High-Resolution Solution Structure of a Designed Peptide Bound to Lipopolysaccharide:  Transferred Nuclear Overhauser Effects, Micelle Selectivity, and Anti-Endotoxic Activity†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (20) ◽  
pp. 5864-5874 ◽  
Author(s):  
Surajit Bhattacharjya ◽  
Prerna N. Domadia ◽  
Anirban Bhunia ◽  
Subbalakshmi Malladi ◽  
Sunil A. David
Keyword(s):  
High Resolution ◽  
Solution Structure ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Endotoxic Activity

The Solution Structure of Yeast tRNAPheas Studied by Nuclear Overhauser Effects in NMR

1983 ◽  
Vol 1 (1) ◽  
pp. 183-207 ◽  
Author(s):  
C. W. Hilbers ◽  
A. Heerschap ◽  
C. A.G. Haasnoot ◽  
J. A.L.I. Walters
Keyword(s):  
Solution Structure ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects

scholarly journals 1H-n.m.r. studies of the isolated activation segment from pig procarboxypeptidase A

1990 ◽  
Vol 267 (1) ◽  
pp. 213-220 ◽  
Author(s):  
J Vendrell ◽  
F X Avilés ◽  
M Vilanova ◽  
C H Turner ◽  
C Crane-Robinson
Keyword(s):  
Solution Structure ◽  
Tyrosine Residue ◽  
Ph Titration ◽  
Tyrosine Residues ◽  
Wide Range ◽  
Activation Segment ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Very High ◽  
Alpha Carbon

The isolated activation segment (asA) from pig pancreatic procarboxypeptidase A was studied by 1H-n.m.r. spectroscopy over a wide range of solution conditions. Isolated asA shows many characteristics of compactly folded globular proteins, such as the observation of perturbed positions for resonances from methyl groups, alpha-carbon atoms, histidine residues and the tyrosine residue. The single tyrosine residue (Tyr-70) exhibits a very high pKa, and both histidine and tyrosine residues show slow chemical modification (deuteration and iodination). In contrast, asA shows rapid NH exchange. Analysis of the spectra by pH titration and nuclear Overhauser effects revealed several residue interactions. Quantitative analysis of deuterium and tritium exchange allowed the assignment of the histidine C-2-H resonances to their respective residues in the sequence. His-66, the closest to the sites of proteolytic attack in the proenzyme, is shown to be the most accessible to solvent in procarboxypeptidase A. It was also shown that asA is thermally very stable [‘melting’ temperature (Tm) 88 degrees C] and requires a high urea concentration for denaturation (6.25 M, at pH 7.5). Evidence is presented for some degree of conformational flexibility in the premelting range, a feature that could be ascribed to the preponderance of helical secondary structure and to the lack of disulphide bridges. The free solution structure of asA is probably unchanged when it binds to carboxypeptidase A.

High Resolution Structure of Half-Cage Isodrin Propionate, a Molecule Suitable for Studying Nuclear Overhauser Effects in the Organic Laboratory

2012 ◽  
Vol 42 (8) ◽  
pp. 790-793
Author(s):  
Eric W. Reinheimer ◽  
Minseok Jang ◽  
Samuel J. Sobelman ◽  
Andrew H. Stewart ◽  
Katherine A. Kantardjieff ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Structure ◽  
Organic Laboratory ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Resolution Structure

scholarly journals Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5′-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies

1989 ◽  
Vol 259 (2) ◽  
pp. 433-441 ◽  
Author(s):  
M S Searle ◽  
J G Hall ◽  
W A Denny ◽  
L P Wakelin
Keyword(s):  
Base Pair ◽  
Solution Structure ◽  
Major Axis ◽  
Base Pairs ◽  
Carbocyclic Rings ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Hoogsteen Base Pairing ◽  
Dyad Symmetry ◽  
Hydroxy Groups

1H- and 31P-n.m.r. spectroscopy were used to characterize the solution structure of the 1:1 complex formed between the antitumour antibiotic luzopeptin and the self-complementary hexanucleotide d(5'-GCATGC)2. Eighteen nuclear Overhauser effects between antibiotic and nucleotide protons, together with ring-current-induced perturbations to base-pair and quinoline 1H resonances, define the position and orientation of the bound drug molecule. Luzopeptin binds in the minor groove of the DNA with full retention of dyad symmetry, its quinoline chromophores intercalating at the 5'-CpA and 5'-TpG steps and its depsipeptide ring spanning the central two A.T base-pairs. The chromophores stack principally on the adenine base with their carbocyclic rings pointing towards the deoxyribose of the cytosine. There is no evidence for Hoogsteen base-pairing in the complex, all glycosidic bond angles and sugar puckers being typical of B-DNA as found for the free hexanucleotide. The ‘breathing’ motions of the A.T and internal G.C base-pairs are substantially slowed in the complex compared with the free DNA, and the observation that two phosphate resonances are shifted downfield by at least 0.5 p.p.m. in the 31P-n.m.r. spectrum of the complex suggests pronounced local helix unwinding at the intercalation sites. The data are consistent with a model of the complex in which luzopeptin bisintercalates with its depsipeptide essentially in the conformation found in the crystal of the free antibiotic [Arnold & Clardy (1981) J. Am. Chem. Soc. 103, 1243-1244]. We postulate only one conformational change within the peptide ring, which involves rotation of the pyridazine-glycine amide group linkage by 90 degrees towards the DNA surface. This manoeuvre breaks the glycine-to-glycine transannular hydrogen bonds and enables the glycine NH groups to bond to the thymine O-2 atoms of the sandwiched A.T base-pairs. It also shortens the major axis of the depsipeptide so that the interchromophore distance is more suitable for spanning two base-pairs. The model further implies that the carboxy and hydroxy groups of the L-beta-hydroxyvaline residue are appropriately positioned for hydrogen-bonding to the 2-amino group of guanine and the O-2 atom of cytosine of the adjacent G.C base-pair.

scholarly journals NMR solution conformation of heparin-derived tetrasaccharide

1996 ◽  
Vol 318 (1) ◽  
pp. 93-102 ◽  
Author(s):  
Dmitri MIKHAILOV ◽  
Kevin H. MAYO ◽  
Ioncho R. VLAHOV ◽  
Toshihiko TOIDA ◽  
Azra PERVIN ◽  
...  
Keyword(s):  
Chair Conformation ◽  
Coupling Constants ◽  
Solution Conformation ◽  
1H And 13C Nmr ◽  
Small Deviations ◽  
J Coupling Constants ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Dynamics Simulations ◽  
Ring Conformations

The solution conformation of the homogeneous, heparin-derived tetrasaccharide ΔUA2S(1 → 4)-α-d-GlcNpS6S(1 → 4)-α-l-IdoAp2S(1 → 4)-α-d-GlcNpS6S (residues A, B, C and D respectively, where IdoA is iduronic acid) has been investigated by using 1H- and 13C-NMR. Ring conformations have been defined by J-coupling constants and inter-proton nuclear Overhauser effects (NOEs), and the orientation of one ring with respect to the other has been defined by inter-ring NOEs. NOE-based conformational modelling has been done by using the iterative relaxation matrix approach (IRMA), restrained molecular dynamics simulations and energy minimization to refine structures and to distinguish between minor structural differences and equilibria between various ring forms. Both glucosamine residues B and D are in the 4C1 chair conformation. The 6-O-sulphate group is oriented in the gauche–trans configuration in the D ring, whereas in the B ring the gauche–gauche rotomer predominates. Uronate (A) and iduronate (C) residues are mostly represented by 1H2 and 2S0 twisted boat forms, respectively, with small deviations in expected coupling constants and NOEs suggesting minor contributions from other A and C ring conformations.

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