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At least 19 recordsLinked to original sources
PubMed1972

Molecular events responsible for modulation of neoantigenic expression: the cleavage-associated neoantigen of fibrinogen (blood coagulation-fibrinogen cleavage products-fibrinolysis-molecular conformation).

Molecular events responsible for modulation of neoantigenic expressions of a defined molecule have been explored in relation to three hypothetical molecular models (see below). Fibrinogen and its cleavage-associated neoantigen have been used as a prototype system. Physicochemical and enzymatic factors influencing neoantigenic expression were evaluated. The cleavage-associated neoantigen was not only exposed by plasmin and enzymes of similar specificity, but also in a qualitatively and quantitatively deficient fashion by enzymes of differing specificities. Denaturation of fibrinogen via reduction or pH alteration did not induce the neoantigen, but oxidation of the native fibrinogen molecule did elicit this neoantigenic expression. The neoantigen, once exposed on the D-fragment, was relatively stable to physical and chemical denaturation. These results are inconsistent with proposed cleavage site specific and neoconformational determinant models and are consistent with a steric model, which postulates that the cleavage-associated neoantigenic determinant is buried in native fibrinogen but is exposed in certain altered molecular species. The importance of molecular conformation in the exposure of antigenic expressions of a molecule and in modulation of the binding affinity of a neoantigen for specific antibody is demonstrated.

Acrylamides↗
PubMedDate not supplied

A new method for fast and accurate derivation of molecular conformations.

During molecular simulations, three-dimensional conformations of biomolecules are calculated from the values of their bond angles, bond lengths, and torsional angles. In this paper we study how to efficiently derive three-dimensional molecular conformations from the values of torsional angles. This case is of broad interest as torsional angles greatly affect molecular shape and are always taken into account during simulations. We first review two widely used methods for deriving molecular conformations, the simple rotations scheme and the Denavit-Hartenberg local frames method. We discuss their disadvantages which include extensive bookkeeping, accumulation of numerical errors, and redundancies in the local frames used. Then we introduce a new, fast, and accurate method called the atomgroup local frames method. This new method not only eliminates the disadvantages of earlier approaches but also provides lazy evaluation of atom positions and reduces the computational cost. Our method is especially useful in applications where many conformations are generated or updated such as in energy minimization and conformational search.

Journal Article↗
PubMed1997

Formation of stable polypeptide monolayers at interfaces: controlling molecular conformation and orientation.

The molecular self-organization and structural properties of peptide assemblies at different interfaces, using either amphipathic or hydrophobic polypeptide helices, is described. The two peptides under investigation form stable monolayers on the water surface under the conservation of their molecular conformation, as studied by circular dichroism and polarization-modulation Fourier transform infrared (FTIR) spectroscopy. Using surface plasmon resonance and reflection-absorption FTIR, we show that such molecular layers can be transferred unaltered to solid substrates. Most importantly, the molecular orientation of the hydrophobic helices on solid supports such as gold can be controlled by choosing a particular procedure for the layer formation. The helices were oriented parallel to the interface in Langmuir-Blodgett monolayers, and perpendicular to the interface in self-assembled monolayers. Our reflection-absorption FTIR measurements have delivered for the first time direct experimental evidence for the molecular conformation and orientation of pure peptide monolayers. Suitable reference spectra of polypeptides with defined conformation and orientation are necessary to use this technique for the determination of the molecular orientation of peptides in monomolecular films. We have solved the problem for alpha-helical polypeptides by using bacteriorhodopsin as a reference in combination with synthetic alpha-helices of defined interfacial orientation. The present study shows the possibility of constructing immobilized peptide monolayers with predefined macroscopic properties and molecular structure by choosing the proper polypeptide amino acid sequence, the technique used for layer formation, and the supporting surface properties.

Amino Acid Sequence↗
PubMed1975

Molecular conformation prostaglandin A1 monoclinic crystalline polymorph.

The molecular conformation of the monoclinic crystalline polymorph of prostaglandin A1 has been determined by X-ray diffraction techniques. The space group is P21 with a = 13.637(2), b = 7.567(1), c = 10.576(2) A, beta = 107.37(3) degrees; Dc = 1.073 g.cm-3 for Z = 2. The molecular conformation is characterized by the nearly parallel arrangement of the C1-C7 and C13-C20 side chains, with a general flattening of the overall structure when compared with the orthorhombic polymorph. The cyclopentenone moiety assumes a C8 envelope conformation with C8 and O9 displaced +0.29 A and -0.18 A from the C9-C10=C11-C12 plane respectively. Concerted, small varations of the torsion angles, primarily about the C8-C12, C14-C15 and C16-C17 bonds, bring the monoclinic and orthorhombic conformations into coincidence.

Models, Molecular↗
PubMed1980

Role of iodine in thyroid hormones: molecular conformation of a halogen-free hormone analogue.

The molecular conformation of the halogen-free thyroid hormone analogue, N-acetyl-4'-methoxy-3,5,3'-trimethyl-L-thyronine ethyl ester, has beeen determined by X-ray diffraction techniques. The observed molecular conformation is similar to that found for the natural hormone 3,5,3'-triiodo-L-thyronine (T3). In this structure, the 3'-methyl group is distal, the overall conformation is cisoid, and the diphenyl ether conformation is twist--skewed. These structural similarities with T3 show that the conformation features required by the active hormone can still be maintained with methyl substitution. The observation that the halogen-free analogues have relatively high activity but extremely low protein binding affinity implies that the role of iodine in hormone transport and biological activity can be deifferentiated. These data suggest that the iodines enhance hormone--protein binding by virtue of their electronic, as well as steric, properties.

Chemical Phenomena↗
PubMed1990

Molecular conformational space analysis using computer graphics: going beyond FRODO.

The molecular graphics program FRODO has been modified to support analytical animation of molecular dynamics trajectories. The enhanced program, mdFRODO, supports all features available in FRODO and is interfaced to GROMOS. A variety of analytical animation modes is included. Extensive coloring and atom selection features are implemented to aid the user in distinguishing features of interest in a set of conformations. Molecular conformational space can be analyzed efficiently and comprehended. Animations may be viewed in stereo, and the animated object can be overlaid with any of the standard FRODO objects. The mdFRODO program is of wide use in molecular dynamics, X-ray crystallography and two-dimensional NMR work. Examples illustrating various aspects of collective motion in protein molecules are given and discussed.

Computer Graphics↗
PubMed1994

Probing specific molecular conformations with the scanning force microscope. Complexes of plasmid DNA and anti-Z-DNA antibodies.

An anti-Z-DNA IgG antibody was used to probe for the left-handed Z-DNA conformation of a d(CG)11 insert in a negatively supercoiled plasmid DNA (pAN022). The complexes were spread on mica in the presence of a quaternary ammonium detergent benzyldimethylalkylammonium chloride and imaged with a scanning force microscope (SFM). The high affinity anti-Z-DNA antibody was retained even after restriction endonuclease cleavage of the DNA. The two arms in the product molecules had unequal lengths in conformity with the known location of the Z-DNA forming insert. Most complexes exhibited one IgG per DNA molecule. The bound antibodies were up to approximately 35 nm in diameter and extended approximately 2 nm from the mica surface. They were generally in a lateral orientation relative to the DNA, in accordance with prior chemical modification experimental data indicating a bipedal mode of binding for an anti-Z-DNA IgG. However, the SFM images also suggest that the DNA bends to accommodate the two Fab combining regions of the antibody. This study demonstrates the utility of the SFM for investigating conformation-dependent molecular recognition.

Antibodies, Monoclonal↗
PubMed2006

Chain-length effects on molecular conformation in and chirality of self-assembled monolayers of alkoxylated benzo[c]cinnoline derivatives on highly oriented pyrolytic graphite.

Self-assembled structures of alkoxylated benzo[c]cinnoline derivatives prepared on highly oriented pyrolytic graphite at room temperature from their solutions in solvents such as 1-phenyloctane, toluene, and 1-octanol were studied by scanning tunneling microscopy. The alkoxy chain length markedly affected the molecular conformations in 2-dimensional assemblies of these derivatives. Long-chain derivatives adopted the trans conformations more often than cis, whereas short-chain derivatives took exclusively the cis conformations in the self-assembled monolayers (SAMs). For the derivatives of intermediate chain lengths, polymorphism existed, with four molecular conformations identified experimentally. Experimental evidence substantiated the formation of chiral SAM structures at the surface, which can be explained by the conformations of the molecules. The chirality was also affected by the chain length of the molecules. A simple method analyzing the angles between different domains in the SAMs was used to identify the molecular conformations and to predict their relative structures.

Graphite↗
PubMed2005

Effects of branched beta-carbon dehydro-residues on peptide conformations: syntheses, crystal structures and molecular conformations of two tetrapeptides: (a) N-(benzyloxycarbonyl)-DeltaVal-Leu-DeltaPhe-Leu-OCH3 and (b) N-(benzyloxycarbonyl)-DeltaIle-Ala-DeltaPhe-Ala-OCH3.

The roles of branched beta-carbon dehydro-residues in the design of peptide conformations have not been systematically explored so far. In order to determine the effects of branched beta-carbon dehydro-residues on the peptide conformations, two N-protected tetrapeptides containing new combinations of DeltaVal and DeltaPhe in (a) N-(benzyloxycarbonyl)-DeltaVal-Leu-DeltaPhe-Leu-OCH(3) and DeltaIle and DeltaPhe in (b) N-(benzyloxycarbonyl)-DeltaIle-Ala-DeltaPhe-Ala-OCH(3) were synthesized by solution procedure. The crystal structures of these peptides were determined by X-ray diffraction methods. Single crystals of both peptides were grown by slow evaporation method from their solutions in acetone-water mixtures (80 : 20) at 25 degrees C. The crystals of these peptides belong to the orthorhombic space group P2(1)2(1)2(1) with cell dimensions of a = 12.342(1) A, b = 15.659(1) A, c = 18.970(1) A for peptide (a) and a = 8.093(1) A, b = 15.791(1) A, c = 23.816(1) A for peptide (b) having Z = 4 in the unit cells of both peptides. The structures were refined by full-matrix least-squares procedure to R-factors of 0.076 and 0.052 respectively. Both peptides adopt the right-handed 3(10)-helical conformations stabilized by two intramolecular (i + 3-->i) hydrogen bonds between the CO of N-terminal benzyloxycarbonyl (Cbz) group and the NH of residue at position 3, and between the CO of residue at position 1 and NH of the residue at position 4. The two consecutive 10-membered rings formed by the hydrogen bonds have dihedral angles corresponding to the standard values for type III beta-turns. DeltaVal and DeltaIle in peptides (a) and (b) respectively are located at the (i + 1) position of the first beta-turn while DeltaPhe is located at the (i + 2) position of the second beta-turn. In the crystals, the molecules are linked head to tail by intermolecular hydrogen bonds to form long helical chains. The axes of helices are parallel to the b-axes while the neighbouring helices run in the opposite directions. The crystal packings are further stabilized by van der Waals forces between the columns of molecular packings.

Amino Acid Sequence↗
PubMed2002

[Molecular conformation and expression efficiency in the hepatocyte targeting gene drug].

OBJECTIVE: To modulate the molecular conformation of the hepatocyte targeting drug to increase exogenous gene expression efficiency in the targeted cell. METHODS: Some specific auxiliary molecules were added to the gene drug its molecular liquid conformation was investigated under the electron-microscope and they were transfected into human hepatoma cell line BEL-7402 in vitro. We detected IFN-gamma gene expression product by ELISA and screened out the most efficient drug molecules. RESULTS: Due to various concentrations of auxiliary molecules, the conformation of hepatocyte targeting drug changed, including floccule, globulous, stringbeads, bacillform and chromosome-like mixture. While the most efficient expression conformation was the bacilliform and chromosome-like mixture and didn't need to inhibit the lysozyme activity, the expression efficiency of such drug molecules was much higher than that of the liposome targeting vector. CONCLUSION: The molecular drug conformation had much influence on targeted gene expression efficiency in gene therapy. Bacilliform and chromosome-like mixture may be the most efficient expression conformation to construct drug molecules in ASOR targeted hepatocyte gene therapy. So we put forward a new concept "chromosome mimic conformation" in screening out the most efficient molecular drug conformation in gene therapy.

Carcinoma, Hepatocellular↗
PubMed2003

Study on relationship between expression level and molecular conformations of gene drugs targeting to hepatoma cells in vitro.

AIM: To increase exogenous gene expression level by modulating molecular conformations of targeting gene drugs. METHODS: The full length cDNAs of both P(40) and P(35) subunits of human interleukin 12 were amplified through polymerase chain reaction (PCR) and cloned into eukaryotic expressing vectors pcDNA3.1(+/-) to construct plasmids of P(+)/IL-12, P(+)/P(40) and P(-)/P(35). These plasmids were combined with ASOR-PLL to form two targeting gene drugs [ASOR-PLL-P(+)/IL-12 and ASOR-PLL-P(+)/P(40) + ASOR-PLL-P(-)/P(35)] in optimal ratios. The conformations of these two drugs at various concentrations adjuvant were examined under electron microscope (EM) and the drugs were transfected into HepG2 (ASGr+) cells. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) was performed with total RNA extracted from the transfected cells to determine the hIL12 mRNA transcript level. The hIL12 protein in the cultured supernatant was measured with enzyme-linked immunosorbent assay (ELISA) 48 hours after transfection. RESULTS: Targeting gene drugs, whose structures were granular and circle-like and diameters ranged from 25 nm to 150 nm, had the highest hIL-12 expression level. The hIL-12 expression level in the group co-transfected with ASOR-PLL-P(+)/P(40) and ASOR-PLL-P(-)/P(35) was higher than that of ASOR-PLL-P(+)/IL-12 transfected group. CONCLUSION: The molecular conformations of targeting gene drugs play an important role in exogenous gene expression level, the best structures are granular and circle-like and their diameters range from 25 nm to 150 nm. The sizes and linking styles of exogenous genes also have some effects on their expression level.

Carcinoma, Hepatocellular↗
PubMed2003

Variety of the molecular conformation in Peptide nanorings and nanotubes.

Possible molecular conformations in peptide nanorings and nanotubes were theoretically investigated by a mathematical conformation analysis as well as ab initio Hartree-Fock calculations. The mathematical analysis predicts not only the conventional nanorings having an extended-type (E-type) backbone (trans zigzag) but also the novel ones having bound-type (B-type) backbones with a smaller internal diameter. Ab initio calculations for the amino acid substitution reveal that all 20 encoded residues can form both types of the above nanorings as a local minimum. However, the energetically stable type is determined in accordance with the kind of the replaced side chains. Moreover, the present work theoretically reveals that both types of nanorings stack to form nanotubes through inter-ring hydrogen bonds, i.e., larger E-type nanotubes and smaller B-type nanotubes. Electronically, the HOMO and LUMO states of the nanoring and nanotube backbones are formed by the in-plane pi state. The replacement by the appropriate residues is furthermore predicted to intrude additional levels in the energy gap and to form the frontier states localized at the side chains.

Hydrogen Bonding↗
PubMed1992

Molecular conformation of ubiquitinated structures and the implications for regulatory function.

The molecular conformation of ubiquitinated structures and the validity of the N-end rule were examined by simulating the molecular mechanics to ascertain the global energy-minimized structure. We examined the chemical linkage involved in attaching the ubiquitin carboxyl terminus to the N-terminus of three different x-hexapeptides, where x is the amino group of the acceptor peptide--either valine, arginine or glutamic acid--(x-K linkage) and to the epsilon-amino group of lysine of the acceptor hexapeptide x-glu1-his2-lys3-gly4-lys5-val6 (K-K linkage) through the formation of an isopeptide bond. Changes in conformation and molecular stability of the multi-ubiquitinated structures were determined by energy-minimization procedures using the SYBYL program developed by Tripos Associates. In the x-K linkage, the ubiquitin molecule is stretched in the beta-pleated sheets and beta-turns while the alpha-helices expand, as the molecule continues to unfold linearly. In the K-K linkage, the ubiquitin molecules have turned into a u-shaped, semi-circular alignment, contracting into a compact, folded structure.

Amino Acid Sequence↗
PubMed2005

Charge on the move: how electron-transfer dynamics depend on molecular conformation.

This tutorial review illustrates the many facets whereby the molecular conformation helps to control the rates of through-bond electron transfer. A brief introduction to Marcus theory is given, highlighting the importance of the coupling element and the super-exchange mechanism, before considering the reasons why the coupling element might depend on the molecular geometry. The methods currently available for determination of both the coupling element and the geometry are reviewed and various examples are given for systems where the structure controls the degree of electronic coupling along the molecular axis. The role of the "bridge" connecting the donor and acceptor is emphasized.

Electrons↗
PubMedDate not supplied

Compare-Conformer: a program for the rapid comparison of molecular conformers based on interatomic distances and torsion angles.

A computer program for comparison of the conformations of a number of related molecular structures is described. The comparisons are performed on either interatomic distances or torsion angles. The comparisons are accomplished on ordered pairs of distances or torsion angles, and the distance comparisons can be performed in a manner that allows permutation of the distance pairs being compared. The algorithm utilizes bit-string Boolean operations that allow the comparisons to be performed rapidly. The program should be useful for computer-assisted molecular modeling studies in which the viable conformers of bioactive analogues are compared in order to locate those conformers that place key substituents in the same spatial orientation.

Acetylcholine↗
PubMed2003

A central partition of molecular conformational space. I. Basic structures.

On the basis of empirical evidence from molecular dynamics simulations, molecular conformational space can be described by means of a partition of central conical regions (cells) characterized by the dominance relations between cartesian coordinates. This work presents a geometric and combinatorial description of the cell arrangement which is polar to a 3x(N-1)-dimensional polytope. Conformations can be precisely located within the face hierarchy of the polytope, whose 1-skeleton provides the framework for determining paths between selected conformations.

HIV Integrase↗
PubMed1983

Dermatan sulfate: molecular conformations and interactions in the condensed state.

The molecular conformations and manner of aggregation has been determined for three allomorphs of the connective tissue polysaccharide dermatan sulfate by analysis of X-ray diffraction from oriented, polycrystalline fibers of sodium salts. One allomorph is unique among glycosaminoglycans in having right-handed (8(3)) helical chains. Two such chains pack antiparallel in a tetragonal unit cell (a = b = 1.267 nm, c = 7.353 nm) with P4(3)2(1)2 space group symmetry. The 3(2) chains of the second allomorph are organized in a trigonal unit cell (a = b = 1.460 nm, c = 2.823 nm, space group symmetry P3(2)21) containing two left-handed antiparallel polysaccharide molecules. (The chirality of this allomorph has been assumed to be the same as in other 3-fold glycosaminoglycan helices, since discrimination between 3(1) and 3(2) symmetries was found not to be possible.) The archiral 2(1) helices of the third allomorph, pack probably in an orthorhombic unit cell (a = 1.151 nm, b = 1.065 nm, c = 1.878 nm, space group symmetry P2(1)2(1)2(1)) that contains again two antiparallel polymer molecules. Each dermatan sulfate chain is stabilized intramolecularly by O3-O5 hydrogen bonds across the beta (1 leads to 4) linkage. There are two intermolecular hydrogen bonds per tetrasaccharide repeat in the tetragonal structure and two per disaccharide in the trigonal structure. Fourier difference syntheses indicated equivalents of four sodium ions per tetrasaccharide and two sodium ions per disaccharide in the tetragonal and trigonal structures, respectively. The cations are either partially or fully hydrated and link dermatan sulfate chains either intra- or intermolecularly by involving besides other polyanion oxygen atoms, carboxylate and sulfate oxygen atoms. The probable mode of packing in the orthorhombic structure indicates a pair of hydrogen bonds between adjacent antiparallel polysaccharide chains and suggests plausible cationic sites in the unit cell.

Carbohydrate Conformation↗