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Biomedical subjects

F M Poulsen

Publications and source records attributed to F M Poulsen.

At least 37 records · Page 2Linked to original sources
PubMed1996

Characterisation of recombinant isoforms of birch pollen allergen Bet v 1.

Three isoforms of the major birch pollen allergen, Bet v, 1 from Betula verrucosa have been expressed as recombinant proteins in E. coli and purified. The immunochemical properties of recombinant isoforms (rBet v 1) differed on immunoblots when compared using Mabs and birch pollen allergic patients serum IgE. 2-D gel analysis showed that recombinant isoforms with different epitope structure can focus under the same protein spot after electrophoresis. The structure of conformational epitopes can be distorted by amino acid substitutions even when T-cell epitopes are not affected as judged by T-cell proliferation studies.

Allergens↗
PubMed1996

X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy.

The three-dimensional structure of the major birch pollen allergen, the 17,500 M(r) acidic protein Bet v 1 (from the birch, Betula verrucosa), is presented as determined both in the crystalline state by X-ray diffraction and in solution by nuclear magnetic resonance (NMR) spectroscopy. This is the first experimentally determined structure of a clinically important inhalant major allergen, estimated to cause allergy in 5-10 million individuals worldwide. The structure shows three regions on the molecular surface predicted to harbour cross-reactive B-cell epitopes which provide a structural basis for the allergic symptoms that birch pollen allergic patients show when they encounter pollens from related trees such as hazel, alder and hornbeam. The structure also shows an unusual feature, a 30 A-long forked cavity that penetrates the entire protein.

Allergens↗
PubMed1995

Modification of a specific tyrosine enables tracing of the end-to-end distance during apomyoglobin folding.

In order to follow the overall geometry of the apomyoglobin molecule during folding, we have converted a specific tyrosine residue into 3-nitro-tyrosine. The specificity of the modification was verified by proteolytic cleavage of the modified protein and mass spectroscopy of the resulting fragments. By measuring the energy transfer from the tryptophanyl side-chains to the modified residue the average end-to-end distance can be followed. The experiment shows that after initiation of folding the N- and C-termini are rapidly brought into proximity, possibly to a near-native distance.

Animals↗
PubMed1995

Local perturbations by ligand binding of hydrogen deuterium exchange kinetics in a four-helix bundle protein, acyl coenzyme A binding protein (ACBP).

Amide hydrogen exchange kinetics of the individual amides in a four-helix bundle protein, acyl-coenzyme A binding protein, have been studied by nuclear magnetic resonance spectroscopy. The kinetics of amides with exchange rate constants in the range of 10(-25) to 10(-6.5) S-1 at pH 6.65 in free protein and the ligand-protein complex have been measured, and the effect of binding the ligand, palmitoyl-coenzyme A, on individual exchange rates has been analysed. Specific correlations between exchange kinetics and the structural properties of the individual amides known from the three-dimensional structure of acyl-coenzyme A binding protein have been examined. Furthermore, an analysis has been performed comparing the structural perturbations of the protein-ligand interactions known from the three dimensional structure of the complex of palmitoyl-coenzyme A and acyl-coenzyme A binding protein with the ligand-induced perturbations on the amides exchange kinetics. Finally, the ligand-induced perturbations on hydrogen exchange have been compared with those on 15N relaxation. The results suggest that hydrogen exchange kinetics in the individual sites of acyl-coenzyme A binding protein are primarily determined by local structural features; they show that ligand binding gives rise mainly to changes localized at the sites of interaction between protein and ligand; they imply that the perturbation of exchange kinetics caused by ligation can be either, as in one example a local stabilisation of the pre-exchange equilibrium induced by formation of a hydrogen bond, or as seen here in several examples a reduction of the dynamic processes that lead to the opening and closing processes of the pre-exchange equilibrium. The results seem not to indicate changes in the rate of the final chemical exchange step.

Amides↗
PubMed1995

Folding of a four-helix bundle: studies of acyl-coenzyme A binding protein.

The refolding from denaturing conditions of a small four-helix bundle, the acyl-coenzyme A binding protein, has been investigated by utilizing an array of fast-reaction techniques. Stopped-flow tryptophan fluorescence for measuring the incorporation of aromatic residues into the protein core and far- and near-ultraviolet circular dichroism to measure the formation of secondary and tertiary structure, respectively, together with the formation of persistent structure measured by hydrogen exchange pulse labeling experiments analyzed by electrospray ionisation mass spectrometry all show that 90% of the acyl-coenzyme A binding protein molecules achieve their fully folded and active, native state with a time constant of less than 5 ms at 25 degrees C and of ca. 30 ms at 5 degrees C. The kinetic parameters measured by the different techniques are closely similar, indicating that the different elements of structure form effectively concomitantly. There is no evidence for a significant population of any partially structured intermediate states, and the kinetics are identical whether refolding occurs from an unfolded state generated either by low pH or by addition of guanidine hydrochloride. The kinetics of both refolding and unfolding are monophasic processes for practically 90% of the molecules, and can be described by a two-state model. The results add to our knowledge of the folding scheme of different structural motifs and are discussed in terms of current views of the mechanisms of protein folding.

Acyl Coenzyme A↗
PubMed1994

A reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints.

Chymotrypsin inhibitor 2 (CI-2) is one of the growing family of proteins for which well-defined solution and crystal structures have been published and for which small, but distinct differences between these were found. It presents an ideal case to address the question of whether a structural difference is physically real or due to the simplifying approximations with respect to averaging that are used in the conventional methods for structure refinement. NOE distance and 3J coupling constant restrained molecular dynamics simulations were performed using conventional and time-averaged restraints, both in vacuo and in aqueous solution, and the trajectories were compared with structural properties of published structures. The time-averaged restrained molecular dynamics simulations sampled more conformations at various times and visited states consistent with both previously published solution and crystal structures. It was found that the difference between these structures is due to the refinement methodology used. Application of time-averaged restraints in structure refinement yields a physically different picture of the molecular mobility.

Computer Simulation↗
PubMed1994

Comparison of backbone dynamics of apo- and holo-acyl-coenzyme A binding protein using 15N relaxation measurements.

15N magnetic relaxation parameters T1, T2 and the nuclear Overhauser effect in the protein acyl-coenzyme A binding protein (ACBP) have been measured in the presence and absence of the ligand, palmitoyl-coenzyme A, in order to obtain information about local and global dynamical properties of the peptide backbone with and without the ligand bound in the binding site. The three-dimensional structures of acyl-coenzyme A binding protein are known for both states of the protein as determined from multidimensional heteronuclear NMR studies, and they have been shown to be essentially identical. However, the dynamics of the backbone is influenced by the presence of ligand in the binding site. The binding of ligand had significant and specific effects on the relaxation time T1 for many of the 15N in the peptide backbone, in particular those near residues with contacts to the ligand. Similarly, the nuclear Overhauser effect at 15N near such residues increased. There were no significant changes in the T2 relaxation. T1 values showing a significant decrease and NOEs increasing in regions close to the binding site when the ligand was bound suggest two modes of action on the dynamics of the protein when the ligand is binding. The reduced T1 indicates motion of lower amplitude in agreement with the structural constraints introduced by protein-ligand interactions. The increased NOEs may be a consequence of shorter time constants for dynamics of the atoms close to the binding site. The Lipari-Szabo model could not be satisfactorily applied to the entire set of experimental data.(ABSTRACT TRUNCATED AT 250 WORDS)

Carrier Proteins↗
PubMed1993

Protein-ligand interactions in the lysine-binding site of plasminogen kringle 4 are different in crystal and solution. Electrostatic interactions studied by site-directed mutagenesis exclude Lys35 as an important acceptor in solution.

Three amino acid residues previously reported to establish the interactions between lysine-like derivatives and plasminogen kringle 4 have been replaced by other residue types using the methods of site-directed mutagenesis. The effect of these modifications on the binding constant have been measured. The residues are Lys35, Asp57, and Arg71, according to the sequence numbering scheme adapted from the plasminogen kringle 5 domain. The plasminogen kringle 4 derivatives where Lys35 of the native molecule is replaced with isoleucine and methionine residues, respectively, were seen to bind the ligands, respectively, with association constants similar to those of the unmodified recombinant kringle 4 domain. The modification of Asp57 to asparagine was shown to eliminate the ability to bind to the lysine affinity column used to purify the protein. Similarly the site-directed mutagenesis for Arg71 to glutamine resulted in a 12-19-fold decrease in binding of each of the two ligands. In addition, the effect of ionic strength on the binding of 6-aminohexanoic acid to the recombinant plasminogen kringle 4 and the three single substituted derivatives was examined. For the unmodified kringle domain as well as for the two derivatives modified only at the position of Lys35, an ionic strength of 0.5 M reduced the binding constant by a factor of 3 to 0.12 x 10(5) M-1. The derivative modified at the position of Arg71 was not effected by the ionic strength and maintained a rather low binding constant of 0.02 x 10(5) M-1. The observations suggest that the carboxylate of Asp57 and the guanidino group of Arg71 provide the electrostatic interaction in the binding site for the epsilon-amino group and the alpha-carboxylate of a C-terminal lysine residue.(ABSTRACT TRUNCATED AT 250 WORDS)

Arginine↗
PubMed1993

The pro region required for folding of carboxypeptidase Y is a partially folded domain with little regular structural core.

The pro region of carboxypeptidase Y (CPY) from yeast is necessary for the correct folding of the enzyme [Winther, J. R., & Sørensen P. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 9330-9334]. Using fluorescence, circular dichroism, and heteronuclear NMR analyses, it is demonstrated that the isolated pro region is a partially folded protein domain under the conditions where it is functional. It is characterized by a relatively high content of secondary structural elements but a very low content of defined tertiary structure. Although these characteristics are reminiscent of the compact denatured states that have been identified as intermediates in protein folding ("molten globules"), the pro region exhibits only very weak binding of the hydrophobic probe 1-anilino-8-naphthalenesulfonate, and it is resistant toward complete thermal unfolding. Altogether the data indicate an extremely flexible structure that has little regular structural core. It is proposed that the feature of a partially folded domain per se is important for the function of the pro region of CPY as a "co-translational chaperone".

Base Sequence↗
PubMed1993

Low energy of activation for amide hydrogen exchange reactions in proteins supports a local unfolding model.

Hydrogen exchange reactions of amides in hen egg white lysozyme that are pH dependent and have a low energy of activation have been shown to be in accordance with a reaction mechanism in two steps, an equilibrium step and an exchange step. These results are not in agreement with the model, proposed by C.K. Woodward & B.D. Hilton, known as the penetration model. Therefore our results suggest that this model should be revised. The amide hydrogen/deuterium exchange rates in hen egg white lysozyme were measured at 4 degrees C, 10 degrees C, 15 degrees C and 25 degrees C at pH 7.0 by 1H nuclear magnetic resonance spectroscopy. Activation energies of the exchange reactions in the range from 20 kJ mol-1 to 333 kJ mol-1 were obtained for 32 of the 129 residues in the protein. The amides of lysozyme studied here could be divided into two groups, one group of amides are characterized by an observed amide exchange rate (ko) in the range 10(-4) to 10(-6) s-1, an equilibrium constant k1/k2 close to 10(-5), a low energy of activation (20 to 50 kJ mol-1) and a distance less than 6 A from solvent. The other group of amides are characterized by a ko less than 10(-6) s-1, a k1/k2 close to 10(-7), higher energies of activation (40 to 330 kJ mol-1) and a distance more than 4 A from solvent. In terms of structure the amides of the last group are from the core of the protein. They are typically involved in a hydrogen bond and form part of the secondary structure either as interior alpha-helices or central strands of beta-sheets. The first group consists of amides that are in the shell of the protein between the core and the surface. These amides are typically hydrogen bonded and involved in secondary structure such as external alpha-helices or outer strands of beta-sheets and turns.

Amides↗
PubMed1993

Context dependence of protein secondary structure formation: the three-dimensional structure and stability of a hybrid between chymotrypsin inhibitor 2 and helix E from subtilisin Carlsberg.

The loop region of chymotrypsin inhibitor 2 from barley has been employed as a scaffold for testing the intrinsic propensity of a peptide fragment to form a secondary structure. The helix formation of the nine amino acid residue segment Lys-Gln-Ala-Val-Asp-Asn-Ala-Tyr-Ala of helix E from subtilisin Carlsberg has been studied by the construction of a hybrid consisting of chymotrypsin inhibitor 2 (CI2) where part of the active loop has been replaced by the nonapeptide. An expression system for a truncated form of CI2 where the 19 structureless residues of the N-terminus have been removed and Leu20 replaced by methionyl was constructed from the entire 83-residue wild-type CI2 gene by polymerase chain reaction methodology. The gene encoding the hybrid was constructed from the truncated inhibitor gene. The stability of the truncated inhibitor and of the hybrid toward guanidinium chloride denaturation was examined. From these measurements, the energy of unfolding in pure water was extrapolated to 30.5 +/- 1.0 kJ/mol for the truncated inhibitor and 10.9 +/- 0.3 kJ/mol for the hybrid. These energies show that the stability of CI2 is unaffected by the N-terminal truncation but severely decreased by the loop mutations. The three-dimensional structure of the hybrid protein has been determined in solution by nuclear magnetic resonance spectroscopy using 893 distance restraints and 84 torsional angle restraints. The average root-mean-square deviation (rmsd) of 15 structures compared to their geometrical average was 0.8 +/- 0.2 A for heavy backbone atoms and 1.3 +/- 0.2 A for all heavy atoms.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1993

Three-dimensional structure of the complex between acyl-coenzyme A binding protein and palmitoyl-coenzyme A.

Multidimensional 1H, 13C and 15N nuclear magnetic resonance spectroscopy has been used to study the complex between palmitoyl-coenzyme A and acyl-coenzyme A binding protein. The 1H and the 15N spectra of the holo-protein have been almost completely assigned and so has most of the 1H spectrum of the coenzyme A part of the protein-bound ligand. The palmitoyl part of the ligand has been uniformly labelled with 13C and the nuclear magnetic resonance signals of the carbon atoms and their protons have been assigned at the two ends of the hydrocarbon chain. A total of 1251 distance restraints from nuclear Overhauser effects and 131 dihedral angle restraints from three-bond coupling constants provided the basis for the structure calculation. A comparison of 20 structures calculated from these data to the average structure showed that they could be aligned with an atomic root-mean-square deviation of 1.3(+/- 0.2) A for all C, N, O, P and S atoms in protein and ligand. The apo-protein is a four-helix protein and this structure is maintained in the holo-protein. The four alpha-helices are Ac1 of residues 3 to 15, Ac2 from residue 20 to 36, Ac3 from 51 to 62, and Ac4 from 65 to 84. For the four alpha-helices of the peptide backbone of the holo-protein the root-mean-square deviation for the C, C alpha and N atoms was 0.42(+/- 0.08) A. The binding site for the palmitoyl-chain stretches between the N-terminal end of Ac3 where the carboxyl part binds, to the N-terminal of Ac3 where the omega-end of the palmitoyl part binds. The adenosine-3'-phosphate is bound near residues of each of the four helices in an arrangement where it can form salt bridges and/or hydrogen bonds to either backbone or side-chain atoms of Ala9, Tyr28, Lys32, Lys54 and Tyr73. The polar parts of the pantetheine and the pyrophosphate are structured in the bound ligand to form an interface with the solvent. Also the ligand forms a set of non-polar intramolecular interactions where the adenine, the pantetheine, and the palmitoyl-chain are associated, so overall the structure of the bound ligand seems to be organized to protect the lipophilic palmitoyl part from the polar solvent.

Amino Acid Sequence↗
PubMed1993

Determination of the rate constants k1 and k2 of the Linderström-Lang model for protein amide hydrogen exchange. A study of the individual amides in hen egg-white lysozyme.

The pH dependence of the amide/solvent hydrogen exchange of individual amide groups in hen egg-white lysozyme has been studied by nuclear magnetic resonance spectroscopy. Lysozyme has been used here as a model for a globular protein to re-examine the hypothesis for the amide/solvent hydrogen exchange reaction proposed by K. Linderstrøm-Lang and described in detail by Hvidt and Nielsen. The work has been focused on the most slowly exchanging amide at the temperature of 21 degrees C and in the pH range between 4 and 8. Exchange rates have been measured for 64 of the 126 amide protons and the pH dependence has been determined for 52 of these. The amides examined represent a sample that includes all the types of secondary structure and they are placed in the globular structure in a range of 3.2 A to 8.5 A from the closest water molecule on the surface. The measured exchange rates at pH 6 have been compared to these structural parameters and the results suggest that the rate constants are determined partly by the distance to the surface and partly by the type of secondary structure the amide is engaged in. Near the surface and in the very interior the distance to the surface seems to be rate-determining. Between the extremes the type of secondary structure is rate determining. The pH dependent exchange of the examined amides was shown to be in agreement with the Linderstrøm-Lang model. For each of the amides examined the rate constants for the opening and the closing reaction in the first reaction step of the Linderstrøm-Lang model has been calculated and compared to structural parameters.

Amides↗
PubMed1993

The three-dimensional structure of acyl-coenzyme A binding protein from bovine liver: structural refinement using heteronuclear multidimensional NMR spectroscopy.

The 3D structure of bovine recombinant acyl-coenzyme A binding protein has been determined using multidimensional heteronuclear magnetic resonance spectroscopy in a study that combines investigations of 15N-labeled and unlabeled protein. The present structure determination is a refinement of the structure previously determined (Andersen, K.V. and Poulsen, F.M. (1992) J. Mol. Biol., 226, 1131-1141). It is based on 1096 distance restraints and 124 dihedral angle restraints of which 69 are for phi-angles and 8 for chiral centers and 47 for prochiral centers. The new experimental input for the structure determination has provided an increase of 263 distance restraints, 5 phi-angle restraints, and 32 chi-angle restraints in 2 chiral centers, and 31 prochiral centers restraining an additional 23 chi 1, 8 chi 2, and 1 chi 3 angles. The increase of 300 distance and dihedral angle restraints representing an additional 30% of input parameters for the structure determination has been shown to be in agreement with the first structure. A set of 29 structures has been calculated and each of the structures has been compared to a mean structure to give an atomic root mean square deviation of 0.44 +/- 0.12 A (1 A is 0.1 nm) for the backbone atoms C, C alpha, and N in the four alpha-helices A1, residues 4-15, A2, residues 21-36, A3, residues 51-62 and A4, residues 65-84. The loop-region of residues Gly45-Lys50 could not be defined by the restraints obtained by NMR. The program PRONTO has been used for the spectrum analysis, assignment of the individual nuclear Overhauser effects, the integration of the cross peaks, and the measurement of the coupling constants. The programs DIANA, X-PLOR and INSIGHT have been used in the structure calculations and evaluations.

Amino Acid Sequence↗
PubMed1992

Primary structure of barwin: a barley seed protein closely related to the C-terminal domain of proteins encoded by wound-induced plant genes.

Barwin is a basic protein with pI above 10 and molecular mass 13.7 kDa isolated from aqueous extracts of barley seed. The complete amino acid sequence of 125 residues has been determined by a combination of conventional protein sequencing, plasma desorption mass spectrometry, and 1H nuclear magnetic resonance spectroscopy. Three disulfide bridges have been localized as Cys31-Cys63, Cys52-Cys86, and Cys66-Cys123 both by 1H nuclear magnetic resonance spectroscopy and by plasma desorption mass spectrometry. The N-terminal residue was identified as pyroglutamate. Barwin is closely related to a peptide segment of 122 residues at the C-terminal region of the proteins encoded by two wound-induced genes in potato plants, win1 and win2, and a protein encoded by the hevein gene of rubber tree. In 77 sequence positions of 125 the barwin, win1, win2, and hevein protein sequences have amino acid sequence identity, when two gaps--one of two residues allowing for the insert of Gly23 and Ala24 and one allowing for the insert of Thr97 in the barwin sequence--are introduced in the latter three. The close sequence similarity with the proteins encoded by the wound-induced potato and rubber tree genes and the ability of the protein to bind saccharides suggest that barwin might belong to a group of proteins involved in a common defense mechanism in plants.

Amino Acid Sequence↗
PubMed1992

Secondary structure in solution of barwin from barley seed using 1H nuclear magnetic resonance spectroscopy.

Barwin, a basic protein from barley seed of 125 amino acid residues, has been studied by two-dimensional 1H nuclear magnetic resonance spectroscopy. This protein is closely related to the C-terminal domain of proteins whose synthesis is induced by wounding, the so-called win proteins. These proteins may, therefore, have a role in the defense against fungal attack. Full assignment of the 1H nuclear magnetic resonances has been obtained for 104 amino acid residues, and 18 amino acid spin systems were partially assigned. Sequence-specific assignment using nuclear Overhauser spectroscopy has been achieved for 122 of the 125 residues. This has revealed that the secondary structure of the protein is dominated by a large four-stranded antiparallel beta-sheet consisting of the strands Gln2-Thr9, Lys65-Asn71, Gln77-Arg81, and His113-Val121, a small parallel beta-sheet of the strands Trp48-Cys52 and Asp84-Ala87, which together account for a third of the protein. Sequential effects indicate the presence of three small alpha-helices, Tyr30-Lys38, Leu40-Tyr46, and Thr97-Asp103. The secondary structure in other regions of the sequence is characterized mainly by loops and turns and regions where no regular secondary structure arrangement could be identified. A large number of long-range nuclear Overhauser effects has been identified, and these have been used, together with sequential and intranuclear Overhauser effects, for a calculation of the protein's three-dimensional structure.

Amino Acid Sequence↗