Biomedical subjects

N H Andersen

Publications and source records attributed to N H Andersen.

At least 19 recordsLinked to original sources

PubMed1997

Formation of a molten-globule-like state of myoglobin in aqueous hexafluoroisopropanol.

The effects of aqueous hexafluoroisopropanol (HFIP) media on the structure of myoglobin are reported. Circular dichroism (CD) spectra of this alpha-helical protein in as little as 4% (v/v) HFIP indicate that native-like amounts of secondary structure remain while rigid tertiary structure is lost. However, thermal studies suggest some residual cooperativity of unfolding in this state. At much higher HFIP concentrations, the helicity exceeds the native value and the protein behaves as a series of independent helices which do not interact with each other. We did not observe cold denaturation of myoglobin, even though this phenomenon has been observed for molten globule states of myoglobin, as well as for monomeric amphipathic alpha-helices when moderate quantities of HFIP are present. The pH dependence of trifluoroethanol-induced disruption of tertiary structure revealed that the degree of disruption increases as the enthalpic advantage of the folded state is diminished at low pH.

Animals↗

PubMed1997

[Arthroscopic subacromial decompression].

The aim of this prospective study was to evaluate the results of arthroscopic subacromial decompression (ASAD) in the treatment of impingement syndrome in patients without full thickness rotator cuff tears. Sixty patients (64 operative procedures) underwent ASAD during the study period; 37 men and 23 women, average age 46 years (range 28-63), average duration of symptoms 37 months (range 8-132). Patients with calcifying tendintis were not included. Evaluation preoperatively and one year postoperatively included: Constant score, clinical examination and radiological evaluation (supraspinatus outlet view). All follow-up examinations were done by an independent observer. Fifty-six patients (60 procedures) were available for follow-up. The average length of follow-up was 13 months (range 10-23). Forty-six patients (77%) achieved a good or excellent result according to Constant score criteria. Preoperatively twenty-four patients had applied for worker's compensation benefits (WCB). Only half of the patients in the WCB group achieved a satisfactory result, whereas 94% of the non-WCB patients had a good or an excellent result. Arthroscopic subacromial decompression is an effective procedure for the majority of patients with stage II impingement syndrome. In this study WCB claims were associated with inferior results.

Adult↗

PubMed1997

Empirical parameterization of a model for predicting peptide helix/coil equilibrium populations.

A modification of the Lifson-Roig formulation of helix/coil transitions is presented; it (1) incorporates end-capping and coulombic (salt bridges, hydrogen bonding, and side-chain interactions with charged termini and the helix dipole) effects, (2) helix-stabilizing hydrophobic clustering, (3) allows for different inherent termination probabilities of individual residues, and (4) differentiates helix elongation in the first versus subsequent turns of a helix. Each residue is characterized by six parameters governing helix formation. The formulation of the conditional probability of helix initiation and termination that we developed is essentially the same as one presented previously (Shalongo W, Stellwagen, E. 1995. Protein Sci 4:1161-1166) and nearly the mathematical equivalent of the new capping formulation incorporated in the model presented by Rohl et al. (1996. Protein Sci 5:2623-2637). Side-chain/side-chain interactions are, in most cases, incorporated as context dependent modifications of propagation rather than nucleation parameters. An alternative procedure for converting [theta]221 values to experimental fractional helicities ( ) is presented. Tests of the program predictions suggest this method may have some advantages both for designed peptides and for the analysis of secondary structure preferences that could drive the formation of molten-globule intermediates on protein folding pathways. The model predicts the fractional helicity of 385 peptides with a root-mean-square deviation (RMSD) of 0.050 and locates (with precise definition of the termini in many cases) helices in proteins as well as competing methods. The propagation and nucleation parameters were derived from NMR data and from the CD data for a 79 peptide "learning set" for which an excellent fit resulted (RMSD = 0.0295). The current set of parameter corrections for capping boxes, helix dipole interactions, and side-chain/side-chain interactions (coulombic, hydrogen bonding and hydrophobic clustering), although still under development provide a significant improvement in both helix/coil equilibrium prediction for peptides and helix location in protein sequences. This is clearly evident in the rms deviations between CD measures and calculated values of fractional helicity for different classes of peptides before and after applying the corrections: for peptides lacking capping boxes and i/i + 3 and i/i + 4 side-chain/side-chain interactions RMSD = 0.044 (n = 164) versus RMSD = 0.054 (0.172 without the corrections, n = 221) for peptides that required context-dependent corrections of the parameters. If we restrict the analysis to N-acylated peptides with helix stabilizing side-chain/side-chain interactions (including N-capping boxes), the degree to which our corrections account for the stabilizing interaction can be judged from the change in helicity underestimation, ( calc- CD): -0.15 +/- 0.10, which is reduced to -0.018 +/- 0.048 (n = 191) upon applying the corrections.

Algorithms↗

PubMed1996

Efforts toward deriving the CD spectrum of a 3(10) helix in aqueous medium.

There have been two recent reports suggesting that 3(10) helices can be distinguished from alpha helices by circular dichroism. The differentiating feature is stated to be a [theta]222:[theta]208 ratio (R2) distinctly smaller than unity. This has been reported for a C(alpha)alpha'-disubstituted homooctamer [Toniolo et al. (1996), J. Am. Chem. Soc. 118, 2744-2745] and for alanine-rich systems of 16-21 residue length with modest fractional helicity [Millhauser (1995) Biochemistry 34, 3873-3877]. We report here the changes in the CD spectrum produced by inserting aminoisobutyric acid (Aib) residues into the helical domain of human pancreatic amylin. In order to examine this effect at comparable net fractional helicities, CD spectra were measured for each species during the course of a helicity titration by trifluoroethanol addition. The addition of five Aib residues gave results of particular interest. At low net fractional helicity, this Aib-rich system displays a diminished pi-->pi* (circa 208 nm) rotational strength versus the less Aib-rich species. However, NMR data and comparisons of CD difference spectra suggest that fluoroalcohol-induced extension of the short Aib-rich helix is in the form of an alpha helix. Given the diminished intensity of the minimum at 208 nm at low net helicity when 3(10) conformations should contribute, we urge extreme caution in using a [theta]222:[theta]208 ratio smaller than unity as a diagnostic for 3(10) helices.

Amino Acid Sequence↗

PubMed1996

[Frozen shoulder. Arthroscopy and manipulation in general anesthesia, followed by early passive mobilization].

Over a 15 month period 20 patients with 20 arthroscopically verified frozen shoulders were treated with manipulation under general anaesthesia and early passive motion. The study had a minimum of six months follow-up. The average duration of the disease before treatment was eight months. Prior to treatment all patients suffered from moderate to severe pain and the average range of motion was less than 40% of the normal shoulder. During the follow-up period 55% had obtained a normal or almost full range of motion and 75% suffered from only slight pain or had no pain at all. Fourteen patients returned to prior work within a mean of nine weeks after treatment. We found no relation between the end-result and the prior pathology. We believe that manipulation with arthroscopy is an effective way of shortening the course of an apparently self-limiting disease and should be considered when conservative treatment fails.

Adult↗

PubMed1995

The receptor binding affinity of monocyclic [Ala3,Xaa11]endothelin-1 analogs correlates with inducible helix length.

Endothelin-1, a bicyclic 21-amino acid peptide with disulfide bridges between cysteines 1 and 15 as well as between cysteines 3 and 11, has been reported to be partially helical based on both CD and NMR data. However, this remains an area of controversy with some claims that CD data indicate no alpha-helical structure (Calas, B.; Harricane, M.-C.; Gulmard, L.; Heitz, F.; Mendre, C.; Chabrier, P.E.; Bennes, R. Peptide Res. 1992, 5, 97) and a recent X-ray crystal structure placing the helix at a different locus (Janes, R.W.; Peapus, D.H.; Wallace, B.A. Structural Biology 1994, 1, 311). The CD studies reported herein indicate that the helical structures reported in NMR studies (e.g. Andersen, N.H.; Chen, C.; Marschner, T.M.; Krystek, Jr. S.R.; Bassolino, D.A. Biochemistry 1992, 31, 1280) apply to pure aqueous media as well. The helix located from Lys9 to the Cys15/His16 juncture is ca 75% populated in pH 4 aqueous buffer. Titration difference CDs reveal that the helix extent increases by one to two residues and that the 'helical conformation' is more completely populated upon addition of TFE to 50+ volume-%. Comparison with a more helical analog suggests that the helix propagates towards (but not to the end of) the C-terminus upon fluoroalcohol addition. A variety of monocyclic derivatives of [Nle7] ET-1 lacking the 3,11-disulfide were evaluated for biological activity and examined by TFE titration difference CD. The series included an Aib11 and a Pro11 analog. The helix promoting Aib analog was the most active while the Pro analog exhibited significantly lower vasoconstrictor activity and binding affinity for the ETA receptor. All of the monocyclic analogs became significantly more helical upon addition of fluoroalcohols. The inclusion of a proline residue at position 11 does not preclude helix formation upon addition of fluoroalcohols. Rather, helix formation is relatively easily induced but limited to a 5 residue span. Apparently this is insufficient to orient required side chains optimally for interaction with the ETA receptor. For the 1,15-monocyclic analogs differing only at position 11, ETA binding affinity and vasoconstrictor potency correlate with the facility which a 7-8 residue long helix can be induced. This presumably includes the segment Glu10-->Cys15 in all cases and may represent the full sequence from Lys9-->His16. CD studies also reveal that the C-terminal fragment of endothelins is not a fully disordered 'random coil' either alone or attached to the endothelin core.

Amino Acid Sequence↗

PubMed1994

Does the solid-state structure of endothelin-1 provide insights concerning the solution-state conformational equilibrium?

Additional NMR data (local NOE ratios and chemical shifts) for endothelin-1 supporting the existence of a relatively regular helix initiated abruptly at Lys9 (with Asp8 as an N-cap) and extending in all cases to Cys15 (and in a frayed form to Asp18 in some analogs) is presented. The recent solids-state structure [Janes et al. (1994), Nature Struct. Biol. 1, 311-319], in contrast, places the helix in the extreme C-terminal section of structure and the Lys9-Tyr13 segment is not helical. The X-ray structure does not predict the NOEs or chemical shifts observed for endothelins in aqueous media containing polar organic co-solvents. An analysis of the chemical shift data for reporter groups indicates that the helical conformational preference of endothelins is not significantly altered by the addition of acetonitrile, acetic acid, or ethylene glycol. The validity of the analytic strategy is supported by results for both more rigid and less helical analogs. We conclude that the structure observed in crystals obtained from purely aqueous media is influenced by intermolecular interactions in the solid state and is not a significant contributor to the conformational equilibrium observed for monomeric ET-1.

Amino Acid Sequence↗

PubMed1994

Beta-structure in human amylin and two designer beta-peptides: CD and NMR spectroscopic comparisons suggest soluble beta-oligomers and the absence of significant populations of beta-strand dimers.

Intensity variation for the positive far UV CD band was observed for three 'beta-sheet' peptides. In 6% HFIP, an amyloidogenic species (human pancreatic amylin) displays, on standing, an extremely intense 192-nm band which diminishes upon physical agitation. A concurrently formed Tyr sidechain band at 274 nm disappears completely with agitation, linking the enhancement of the 192-nm band to the highly ordered stacking of beta-sheets. NMR studies indicate that the beta-states of the three peptides are oligomeric, not beta dimers. A membrane-forming EAK peptide displays NMR peaks due to the low concentration of 'random coil' monomers present in slow equilibrium with beta-oligomers; solutions of a more hydrophobic ELKA peptide, which displays an intense 195-nm band, contain only oligomeric species. NMR studies at 25% HFIP revealed the structural requirements for inhibition of beta-oligomer formation.

Amino Acid Sequence↗

PubMed1993

Hevein: NMR assignment and assessment of solution-state folding for the agglutinin-toxin motif.

The first high-resolution solution-state structure of a member of the toxin-agglutinin folding motif with the WGA disulfide linkage is presented. The 1H NMR spectrum of hevein has been 100% assigned from residue 2 through residue 43, the C-terminus, using two-dimensional correlation and NOE spectroscopy. During the course of the NOESY analysis, the three-dimensional structural features of hevein were derived, using nonstereospecific distance constraints (with tight bounds) for XPLOR simulated annealing followed by unconstrained relaxation in the CHARMm force field, at two levels of long-range constraint density. In addition, a large number of low-bound-only constraints, corresponding to unobserved NOE's, were used in both refinements. The first structure elucidation employed a total of 180 distance constraints (60 of which were medium or long range, i/i+n with n < or = 2). The second refinement employed 244 (101 medium or long range) constraints: some conformation-insensitive intraresidue constraints were deleted, two misassigned long-range constraints were corrected, and 41 new i/i+n (n > or = 2) constraints were added. The average bounds precisions of the two refinements were comparable (+/- 0.44 A) and significantly tighter than those that result when a universal low bound corresponding to the sum of the van der Waals radii was used. (The more conservative treatment of NOE's gave the same final structure but required a higher constraint density before assignment errors would stand out during the refinement.) Constraint density also has a significant influence on convergence and accuracy using tight constraints. The study demonstrates that convergence within an ensemble of solution structures is not a dependable criterion for either the accuracy or precision of the derived structure. The best fitting conformers from the refinement at the higher constraint density bear a greater similarity to the solid-state structure of the domains of wheat germ agglutinin (0.95 A rmsd over residues 2-32) than to the recently reported 2.8-A X-ray structure of hevein (1.25 A rmsd over residues 2-32, 2.83 A rmsd over residues 2-42). The consensus conformer from the solution data is defined to a backbone rmsd of < 0.6 A over the full sequence for which NMR data could be collected.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed1992

Peptide/protein structure analysis using the chemical shift index method: upfield alpha-CH values reveal dynamic helices and alpha L sites.

The alpha-CH shifts observed by 1H NMR for medium-sized peptides and for an unusual small protein, herein, which has a high density of alpha L conformations within its 43 residue length, reveal that the recently introduced chemical shift index (CSI) analysis places short dynamic helices (alpha R) and alpha L residues in the same category as stable helices. The method appears to be a promising addition to the arsenal of methods for peptide structure analysis and is clearly not limited to rigid protein systems.

Amino Acid Sequence↗

PubMed1992

Solution conformation of a cyclic pentapeptide endothelin antagonist. Comparison of structures obtained from constrained dynamics and conformational search.

The structure of a cyclic pentapeptide, cyclo-(D-Trp-D-Asp-L-Pro-D-Val-L-Leu), that has high selectively for the endothelin ETA receptor has been determined by NMR spectroscopy using constrained molecular dynamics and conformational search procedures. Structures obtained using two methods of refinement, namely (i) constrained molecular dynamics; and (ii) systematic searches of conformational space for optimal satisfaction of distance constraints, were compared to those obtained from systematic searches of conformational space without NMR data. The two different procedures of refinement produce similar conformations that are consistent with the NMR distance constraints. Conformational searches for optimal energy without any NMR distance constraints produced several low-energy structures, two of which have essentially the same backbone as those structures derived from distance-constrained procedures and one of these even reproduces several side-chain positions well. The pentapeptide backbone consists of a linked gamma- and beta-turn conformation, with the leucine and tryptophan as corner residues of the type II beta-turn. The side chains are highly ordered both in aqueous solvent and in dimethyl sulfoxide. In aqueous media the leucine side chain is directed towards the indole ring, presumably to reduce the non-polar surface exposure, producing unusual upfield shifts for the methyls (and particularly H gamma). This structural feature was reproduced in one of the structures obtained from conformational searches performed without NMR data. Exhaustive conformational searches appear to provide an alternative method for structure generation for cyclic peptides.

Endothelins↗

PubMed1992

Conformational isomerism of endothelin in acidic aqueous media: a quantitative NOESY analysis.

The conformational features of endothelin-1 (ET-1) in mixed water/ethylene glycol media have been studied by two-dimensional 1H NMR experiments throughout the pH range 3.2-7.2. At pH less than 5 all backbone NH signals can be observed, and NOESY experiments provided a large set of dipolar cross-peaks. Cross-peak intensities from each experiment (different mixing times and H2O versus D2O) were converted to distance constraints using a novel algorithm (program DISCON) for removing spin diffusion effects and thus obtain cross-rates rather than cross-peak intensities. A set of 168 nonstereospecific distance bounds (average experimental precision, +/- 0.38 A) was used in dynamics simulated annealing refinements. Two consensus structural features were found--a reverse turn at Ser5----Asp8 and an alpha-helical stretch from Lys9 to Cys15; however, after constraint-free minimization, structures generated using XPLOR-1.5, CONGEN, and DISCOVER all violated at least 32% of the bounds by more than 0.2 A, which we ascribe to conformational isomerism. When the constraints were modified to reflect subsequent experimental data and to eliminate constraints that could not be obeyed by any single conformer structure, the relaxed structures still violated at least 15% of this more limited and looser set of constraints. Therefore, a modified procedure for constrained dynamics refinement (using XPLOR-2.1), which allows for conformational isomerism outside of the central helical core region, was developed. This "conformer search procedure" produced structures which fell into five tightly defined conformational clusters. The two most populated clusters correspond to a rotation of the 8,9-amide unit. The conformer which we propose as the major contributor at pH 3.2-5.8 was defined to a backbone rmsd of 0.51 A over residues 1----15. An alternative description of the motional averaging in segments of the endothelin structure as extensive randomization rather than rapid interconversion between a small number of discreet conformers was ruled out by an analysis of NH shift-temperature gradients and exchange rates. This analysis suggests that small delta delta/delta T values need not correlate with H-bonding for conformational mixtures. In ET-1 the greatest motional averaging occurs from Ser2 through Ser5 (not in the C-terminus) and may be so extensive as to approximate a flexible random coil population as high as 30%. The C-terminus shows less rapid and less extensive conformational averaging, but no definitive structures for individual conformers could be derived in the absence of stereospecific constraints. The pharmacological implications of the consensus structural features are discussed.

Amino Acid Sequence↗

PubMed1992

Dactylocyclines, novel tetracycline derivatives produced by a Dactylosporangium sp. II. Structure elucidation.

Fermentation of Dactylosporangium sp. (ATCC 53693) produces a mixture of tetracycline derivatives from which several related tetracycline glycosides, the dactylocyclines, were isolated and their structures determined. The most abundant glycoside in initial fermentations was found to be dactylocycline A. Each glycoside proved to be acid sensitive and readily hydrolyzed to a common aglycone, dactylocyclinone. While the aglycone was cross resistant with tetracycline, the dactylocyclines proved active against certain tetracycline-resistant organisms.

Actinomycetales↗

PubMed1991

[Peritonsillar abscess. Occurrence of disease requiring surgery in the remaining tonsil after unilateral tonsillectomy à chaud].

The occurrence of disease requiring surgery of the remaining tonsil after unilateral tonsillectomy à chaud in the treatment of peritonsillar abscess was studied in 536 patients. None of the patients histories of previous severe tonsillitis at the time of the unilateral had tonsillectomy. 9.3% of the patients under 30 years of age were readmitted for surgery on the remaining tonsil during the follow up period. Only 0.5% of the patients over 30 years were readmitted. Previous investigations have shown increasing frequency of pharyngitis after bilateral tonsillectomy. The present authors suggest bilateral tonsillectomy in all patients under 30 years of age who suffer from peritonsillar abscess irrespectively of previous tonsillar disease. In patients over 30 years, unilateral ablation is recommended unless clear indication for bilateral tonsillectomy are present.

Adolescent↗

PubMed1991

Conformation of endothelin in aqueous ethylene glycol determined by 1H-NMR and molecular dynamics simulations.

The solution conformation of a 21-residue vasoconstrictor peptide endothelin-1 (ET-1) in water-ethylene glycol has been determined by two-dimensional 1H-NMR spectroscopy and constrained molecular dynamics simulations. The N-terminus (residues 1-4) appears to undergo conformational averaging and no single structure consistent with the NMR constraints could be found for this region. Residues 5-8 form a turn, and residues 9-16 exist in a helical conformation. A flexible 'hinge' between residues 8-9 allows various orientations of the turn relative to the helix. Another 'hinge' at residue 17 connects the extended C-terminus to the bicyclic core region (residues 1-15). Residues important for binding and biological activity form a contiguous surface on one side of the helix, with the two disulfides extending from the other side of the helix.

Computer Simulation↗

PubMed1991

Peritonsillar abscess: risk of disease in the remaining tonsil after unilateral tonsillectomy à chaud.

The occurrence of disease in the remaining tonsil after unilateral tonsillectomy à chaud in the treatment of peritonsillar abscess, was studied in 536 patients. No patient had a history of previous severe tonsillitis at the time of the unilateral tonsillectomy, 6.1 per cent of the patients were readmitted for surgery of the remaining tonsil during the follow-up period. Ninety-seven per cent of these patients were younger than 30 years of age. Previous investigations have shown increasing frequency by age of pharyngitis after bilateral tonsillectomy. We suggest bilateral tonsillectomy in all cases of patients younger than 30 years old who suffer from peritonsillar abscess irrespective of previous tonsillar disease. Patients older than 30 should be treated with unilateral ablation, unless there is a clear indication for bilateral tonsillectomy.

Adolescent↗

PubMed1990

Computer-aided conformational analysis based on NOESY signal intensities.

The basis for the development of a suite of programs that allow the user to determine motional features (the correlation time and the significance of segmental motion) and the optimum conditions for future experiments from a NOESY signal matrix is presented. This automated evaluation of NOESY data serves as the initial step of an iterative conformational analysis which uses the molecular model manipulation capabilities of modern graphics workstations. Incorporated in these programs is NOESYSIM, a calculation subroutine which uses a set of molecular coordinates (and a correlation time estimate) together with user entered experimental parameters (acquisition time, sweep width, mixing time and cycle repetition time) to generate an accurately calculated NOESY signal matrix reflecting those conditions and the specified conformational model. Conformational refinement then consists of iterative comparisons of the experimental signal matrix with a series (or systematically sampled set) of model coordinates corresponding to a dynamics' course, driven-minimization or torsional grid search. These procedures and developments are illustrated with examples including: solution conformations of prostanoids; studies of the folding preferences and media-dependent changes in conformation for peptide hormones; and the structure elucidation of a novel undecapeptide macrolide antibiotic (lysobactin). For larger molecules, even constrained grid searches have too high a dimensionality and one must resort to distance-constraint based minimizations. A novel procedure for deriving more accurate distance constraints (corrected for secondary NOEs) is detailed and a new strategy for conformation elucidation, based on this procedure, is outlined.

Amino Acid Sequence↗

PubMed1988

1H-n.m.r. analysis of type-2 chain lacto-gangliosides. Confirmation of structure of a novel cancer-associated fucoganglioside, alpha-NeuAc-(2----6)- beta-D-Galp-(1----4)-beta-D-GlcpNAc-(1----3)-beta-D-Galp-(1----4)-[alp ha-L- Fucp-(1----3)]-beta-D-GlcpNAc-(1----3)-beta-D-Galp-(1----4)-beta -D-Glc p- (1----1)-Cer (VI6NeuAcIII3FucnLc6Cer).

Neolacto-glycosphingolipids, substituted with alpha-NeuAc-(2----3)- and -(2----6)-linked D-Galp residues were analyzed by one- and two-dimensional 1H-n.m.r. spectroscopy at 500 MHz in 49:1 (v/v) di(2H3)methyl sulfoxide-deuterium oxide solution. For the simplest structures analyzed, nLc4Cer, IV3NeuAcnLc4Cer, and IV6NeuAcnLc4Cer, sialosylation-induced changes in shifts of terminal and subterminal core residues were interpretable in terms of existing conformational models. Chemical shifts for H-3e and H-3a of NeuAc characteristic for the type of linkage, were also determined. In addition, regularly reproducible shifts were seen for H-1 and other resonances of terminal and subterminal core residues of all structures tested. Chemical-shift correlations proved to be useful in elucidating the structure of a unique ganglioside bearing an internal beta-D-Galp-(1----4)-[alpha-L-Fucp-(1----3)]-beta-D-GlcpNAc-(1---- 3) residue ("X-trisaccharide") with an alpha-NeuAc-(2----6)-substituted terminal group.

Carbohydrate Sequence↗