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Biomedical subjects

D A Langs

Publications and source records attributed to D A Langs.

At least 55 records · Page 3Linked to original sources
PubMed1991

Monoclinic uncomplexed double-stranded, antiparallel, left-handed beta 5.6-helix (increases decreases beta 5.6) structure of gramicidin A: alternate patterns of helical association and deformation.

A comparison of the monoclinic and orthorhombic crystal structures of the uncomplexed double-stranded, antiparallel, left-handed beta-helix (5.6 amino acid residues per turn) (increases decreases beta 5.6) conformers of gramicidin A reveals marked differences in the tryptophan side-chain orientations and the degree of helical uniformity of the dimer and in the manner in which these helical dimers associate with one another in the crystal. The helix of the orthorhombic dimer exhibits a regular pattern of bulges and constrictions that appears to be induced by crystal packing forces affecting tryptophan side chains that are aligned parallel to the helix axis. The monoclinic dimer is more uniform than the orthorhombic dimer as a consequence of pi stacking interactions between dimers in which orientation of tryptophan side chains is normal to the helix axis to relieve the lateral crystal packing forces that may locally twist and deform the helix. It may be inferred from these observations that lipid interactions may be expected to destabilize the increases decreases beta 5.6 helix when it is inserted into a membrane bilayer.

Crystallization↗
PubMed1991

The structure of [D-Hyi2,L-Hyi4]meso-valinomycin revealed by X-ray analysis.

Direct x-ray analysis has been used to determine the crystal structure of [D-Hyi2, L-Hyi4]meso-valinomycin (cyclo[-D-Val-D-Hyi-L-Val-L-Hyi-(D-Val-L-Hyi-L-Val-D-+ ++Hyi)2-], C60H102N6O18), which crystallized from acetone with two solvent molecules. The crystals are trigonal, space group P32, number of molecules per unit cell Z = 3, cell parameters a = b = 15.2085 (8) A, c = 29.3250 (9) A, gamma = 120 degrees. The standard (R) and weighted (Rw) reliability factors after refinement of the atomic coordinates for C, N, and O atoms in the anisotropic thermal motion approximation, allowing for isotropic H atom contributions, were 0.070 and 0.082, respectively. The molecule adopts a distorted bracelet structure which is stabilized by six N-H ... O = C 4----1 type intramolecular hydrogen bonds. The side chains predominantly occupy external pseudoaxial positions relative to the cylindrical axis of the molecule. In contrast to meso-valinomycin, only four of the six Val carbonyl oxygen atoms are directed inwards to form a coordination centre for the molecule, and the carbonyl oxygen atoms of residues D-Val1 and L-Val3 are twisted outward and point away from the centre of the molecule. Although the analogue has a partially formed ion-binding center, it is inaccessible because the hydrophobic isopropyl groups of the D-Hyi2 and L-Hyi4 residues screen the molecular cavity on both sides.

Amino Acid Sequence↗
PubMed1991

Molecular conformation of a D,L stereoisomeric analogue of valinomycin, cyclo[-(L-Val-L-Hyi-L-Val-D-Hyi)2-(D-Val-L-Hyi-L-Val-D-Hyi)-].

The crystal structure of a synthetic analogue of valinomycin, cyclo[-(L-Val-L-Hyi-L-Val-D-Hyi)2-(D-Val-L-Hyi-L-Val-D -Hyi)-] ([L-Val1, L-Val5]meso-valinomycin), C60H102N6O18, has been determined. Crystals grown from petroleum ether are orthorhombic, space group P2(1)2(1)2(1), with cell parameters a = 16.41(1), b = 18.76(1), c = 25.86(1) A, and Z = 4. The atomic coordinates for nonhydrogen atoms, except those of terminal carbons on one side chain, were refined in the anisotropic thermal motion approximation. The coordinate parameters of the H atoms were incorporated into the structure factor calculations at geometrically expected positions. Values of the standard and weighted R factors after refinement are 0.074 and 0.083, respectively. The crystal structure of the molecule is asymmetric and adopts a conformation with four 4----1 type and one 6----1 type intramolecular hydrogen bonds between amide nitrogens and carbonyl oxygens. Valinomycin binds potassium more than 100 times strongly than the D,L stereoisomeric analogue, as a result of a different spatial orientation of potentially interacting carbonyl groups.

Amino Acid Sequence↗
PubMed1991

Molecular level model for the agonist/antagonist selectivity of the 1,4-dihydropyridine calcium channel receptor.

Crystal structures of the 1,4-dihydropyridine (1,4-DHP) calcium channel activators Bay K 8643 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(3-nitrophenyl)-pyridine-5-carboxy lat e], Bay O 8495 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(3-trifluoromethylphenyl)-pyridine-5- carboxylate], and Bay O 9507 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(4-nitrophenyl)-pyridine-5-carboxy lat e] were determined. The conformations of the 1,4-DHP rings of these activator analogues of Bay K 8644 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(2-trifluoromethylphenyl)-pyridine-5- carboxylate] do not suggest that their activator properties are as strongly correlated with the degree of 1,4-DHP ring flattening as was indicated for members of the corresponding antagonist series. The solid state hydrogen bonding of the N(1)-H groups of the activators is not, unlike that of their antagonist counterparts, to acceptors that are directly in line with the donor. Rather, acceptor groups are positioned within +/- 60 degrees of the N(1)-H bond in the vertical plane of the 1,4-DHP ring. Previously determined structure-activity relationships have indicated the importance of this N(1)-H group to the activity of the 1,4-DHP antagonists. Based on these observations, a model is advanced to describe the 1,4-DHP binding site of the voltage-gated Ca2+ channel and its ability to accommodate both antagonist and activator ligands.

Calcium Channel Agonists↗
PubMed1990

Receptor model for the molecular basis of tissue selectivity of 1, 4-dihydropyridine calcium channel drugs.

Our analysis of the solid state conformations of nifedipine [dimethyl 1,4-dihydro-2,6-dimethyl-4-(2-nitrophenyl)-3,5-pyridinecarboxylate ] and its 1,4-dihydropyridine (1,4-DHP) analogues produced a cartoon description of the important interactions between these drugs and their voltage-dependent calcium channel receptor. In the present study a molecular-level detailed model of the 1,4-DHP receptor binding site has been built from the published amino acid sequence of the alpha 1 subunit of the voltage-dependent calcium channel isolated from rabbit skeletal muscle transverse tubule membranes. The voltage-sensing component of the channel described in this work differs from other reported for the homologous sodium channel in that it incorporates a water structure and a staggered, rather than eclipsed, hydrogen bonded S4 helix conformation. The major recognition surfaces of the receptor lie in helical grooves on the S4 or voltage-sensing alpha-helix that is positioned in the center of the bundle of transmembrane helices that define each of the four calcium channel domains. Multiple binding clefts defined by Arg-X-X-Arg-P-X-X-S 'reading frames' exist on the S4 strand. The tissue selectivity of nifedipine and its analogues may arise, in part, from conservative changes in the amino acid residues at the P and S positions of the reading frame that define the ester-binding regions of receptors from different tissues. The crystal structures of two tissue-selective nifedipine analogues, nimodipine [isopropyl (2-methoxyethyl) 1,4-dihydro-2,6-dimethyl-4-(3-nitrophenyl)-3,5-pyridinecarboxylate ] and nitrendipine [ethyl methyl 1,4-dihydro-2,6-dimethyl-4-(3-nitrophenyl)-3, 5-pyridinecarboxylate] are reported. Nimodipine was observed to have an unusual ester side chain conformation that enhances the fit to the proposed ester-sensing region of the receptor.

Amino Acid Sequence↗
PubMed1990

Factors governing helical preference of peptides containing multiple alpha,alpha-dialkyl amino acids.

The presence of multiple alpha,alpha-dialkyl amino acids such as alpha-methylalanine (alpha-aminoisobutyric acid, Aib) leads to predominantly helical structures, either with alpha-helical or 3(10)-helical hydrogen bonding patterns. The crystal structure of emerimicin-(1-9) benzyl ester (Ac-Phe-Aib-Aib-Aib-Val-Gly-Leu-Aib-Aib-OBzl) reported here shows essentially pure alpha-helical character, whereas other similar compounds show predominantly 3(10)-helical structures. The factors that govern helical preference include the inherent relative stability of the alpha-helix compared with the 3(10)-helix, the extra hydrogen bond seen with 3(10)-helices, and the enhanced electrostatic dipolar interaction of the 3(10)-helix when packed in a crystalline lattice. The balance of these forces, when combined with the steric requirements of the amino acid side chains, determines the relative stability of the two helical conformations under a given set of experimental conditions.

Amino Acid Sequence↗
PubMed1989

Structure of the ion channel peptide antibiotic gramicidin A.

The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 0.86 A resolution. The polypeptide crystallizes from ethanol as a left-handed, double-stranded, antiparallel beta 5.6-helical dimer that is 31 A long and an average of 4.8 A in diameter. The uncomplexed channel does not contain ions or solvent molecules, and its diameter is not uniform but varies from a minimum of 3.85 A to a maximum of 5.47 A. There are three empty cavities in the channel that have a diameter exceeding 5.25 A and appear to be large enough to accommodate water molecules or potassium ions in a chemically reasonable coordination environment. The observed crystal structure does not offer any obvious clues as to why an antiparallel beta 5.6-helix cannot function as an ion channel in lipid bilayers.

Gramicidin↗
PubMed1989

Molecular conformation and ion transport of cyclic and linear ionophores.

X-ray crystal structure determinations and energy-minimization techniques provide conformational data on the complexed and uncomplexed forms of ion transport antibiotics of the shuttle and channel types. In the solid state, hexadecaisoleucinomycin (HEXIL), an analogue of valinomycin, is observed as an asymmetric macrocycle stabilized by eight intramolecular (4----1) hydrogen bonds. The structure obtained from energy-minimization procedures exhibits a greater variation in phi and psi angles of chemically equivalent residues than does the crystallographically observed structure. The structure has eight carbonyl groups directed toward its interior and is capable of providing flexible coordination to a positively charged ion or molecule. These structural findings are consistent with the observed capacity of HEXIL to complex cesium ions, tetramethyl ammonium ions and acetylcholine. Gramicidin A is a pentadecapeptide that functions as a transmembrane channel for transporting monovalent cations. Uncomplexed gramicidin A crystallizes as a left-handed, antiparallel, double-stranded, helical dimer with 5.6 amino acid residues per turn. The helix has an overall length of 31 A and an average inner channel diameter of 4.8 A. The channel of this crystalline form does not contain ions or solvent molecules. Transporting ions through this channel could be achieved only by some expansion of the channel opening that would involve breaking and reforming hydrogen bonds that stabilize the double-stranded helix.

Gramicidin↗
PubMed1988

Direct methods: the identification of conditions which simplify the generation of inconsistent quadrupoles.

An algorithm is implemented to determine the form and phase shift for inconsistent type II quadrupoles for any space group having glide or screw-axis translations which are not a consequence of lattice centering. Cumulatively there are only six different Miller index restrictions and nine different phase shift forms common to all space groups of orthorhombic or lower symmetry. A similar analysis has been performed for a newly discovered type III class of quadrupoles. The configuration of the phase connections among the four triples of the type III quadrupole is different from the common configuration previously described for both normal (type I) and inconsistent (type II) quadrupoles. A knowledge of these constraint conditions for type II and III quadrupoles greatly simplifies a procedure for generating these relationships.

Crystallography↗
PubMed1988

A priori estimation of scale and overall anisotropic temperature factors from the Patterson origin peak.

An idea due to D. Rogers [Computing Methods in Crystallography (1965), edited by J. S. Rollett, pp. 117-148. Oxford: pergamon Press] has been developed and implemented. The method is an advantageous alternative to Wilson plot or K-curve scaling of intensity data. On the relative experimental scale the structure factor can be written in matrix notation as F(h) = kappa -1 sigma j fj(h) exp (2 pi ih tau xj) exp (-h tau bjh); and the squared structure-factor magnitude can be written as magnitude of F(h)2 = kappa -2 exp (-2h tau bh) [sigma j fj2+ 2 sigma j sigma k greater than jfjfk exp [2 pi ih tau (xj-xk)]], if a a common, or average, anisotropic temperature factor is factored out of the atomic summations. The fj2 summation corresponds to the Patterson origin peak, and the fjfk double summation to the off-origin Patterson peaks. A tovariate Gaussian density function, P(u)-Pmin = Po exp (-u tau pu), is fitted by least squares to the origin peak from a Patterson synthesis with coefficients magnitude of F2 meas/sigma jf2j. Fourier inversion of the fitted Gaussian gives the scale and thermal parameters, k2 = (detp)1/2/(pi 3/2 Vcell Po) and b = (pi 2/2)p-1. The fit of the parameter Pmin is constrained by the condition that Pmin = -F(000)2/(k2Vcell sigma j Zj2), and thus only po and the six coefficients pij (i less than j = 1,2,3) are independent parameters.

Crystallography↗
PubMed1988

Three-dimensional structure at 0.86 A of the uncomplexed form of the transmembrane ion channel peptide gramicidin A.

The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 120 K and at 0.86 angstrom resolution. The pentadecapeptide crystallizes as a left-handed antiparallel double-stranded helical dimer with 5.6 amino acid residues per turn. The helix has an overall length of 31 angstroms and an average inner channel diameter of 4.80 angstroms. The channel of this crystalline form is void of ions or solvent molecules. The channel diameter varies from a minimum of 3.85 angstroms to a maximum of 5.47 angstroms and contains three pockets where the cross-channel contacts are 5.25 angstroms or greater. The range of variation seen for the phi and psi torsion angles of the backbone of the helix suggests that these potential ion binding sites can be induced to travel the length of the channel in a peristaltic manner by cooperatively varying these angles. The indole rings of the eight tryptophan residues of the dimer are overlapped in three separate regions on the outer surface of the helix when viewed down the barrel of the channel. This arrangement would permit long-chained lipid molecules to nest parallel to the outer channel surface between these protruding tryptophan regions and act like molecular splines to constrain helical twist deformations of the channel.

Binding Sites↗
PubMed1988

Direct methods: the identification of space-group-specific inconsistent three-phase structure invariants.

Certain space groups often permit the generation of pairs of triple relationships involving the same three parent reflections in different symmetry forms, giving rise to two equally probable invariant estimates which, because of the space-group symmetry, must disagree by an a priori known phase shift. The 230 space groups have been examined to identify those which permit inconsistent triples, and the complete list which describes the forms of the pair of triples and their phase inconsistency is given.

Crystallography↗
PubMed1986

Structure of pressinoic acid: the cyclic moiety of vasopressin.

Arginine vasopressin consists of a 20-membered, disulfide-linked macrocyclic ring system called pressinoic acid to which is attached a COOH-terminal tripeptide. The molecular conformation of pressinoic acid has been determined from single crystal x-ray diffraction data. The 20-membered macrocyclic ring, stabilized by two intramolecular hydrogen bonds, has a type I beta-bend centered on Gln4 and Asn5 and a highly distorted type II' bend centered on Phe3 and Gln4. In vasopressin the Asn5 side chain extends away from the macrocyclic ring system and hydrogen bonds to the terminal tripeptide, but in pressinoic acid the Asn5 side chain lies over the molecule and forms a strong hydrogen bond to the nitrogen of Tyr2. The absence of pressor activity in pressinoic acid may be a result of both the loss of the COOH-terminal tripeptide and the incorrect orientation of the Asn5 side chain. Whether this class of hormones has pressor or oxytocic activity is determined by the orientation of the Tyr2 side chain, that is, whether it is extended away from or over the ring system, respectively. In pressinoic acid, the Tyr2 side chain is in the expected "pressor conformation," that is, extended away from the ring system, and is stabilized through a hydrophobic interaction with the Phe3 side chain. Thus, the conformation of the pressinoic acid molecule partly explains the activity of vasopressin-like hormones.

Arginine Vasopressin↗
PubMed1986

The crystal structures of [Met5]enkephalin and a third form of [Leu5]enkephalin: observations of a novel pleated beta-sheet.

The structures of [Met5]enkephalin (Tyr-Gly-Gly-Phe-Met) and [Leu5]enkephalin (Tyr-Gly-Gly-Phe-Leu) have been determined from single crystal x-ray diffraction data and refined to residuals of 0.100 and 0.092, respectively. The [Met5]enkephalin structure consists of dimers forming antiparallel beta-sheets extending in the monoclinic ac plane with 10.6 water molecules per dimer. The two molecules, related by pseudo two-fold axes, have similar backbone conformations and similar tyrosine and phenylalanine side-chain conformations. Both methionine residues are disordered and the disorder is different in the two independent molecules. Additional hydrogen bonds connect adjacent dimers to form infinite sheets normal to the b axis. The water molecules are found mainly in the interstices between the sheets. [Leu5]Enkephalin crystallizes as a monohydrate that is isomorphous with the [Met5]enkephalin structure with respect to the beta-sheet but different with respect to the tyrosine and phenylalanine side-chain conformations and water content. The peptide chains in both structures are fully extended and more nearly planar than pleated. The planes of the peptide chains in the dimers form an angle of 143.3 degrees with one another in [Met5]enkephalin and 156.0 degrees in [Leu5]enkephalin. This produces a zigzag pattern or pleat in the beta-sheets perpendicular to the direction of the peptide chains and, therefore, perpendicular to the normal beta-sheet pleat. The average repeat distance between Ni and Ni+2 in the peptide chains of both structures is 7.10 A, versus an ideal value of 6.68 A.

Crystallography↗
PubMed1985

Conformational features of calcium channel agonist and antagonist analogs of nifedipine.

The crystal and molecular structures of methyl 2,6-dimethyl-5-nitro-4-(2-trifluoromethylphenyl)-1,4- dihydropyridine-3-carboxylate and ethyl 4-(2-difluoromethoxyphenyl)-1,4,5,7,-tetrahydro-2-methyl-5-oxof uro[3,4-b]pyridine-3-carboxylate, which are analogs of the calcium channel antagonist nifedipine reported to have agonist activity, have been determined. The conformations of these two agonists are compared with the conformational features shown by nifedipine and related 1,4-dihydropyridine calcium channel antagonists. Common conformational features shown by these agonists and antagonists allow both to bind to the same plasma membrane receptor while subtle differences in hydrogen-bonding activity of the amine group, and ester group orientation and hydrophobic fit, may control the availability of channel open and closed states.

Calcium↗
PubMed1979

Thromboxane molecules do not adopt the prostaglandin hairpin conformation.

The hairpin conformational hypothesis has been proposed to rationalise much of the structure-activity and receptor-binding data which have accumulated for the prostaglandin (PG) hormones. The hairpin conformation, thought to be necessary for PG activity, requires that the alpha- and omega-chains of the molecule be extended and in parallel alignment, separated by a van der Waals contact distance for the full length of the chains, with the ends of the chains approximately 5.5 A apart. The similarity between the structures of the thromboxanes (TXs) and the PGs suggests that the profile of activity of TXs, like that of PGs, centres on subtle conformational variation of the hairpin geometry. Thromboxane B2 (TXB2) is a stable hydrolysis product of a highly reactive, short-lived intermediate, thromboxane A2 (TXA2), which is formed from the prostaglandin endoperoxide (PGH2) as indicated in Fig. 1. An examination of molecular models of TXA2 and TXB2 suggests that the structural differences between the ring moieties may have much less influence in altering the side-chain conformation of TXs than do substitutents on the relatively more flexible cyclopentane ring of a PG molecule. We report here the first diffraction analysis of a thromboxane structure and note that the molecular conformation is not hairpin shaped.

Molecular Conformation↗