			Home About us Contact

Conformational Differences (conformational + difference)

Distribution by Scientific Domains

Chemistry	85%
Medical Sciences	14%

Selected Abstracts

Hydrogen Atom Transfer Experiments Provide Chemical Evidence for the Conformational Differences between C - and O -Disaccharides

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 27 2010
Elisa I. León
Abstract The glycopyran-6- O -yl radical promoted hydrogen atom transfer reaction (HAT) between the two pyranose units of ,- D -Manp -(1,4)-,- D -Glcp and ,- D -Manp -(1,4a)-4a-carba-,- D -Glcp disaccharides provides supporting chemical evidence for the conformational differences between O - and C -glycosyl compounds. In the O -disaccharide the 6-alkoxyl radical, generated under oxidative or reductive conditions, abstracts exclusively the hydrogen at C-5, via a completely regioselective 1,8-HAT reaction. This may be attributable to the conformational restriction of the glycosidic and aglyconic bonds due principally to steric and stereoelectronic effects. On the contrary, very little regioselectivity is observed in the homologous C -disaccharide and a mixture of compounds generated by 1,5-, 1,6-, and 1,8-HAT processes where the abstraction occurs at hydrogen atoms positioned at C-4a, C-1,, and C-5,, respectively, has been obtained. This study has been extended to simpler O - and C -glycosides, where the aglycon was a straight n -alkyl alcohol tether of five atoms; in general, all of the results obtained are shown to be consistent with a major conformational flexibility of the C -glycosidic bond. [source]

3-[5-(4-Chlorophenyl)-1-(4-methoxyphenyl)-1H -pyrazol-3-yl]propionic acid and the corresponding methyl ester

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2009
Isuru R. Kumarasinghe
The synthesis of 3-[5-(4-chlorophenyl)-1-(4-methoxyphenyl)-1H -pyrazol-3-yl]propionic acid, C19H17ClN2O3, (I), and its corresponding methyl ester, methyl 3-[5-(4-chlorophenyl)-1-(4-methoxyphenyl)-1H -pyrazol-3-yl]propionate, C20H19ClN2O3, (II), is regiospecific. However, correct identification of the regioisomer formed by spectroscopic techniques is not trivial and single-crystal X-ray analysis provided the only means of unambiguous structure determination. Compound (I) crystallizes with Z, = 2. The propionic acid groups of the two crystallographically unique molecules form a hydrogen-bonded dimer, as is typical of carboxylic acid groups in the solid state. Conformational differences between the methoxybenzene and pyrazole rings give rise to two unique molecules. The structure of (II) features just one molecule in the asymmetric unit and the crystal packing makes greater use than (I) of weak C,H...A interactions, despite the lack of any functional groups for classical hydrogen bonding. [source]

Simulation of pH-dependent edge strand rearrangement in human ,-2 microglobulin

PROTEIN SCIENCE, Issue 1 2006
Sheldon Park
Abstract Amyloid fibrils formed from unrelated proteins often share morphological similarities, suggesting common biophysicalmechanisms for amyloidogenesis. Biochemical studies of human ,-2 microglobulin (,2M) have shown that its transition from a water-soluble protein to insoluble aggregates can be triggered by low pH. Additionally, biophysical measurements of ,2M using NMR have identified residues of the protein that participate in the formation of amyloid fibrils. The crystal structure of monomeric human ,2M determined at pH 5.7 shows that one of its edge ,-strands (strand D) adopts a conformation that differs from other structures of the same protein obtained at higher pH. This alternate ,-strand arrangement lacks a ,-bulge, which may facilitate protein aggregation through intermolecular ,-sheet association. To explore whether the pH change may yield the observed conformational difference, molecular dynamics simulations of ,2M were performed. The effects of pH were modeled by specifying the protonation states of Asp, Glu, and His, as well as the C terminus of the main chain. The bulged conformation of strand D is preferred at medium pH (pH 5,7), whereas at low pH (pH < 4) the straight conformation is observed. Therefore, low pH may stabilize the straight conformation of edge strand D and thus increase the amyloidogenicity of ,2M. [source]

Functional role of human NK cell receptor 2B4 (CD244) isoforms

EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 6 2009
Stephen O. Mathew
Abstract 2B4 (CD244), a member of the signaling lymphocyte-activation molecule (SLAM/CD150), is expressed on all NK cells, a subpopulation of T cells, monocytes and basophils. Human NK cells express two isoforms of 2B4, h2B4-A and h2B4-B that differ in a small portion of the extracellular domain. In the present investigation, we have studied the functions of h2B4-A and h2B4-B. Our study demonstrated that these two isoforms differ in their binding affinity for CD48, which results in differential cytotoxic activity as well as intracellular calcium release by NK cells upon target cell recognition. Analysis of the predicted 3-D structure of the two isoforms showed conformational differences that could account for their differences in binding affinity to CD48. h2B4-A was able to mediate natural cytotoxicity against CD48-expressing K562 target cells and induce intracellular calcium release, whereas h2B4-B showed no effects. NK-92MI, U937, THP-1, KU812, primary monocytes, basophils and NK cells showed expression of both h2B4-A and h2B4-B whereas YT and IL-2-activated NK cells did not show any h2B4-B expression. Stimulation of NK cells through 2B4 resulted in decreased mRNA levels of both h2B4-A and h2B4-B indicating that down-regulation of 2B4 isoforms may be an important factor in controlling NK cell activation during immune responses. [source]

Hydrogen Atom Transfer Experiments Provide Chemical Evidence for the Conformational Differences between C - and O -Disaccharides

Conformational restrictions in the active site of unliganded human caspase-3

JOURNAL OF MOLECULAR RECOGNITION, Issue 3 2003
Chao-Zhou Ni
Abstract Caspases are cysteine proteases that play a critical role in the initiation and regulation of apoptosis. These enzymes act in a cascade to promote cell death through proteolytic cleavage of intracellular proteins. Since activation of apoptosis is implicated in human diseases such as cancer and neurodegenerative disorders, caspases are targets for drugs designed to modulate their action. Active caspases are heterodimeric enzymes with two symmetrically arranged active sites at opposite ends of the molecule. A number of crystal structures of caspases with peptides or proteins bound at the active sites have defined the mechanism of action of these enzymes, but molecular information about the active sites before substrate engagement has been lacking. As part of a study of peptidyl inhibitors of caspase-3, we crystallized a complex where the inhibitor did not bind in the active site. Here we present the crystal structure of the unoccupied substrate-binding site of caspase-3. No large conformational differences were apparent when this site was compared with that in enzyme-inhibitor complexes. Instead, the 1.9,Å structure reveals critical side chain movements in a hydrophobic pocket in the active site. Notably, the side chain of tyrosine204 is rotated by ,90° so that the phenol group occupies the S2 subsite in the active site. Thus, binding of substrate or inhibitors is impeded unless rotation of this side chain opens the area. The positions of these side chains may have important implications for the directed design of inhibitors of caspase-3 or caspase-7. Copyright © 2003 John Wiley & Sons, Ltd. [source]

Structural analysis of an "open" form of PBP1B from Streptococcus pneumoniae

PROTEIN SCIENCE, Issue 7 2006
Andrew L. Lovering
Abstract The class A PBP1b from Streptococcus pneumoniae is responsible for glycosyltransferase and transpeptidase (TP) reactions, forming the peptidoglycan of the bacterial cell wall. The enzyme has been produced in a stable, soluble form and undergoes time-dependent proteolysis to leave an intact TP domain. Crystals of this TP domain were obtained, diffracting to 2.2 Å resolution, and the structure was solved by using molecular replacement. Analysis of the structure revealed an "open" active site, with important conformational differences to the previously determined "closed" apoenzyme. The active-site nucleophile, Ser460, is in an orientation that allows for acylation by ,-lactams. Consistent with the productive conformation of the conserved active-site catalytic residues, adjacent loops show only minor deviation from those of known acyl-enzyme structures. These findings are discussed in the context of enzyme functionality and the possible conformational sampling of PBP1b between active and inactive states. [source]

Structures of S. aureus thymidylate kinase reveal an atypical active site configuration and an intermediate conformational state upon substrate binding

PROTEIN SCIENCE, Issue 4 2006
Masayo Kotaka
Abstract Methicillin-resistant Staphylococcus aureus (MRSA) poses a major threat to human health, particularly through hospital acquired infection. The spread of MRSA means that novel targets are required to develop potential inhibitors to combat infections caused by such drug-resistant bacteria. Thymidylate kinase (TMK) is attractive as an antibacterial target as it is essential for providing components for DNA synthesis. Here, we report crystal structures of unliganded and thymidylate-bound forms of S. aureus thymidylate kinase (SaTMK). His-tagged and untagged SaTMK crystallize with differing lattice packing and show variations in conformational states for unliganded and thymidylate (TMP) bound forms. In addition to open and closed forms of SaTMK, an intermediate conformation in TMP binding is observed, in which the site is partially closed. Analysis of these structures indicates a sequence of events upon TMP binding, with helix ,3 shifting position initially, followed by movement of ,2 to close the substrate site. In addition, we observe significant conformational differences in the TMP-binding site in SaTMK as compared to available TMK structures from other bacterial species, Escherichia coli and Mycobacterium tuberculosis as well as human TMK. In SaTMK, Arg 48 is situated at the base of the TMP-binding site, close to the thymine ring, whereas a cis -proline occupies the equivalent position in other TMKs. The observed TMK structural differences mean that design of compounds highly specific for the S. aureus enzyme looks possible; such inhibitors could minimize the transfer of drug resistance between different bacterial species. [source]

Diastereomers (RC,SP)- and (RC,RP)- S -methyl P -(3-azidopropyl)- N -[(1R)-1-phenylethyl]phosphonamidothioate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2009
Lilu Guo
Diastereoisomers of the title organophosphorus compound, C12H19N4OPS, denoted RCSP, (I), and RCRP, (II), were structurally characterized and compared. Asymmetric phosphorus compounds are of interest with regard to the use of these systems as possible protein probes via the stereoselective delivery of an azide group tethered to the P atom into key protein regions. The diastereomers were produced in a 1:1 mixture and isolated by chromatography. Although both isomers crystallize in the same space group with superficially similar cell constants, conformational and packing differences are pronounced. Despite the conformational differences, strong intermolecular hydrogen bonding links both isomers into chains parallel to the a axis [N...O = 2.8609,(18) and 2.966,(3),Å in (I) and (II), respectively], with C,H..., interchain interactions of ca 3.5,Å. [source]

HLA,B27 heavy chains distinguished by a micropolymorphism exhibit differential flexibility

ARTHRITIS & RHEUMATISM, Issue 4 2010
Heinz Fabian
Objective Although the products of the HLA subtypes B*2705 and B*2709 differ only in residue 116 (Asp versus His) within their peptide-binding grooves, they are differentially associated with inflammatory rheumatic diseases such as ankylosing spondylitis (AS): B*2705 occurs in AS patients, whereas B*2709 is only rarely encountered. The reasons for this distinct association are still unclear but could include subtype-specific conformational and dynamic properties of these antigens. The present study was undertaken to investigate structural and dynamic differences between B*2705 and B*2709 and their possible relationship to subtype-specific disease association. Methods The membrane-distal segments of the B*2705 and B*2709 heavy chains were expressed in vitro and reconstituted together with ,2 -microglobulin and a peptide. HLA,B27 complexes loaded with 2 self peptides (TIS [RRLPIFSRL] and pVIPR [RRKWRRWHL]) and a sequence-related viral peptide (pLMP2 [RRRWRRLTV]) were studied by isotope-edited infrared spectroscopy to detect differences in their structure and flexibility at physiologic temperature. Results Our analyses revealed the existence of subtype-specific conformational differences between the 2 HLA,B27 heavy chains at physiologic temperature, which are undetectable using x-ray crystallography. Irrespective of the bound peptide, the heavy chain of the B*2705 complex exhibited higher conformational flexibility than the B*2709 heavy chain. Conclusion The present study demonstrates the existence of previously undetected systematic conformational and dynamic differences between the heavy chains of the 2 HLA,B27 subtypes. Since effector cell recognition of cells expressing HLA antigens is dependent on the dynamic properties of the interacting cell surface molecules, this HLA,B27 subtype,specific heavy chain flexibility could have a role in the distinct association of HLA,B27 subtypes with spondylarthritides. [source]

Structure of d -tyrosyl-tRNATyr deacylase using home-source Cu,K, and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010
Manickam Yogavel
d -Tyrosyl-tRNATyr deacylase (DTD) is an editing enzyme that removes d -amino acids from mischarged tRNAs. The crystal structure of Plasmodium falciparum DTD (PfDTD) was determined using the iodide-SAD phasing method. Iodide-derivatized PfDTD crystals were obtained using the quick cryo-soaking procedure in which native crystals were soaked for a short period of 10,30,s in cryoprotectant solution containing 0.2,1,M NaI. Iodide-SAD data sets were collected to 3.3 and 2.74,Å resolution from PfDTD crystals that belonged to two different space groups, P43 and P1, using an in-house X-ray copper-anode source. This is the first report to detail structure solution using low iodide anomalous signal, modest resolution and redundancy and average solvent content for SAD phasing of 984 and 1312 amino acids in the triclinic P1 and tetragonal P43 space groups, respectively. A total of 85% and 56% of the residues were automatically built into the iodide-phased electron-density maps using PHENIX AutoBuild. The structure of HEPES-bound PfDTD was subsequently determined by molecular replacement and refined to 2.83,Å resolution. The crystals obtained from various batches of crystallization trials of PfDTD exhibited polymorphism in terms of belonging to different crystal forms and space groups. Even within a given crystal system the unit-cell parameters showed high non-isomorphism. These packing variations were exploited in order to conduct a systematic study of conformational changes in PfDTD. It is shown that the disposition of a ten-residue insertion loop affects packing within the PfDTD crystals and seems to determine the non-isomorphism in unit-cell parameters. By tracking the changes in PfDTD unit cells, it was possible to map conformational differences within PfDTD that may be of significance for enzyme activity. [source]

Structural comparison of Escherichia colil -asparaginase in two monoclinic space groups

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2003
Mario Sanches
The functional l -asparaginase from Escherichia coli is a homotetramer with a molecular weight of about 142,kDa. The X-ray structure of the enzyme, crystallized in a new form (space group C2) and refined to 1.95,Å resolution, is compared with that of the previously determined crystal form (space group P21). The asymmetric unit of the new crystal form contains an l -asparaginase dimer instead of the tetramer found in the previous crystal form. It is found that crystal contacts practically do not affect the conformation of the protein. It is shown that subunit C of the tetrameric form is in a conformation which is systematically different from that of all other subunits in both crystal forms. Major conformational differences are confined to the lid loop (residues 14,27). In addition, the stability of this globular protein is analyzed in terms of the interactions between hydrophobic parts of the subunits. [source]

The X-ray structure of a recombinant major urinary protein at 1.75,Å resolution.

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2001
A comparative study of X-ray, NMR-derived structures
Major urinary proteins belong to the lipocalin family and are present in the urine of rodents as an ensemble of isoforms with pheromonal activity. The crystal structure of a recombinant mouse MUP (rMUP) was solved by the molecular-replacement technique and refined to an R factor and Rfree of 20 and 26.5%, respectively, at 1.75,Å resolution. The structure was compared with an NMR model and with a crystallographic structure of the wild-type form of the protein. The crystal structures determined in different space groups present significantly smaller conformational differences amongst themselves than in comparison with NMR models. Some, but not all, of the conformational differences between the crystal and solution structures can be explained by the influence of crystallographic contacts. Most of the differences between the NMR and X-ray structures were found in the N-terminus and loop regions. A number of side chains lining the hydrophobic pocket of the molecule are more tightly packed in the NMR structure than in the crystallographic model. Surprisingly, clear and continuous electron density for a ligand was observed inside the hydrophobic pocket of this recombinant protein. Conformation of the ligand modelled inside the density is coherent with the results of recent NMR experiments. [source]