction in force sensation in trained muscles at any exercise intensity. To study the central and peripheral contributions to this adaptation, we trained six male subjects with single-leg cycling at 60% VO2 peak (30 min/day x 3 days/week x 8 weeks); six others were matched controls. Measurements were made during separate 20-min, single-leg rides at 70% pre-training VO2 peak, with trained (TR), untrained (UT), and control (CT) legs, before and after training. No pre-post differences were observed in the control group. VO2 peak increased 18% (p < 0.05) in the TR leg and 6% (p < 0.05) in the UT leg of the trained subjects. Force sensation was significantly less in both the TR (70%; p < 0.05) and UT (50%; p < 0.05) legs during 20 min of single-leg cycling after training. Vastus lateralis EMG, plasma lactate, and heart rate were all significantly (p < 0.05) lower when cycling with either the TR or UT leg, which were both lower than when cycling with the CT leg, at the end of each 20-min ride. These data reflect an intramuscular environment that is better adapted to endurance performance by virtue of both central and peripheral mechanisms. Thus, there is less need to recruit additional motor units to maintain the same power output, and this reduced motor outflow leads to a decline in force sensation.

Conformations and internal mobility of a glycopeptide derived from bromelain using molecular dynamics simulations and NOESY analysis

The conformation and internal flexibility of a glycopeptide Manalpha1-6 (Xylbeta1-2)Manbeta1-4GlcNAcbeta1-4(Fucalpha1-3) GlcNAcbeta1-N(Asn-Glu-Ser-Ser), prepared from pineapple stem bromelain, have been analyzed using a combination of molecular dynamics (MD) simulations in water with NOESY 1H NMR spectroscopy. Theoretical NOESY cross-peak intensities were calculated by the CROSREL program on the basis of models, obtained from MD simulations, using a full relaxation matrix approach. Special attention was paid to the description of internal flexibility of the hexasaccharide moiety by the use of generalized order parameters, in combination with the application of an individual rotation correlation tme for each monosaccharide residue. The tetrapeptide moiety appeared to be very mobile during the MD simulations, which was confirmed by the absence of NOE cross peaks. For the oligosaccharide part a model was developed to estimate characteristic times for large reorientational motions around the glycosidic linkages, associated with conformational transitions. For the Manalpha1-6Man and the Fucalpha1-3GlcNAc linkages such a flexibility was found with a characteristic time of 2 ns. In contrast, the Xylbeta1-2Manbeta1-4GlcNAcbeta1-4GlcNAc part of the glycan appears to be relatively rigid.

Peptides containing the sulfonamide transition-state isostere: synthesis and structure of N-acetyl-tauryl-L-proline methylamide

The structure of the sulfonamide isostere-containing peptide N-acetyl-tauryl-proline methylamide 4 was compared to information on the structure of the peptide N-acetyl-beta-alanyl-proline methylamide 6. NMR measurements of the beta-alanine containing peptide 6 showed the presence of two conformations due to cis/trans isomerism of the beta-Ala-Pro amide bond, whereas the sulfonamide-containing peptide 4 appeared in only one conformation. The crystal structure of N-acetyl-tauryl-proline methylamide 4 gave additional evidence for the absence of cis/trans isomerism. The crystals are orthorhombic, space group P2(1)2(1)2(1), Z = 4, F(000) = 592, a = 7.5919(3), b = 10.3822(2), c = 17.1908(7) A, V = 1354.99(8) A3, Dx = 1.359 g cm-3. The oxygen atoms connected to the sulfur take positions similar to both the cis and trans positions of the carbonyl oxygen of an amide. Consequently the tauryl part is placed perpendicular to the proline alpha-C-C(O) bond, giving it an extended conformation in contrast to the cis/trans isomers of N-acetyl-beta-alanyl-proline methylamide 6.