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C M Dobson

Publications and source records attributed to C M Dobson.

At least 235 records · Page 13Linked to original sources
PubMed1985

The study of conformational states of proteins by nuclear magnetic resonance.

By the use of examples, mainly of rather rigid proteins, we hope to have shown that conformational analysis of proteins is a problem that is not simply related to the conformational analysis of small molecules. The primary difficulties with proteins are (1) the multitude of possible conformers, (2) the complex dynamical behaviour and (3) the degree of co-operativity within the molecules. Any experimentally derived structural description of a protein is an attempt to represent some average of a complex time dependence. N.m.r. techniques have now reached the point where it is possible to use them to describe many detailed structural features of small globular proteins in solution and to detect and to describe conformational changes in such proteins. In addition, analysis is becoming possible of much less ordered regions of polypeptides, such as are found in less compact proteins, of for example myosin, histones and virus coat proteins, or in denatured states. The limits to the detailed conformational analysis of such proteins are likely to be ones of reality rather than method but the description of the properties shown in Table 1 is by its very nature an extremely important problem in conformational analysis of dynamic macromolecules.

Cytochrome c Group↗
PubMed1985

Vicinal coupling constants and protein dynamics.

The effects of motional averaging on the analysis of vicinal spin-spin coupling constants derived from proton NMR studies of proteins have been examined. Trajectories obtained from molecular dynamics simulations of bovine pancreatic trypsin inhibitor and of hen egg white lysozyme were used in conjunction with an expression for the dependence of the coupling constant on the intervening dihedral angle to calculate the time-dependent behavior of the coupling constants. Despite large fluctuations, the time-average values of the coupling constants are not far from those computed for the average structure in the cases where fluctuations occur about a single potential well. The calculated differences show a high correlation with the variation in the magnitude of the fluctuations of individual dihedral angles. For the cases where fluctuations involve multiple sites, large differences are found between the time-average values and the average structure values for the coupling constants. Comparison of the simulation results with the experimental trends suggests that side chains with more than one position are more common in proteins than is inferred from X-ray results. It is concluded that for the main chain, motional effects do not introduce significant errors where vicinal coupling constants are used in structure determinations; however, for side chains, the motional average can alter deductions about the structure. Accurately measured coupling constants are shown to provide information concerning the magnitude of dihedral angle fluctuations.

Amino Acids↗
PubMed1985

Identification of glycine spin systems in 1H NMR spectra of proteins using multiple quantum coherences.

Double-quantum filtered COSY and triple-quantum filtered COSY techniques have been compared for the tripeptide Gly-Tyr-Gly and for human lysozyme. The insertion of a triple-quantum filter in the COSY experiment leads to dramatic spectral simplification in the fingerprint region of the spectrum and permits the specific identification of glycine spin systems in the complex 1H NMR spectra of proteins. The assignment of these peaks to glycine H alpha can be confirmed using 2D double-quantum correlated spectroscopy.

Glycine↗
PubMed1985

Surface accessibility of aromatic residues in human lysozyme using photochemically induced dynamic nuclear polarization NMR spectroscopy.

Resonances in the photo-CIDNP spectrum of human lysozyme have been assigned to specific spin systems despite extensive spectral overlap using the two-dimensional photo-CIDNP COSY experiment. Five of the 12 tyrosine, tryptophan and histidine residues of human lysozyme are found to be accessible to flavin dye in solution. This result is in good agreement with surface accessibility calculations carried out on the human lysozyme crystal structure. When amino acid differences are considered the photo-CIDNP results obtained for human lysozyme are in good agreement with results obtained previously for hen lysozyme.

Amino Acids↗
PubMed1985

Lysozyme: a major secretory product of a human colon carcinoma cell line.

One of the major proteins secreted by an established human colon adenocarcinoma cell line has been isolated in 25% yield from the serum-free medium in which the cells were grown and identified as lysozyme. Its purification was achieved by sequential steps of acidification, cation-exchange chromatography, and reversed-phase high-performance liquid chromatography. It was recognized to be a human lysozyme on the basis of its molecular weight (14 000), isoelectric point (10.5), amino acid composition, and enzymatic activity. Its identity with previously characterized human lysozymes was established by amino-terminal sequence, peptide composition, immunological properties, NMR, and crystallography. A 4-day, 7-L collection of conditioned medium contained 20.3 mg of secreted protein of which 4.9 mg or approximately 24% of the total was tumor-derived lysozyme. The intracellular level of lysozyme was approximately 18 ng per 10(6) carcinoma cells. The possible significance of these findings in regard to the malignant process and tumor maintenance is discussed.

Adenocarcinoma↗
PubMed1984

High-resolution nitrogen-15 nuclear magnetic resonance studies of alpha-lytic protease in solid state. Direct comparison of enzyme structure in solution and in the solid state.

Histidine enriched in 15N in the imidazole nitrogens was incorporated into the catalytic triad of alpha-lytic protease, and high-resolution solid-state 15N NMR spectra of lyophilized enzyme powders were recorded. The lyophilized powders were prepared from aqueous solutions with pH values ranging from 4.9 to 9.3. The behavior of the 15N resonances as a function of "pH" in these solid samples closely parallels that observed previously in the corresponding solution-state study, with the exception that in the powders proton exchange at His-57 is slow on the NMR time scale whereas in solutions it is fast. Thus, the 15N isotropic shifts demonstrate that the N pi-H tautomer of His-57 predominates in powders prepared at high pH and that N pi(H) participates in a strong hydrogen bond, as the hydrogen-bond donor, in powders prepared at both high pH and low pH. The simplest interpretation of these results is that the active site catalytic triad structure of Asp-His-Ser is maintained in these lyophilized powders. Because Asp-102 and His-57 are sequentially separated, their interaction in these lyophilized powders suggests that the tertiary structures of alpha-lytic protease in the powder and in solution are very similar. The 15N isotropic shifts further indicate that His-57 located within the intact triad in lyophilized enzyme powders has what can be taken as a normal "pKa" for a histidyl residue, undergoing a transition from the protonated to the neutral state with a midpoint between pH 6.0 and 7.0.

Endopeptidases↗
PubMed1984

Identification using 1H NMR spectroscopy of slowly exchanging amide hydrogens of hen lysozyme in solution.

Resonances of over 20 of the most slowly exchanging amide hydrogens have been identified and assigned in the 1H NMR spectrum of hen lysozyme. This was achieved by combining information about spin-spin coupling patterns with nuclear Overhauser enhancement measurements. A computer-based search program was used to permit the assumptions and constraints in this procedure to be closely defined and to reveal possible ambiguities. In addition, experimental values of coupling constants were compared with values calculated on the basis of the torsion angles found in the crystal structure. The close correlation between these gave further confidence in the assignment procedures and provided information concerning the nature of fluctuations about the average solution structure. The very slowly exchanging amide hydrogens are largely buried in alpha-helical and beta-sheet regions of the protein structure.

Amides↗
PubMed1984

A new two-disulphide intermediate in the refolding of reduced bovine pancreatic trypsin inhibitor.

The apparently complete refolding of reduced bovine pancreatic trypsin inhibitor (BPTI) is shown to produce a mixture of two species. One of these is native BPTI, but the other lacks the disulphide bond between cysteines 30 and 51. The latter species has a folded conformation very like that of native BPTI, and is oxidized by air to native BPTI on warming in aqueous solution. The two unreactive cysteine thiol groups appear to be buried in the interior of the molecule, which restricts access by reagents that can alkylate them or oxidize them to form the disulphide bond. The implications of this intermediate and its conformation for the understanding of protein folding are discussed.

Amino Acid Sequence↗
PubMed1984

Proton NMR studies of denatured lysozyme.

Evidence is presented from 1H NMR studies for non-random conformational behaviour in denatured lysozyme in aqueous solution. A method is presented which permits the assignment of resonances in the 1H NMR spectrum of the denatured protein by observing magnetisation transfer from resonances of the native state. The use of these experiments in characterising the denatured state and the significance of these studies for the investigation of protein folding are discussed.

Hot Temperature↗
PubMed1983

Exchange of individual hydrogens for a protein in a crystal and in solution.

A preliminary comparison of the solvent exchange of individual hydrogens of a protein in solution and in a crystal has been possible by using data for lysozyme from 1H nuclear magnetic resonance and neutron diffraction studies. It is suggested that this approach enables a direct comparison of local dynamical behaviour in the two states. The results indicate markedly similar behaviour for many residues, but significant differences are indicated in several regions of the protein.

Animals↗
PubMed1983

Correlation of hydrogen exchange behaviour and thermal stability of lysozyme.

The solvent exchange rates of individual indole NH hydrogens of tryptophan residues of lysozyme have been measured, by using 1H nuclear magnetic resonance spectroscopy, as a function of temperature in the presence of urea and following chemical modification. The results have been interpreted in terms of a low activation energy process which is not dependent on the thermal stability of the protein, and a higher activation energy process that is directly correlated with the thermal stability. The significance of these observations for an understanding of the dynamics of the protein is discussed.

Hydrogen↗
PubMed1982

Complete assignment of the 1H NMR spectrum of the aromatic residues of lysozyme.

Assignment of the nuclear magnetic resonance (NMR) spectrum of the 59 non-exchangeable protons of the 13 aromatic amino acid residues of lysozyme has been completed using a combination of selective spin decoupling and nuclear Overhauser experiments. The experimental chemical shift data were used to simulate the aromatic region of the NMR spectrum at 300 MHz and at 470 MHz. Excellent agreement with the experimental spectra was obtained and the simulations permitted more accurate chemical shift values and resonance linewidths to be obtained. The current set of assignments is compared with those of the assignments made previously. Evidence for the motional behaviour of the aromatic amino acid side chains is presented.

Animals↗
PubMed1982

Studies of beta-sheet structure in lysozyme by proton nuclear magnetic resonance. Assignments and analysis of spin-spin coupling constants.

Resonances of H alpha, H beta, and HN (amide) protons have been assigned in the NMR spectrum for ten residues in a region of beta-sheet structure of lysozyme. The assignments were achieved primarily by interpretation of nuclear Overhauser effects in conjunction with spin decoupling. The HN hydrogens involved in main-chain hydrogen bonding were found to exchange slowly with D2O solvent, although one of the most slowly exchanging HN hydrogens is not classified as being involved in a hydrogen bond in the crystal structure. Spin-spin coupling constants between H alpha protons and HN and H beta protons correlated well with values predicted from the crystal structure by means of the Karplus relationship. For no residues are the coupling constant discrepancies greater than 2.5 HZ. This indicates that for the residues studied here the torsion angles phi and chi 1 defined in the crystal structure describe accurately, generally well within 20 degrees, those for the average solution state.

Animals↗
PubMed1982

Fluctuations and averaging of proton chemical shifts in the bovine pancreatic trypsin inhibitor.

The effects of motional averaging on the aromatic ring-current contribution to the proton chemical shifts in proteins are examined. Atomic trajectories obtained from a 96-ps molecular dynamics simulation of the bovine pancreatic trypsin inhibitor are used in conjunction with the Johnson-Bovey model of ring-current shifts to calculate the time evolution of the proton chemical shifts. Although large high-frequency fluctuations are observed (often greater than +/- 1 ppm), the average shift values in most cases are close to those obtained from the average structure; for some protons, significant differences are found. The calculated trends are used to probe the relationship between the average structure, atomic motions, and observed values of the proton chemical shifts. It is concluded that chemical shift values are in general most sensitive to the average structure of the protein and, because of the averaging involved, cannot be used directly to probe the short time structural fluctuations.

Animals↗
PubMed1982

Mechanisms of hydrogen exchange in proteins from nuclear magnetic resonance studies of individual tryptophan indole NH hydrogens in lysozyme.

The individual rates of solvent exchange of the six tryptophan indole NH hydrogens of lysozyme in 2H2O have been measured over a wide range of temperatures by using 1H NMR. Two distinct mechanisms for exchange have been identified, one characterized by a high activation energy and the other by a much lower activation energy. The high-energy process has been shown to be associated directly with the cooperative thermal unfolding of the protein and is the dominant mechanism for exchange of the most slowly exchanging hydrogen even 15 degrees C below the denaturation temperature. Rate constants and activation for the folding and unfolding reactions were obtained from the experimental exchange rates. At low temperatures, a lower activation energy mechanism is dominant for all hydrogens, and this can be associated with local fluctuations in the protein structure which allows access of solvent. The relative exchange rates and activation energies can only qualitatively be related to the different environments of the residues in the crystal structure. There is provisional evidence that a mechanism intermediate between these two extremes may be significant for some hydrogens under restricted conditions.

Hydrogen↗
PubMed1982

Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects.

The crystal structure and a 96-ps molecular dynamics simulation used to analyze structural and motional contributions to spin-lattice (T1) relaxation times of phenylalanine and tyrosine C gamma carbons of the pancreatic trypsin inhibitor. The H beta and H delta protons geminal to C gamma are calculated to account for approximately 80% of the dipolar relaxation for each residue. Experimental T1 values for the phenylalanine residues obtained at 25 MHz are observed to be 15-25% longer than estimates based on the rigid crystal structure. It is shown how an increase in T1 can be related to order parameters for the picosecond motional averaging of the important C,H dipolar interactions, and how these order parameters can be calculated from a protein molecular dynamics trajectory.

Animals↗