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Biomedical subjects

J M Goodfellow

Publications and source records attributed to J M Goodfellow.

At least 19 recordsLinked to original sources
PubMed1999

DNA conformation and dynamics.

Nucleotide conformation and dynamics are important for the study of radiation damage to DNA at the atomic level. It is necessary to study not only normal oligonucleotide structure but also those containing modified bases which result from interaction with OH-radicals. There are now over 8000 atomic coordinate entries in the Brookhaven Protein Data Bank, of which over 900 relate to experimentally determined structures of nucleic acids and nucleic acid/protein complexes. We review some of these data which have led to the elucidation of novel DNA conformations, insight into DNA sequence specificity and knowledge of protein/DNA interactions. Further understanding of the conformation, stability and dynamics of nucleic acids has come from molecular modelling. We have used such techniques to study chemical modifications to bases such as alkylation of thymine and guanine and the effects of curvature in longer sequences. Recent improvements in this area include the inclusions of explicit counter-ions and solvent molecules, the use of Particle Mesh Ewald methods to incorporate the long-range electrostatic interactions and the use of longer time scale simulations. We have employed these methods to analyse the effects of incorporation of 8-oxodeoxyguanosine into duplex DNA. This lesion is a common result of radiation damage and is known to have important effects in mutagenesis, cancer and ageing.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed1998

The pH-induced release of iron from transferrin investigated with a continuum electrostatic model.

A reduction in pH induces the release of iron from transferrin in a process that involves a conformational change in the protein from a closed to an open form. Experimental evidence suggests that there must be changes in the protonation states of certain, as yet not clearly identified, residues in the protein accompanying this conformational change. Such changes in protonation states of residues and the consequent changes in electrostatic interactions are assumed to play a large part in the mechanism of release of iron from transferrin. Using the x-ray crystal structures of human ferri- and apo-lactoferrin, we calculated the pKa values of the titratable residues in both the closed (iron-loaded) and open (iron-free) conformations with a continuum electrostatic model. With the knowledge of a residue's pKa value, its most probable protonation state at any specified pH may be determined. The preliminary results presented here are in good agreement with the experimental observation that the binding of ferric iron and the synergistic anion bicarbonate/carbonate results in the release of approximately three H+ ions. It is suggested that the release of these three H+ ions may be accounted for, in most part, by the deprotonation of the bicarbonate and residues Tyr-92, Lys-243, Lys-282, and Lys-285 together with the protonation of residues Asp-217 and Lys-277.

Apoproteins↗
PubMed1998

The intrinsic curvature of a 51 bp K-DNA fragment of Leishmania tarentolae: a molecular model.

DNA intrinsic structure and curvature is a subject of debate because of the importance of these attributes in processes such as DNA packaging, transcription, and gene regulation. X-ray crystallography of DNA single crystals has provided a wealth of information about the local, short range conformational features of DNA. On the other hand, gel electrophoresis analysis of DNA has not only uncovered the macroscopic curvature of DNA but it also provides most of the available data on DNA intrinsic curvature. However, gel electrophoresis can not identify features of DNA structure at the nucleotide or atomic level. In order to address the problem of DNA intrinsic curvature in an attempt to bridge the gap between X-ray crystallography and gel electrophoresis, we use the computational method of molecular dynamics (MD). In this study, we report the results of 2.0 ns MD simulations on a 51 bp fragment of the K-DNA of Leishmania tarentolae containing several A-tracts. The K-DNA double helix is very stable and remains in an intermediate state between the canonical A and B forms of the duplex. The magnitude of global curvature (75 degrees) agrees well with the experimental estimate (72 degrees) available. Analysis of local (every base triplet) and sublocal (every helix turn) curvature shows that the 51 bp K-DNA fragment has curvature features also present in the Wedge, Junction and Calladine's models of DNA intrinsic curvature. We further characterize the flexibility of individual nucleotides in the molecule and find the sugar flexibility within the A-tracts to be strongly correlated with the pattern of A-tract cleavage by the hydroxyl radical. Differential curvature and flexibility at the 5' and 3'junctions between A-tracts and general-sequence DNA are found to modulate the global curvature of the K-DNA fragment.

Animals↗
PubMed1998

The biological implications of damage to DNA incorporating an 8-oxodeoxyguanine:cytosine basepair.

DNA damage produced by free radicals is probably the most frequent lesion encountered by cells (Wallace, S.S., Environmental and Molecular Mutagenesis 12, 431-477, 1988 (1)). One of the most common effects is the formation of 7-hydro-8-oxodeoxyguanine due to oxygen radicals interacting with the normal guanine base. Such chemical changes appear to be important in mutagenesis, cancer and aging. We have used computer simulation techniques to model the effect of inclusion of such a modified base within a duplex strand of DNA. We find that such modifications can be stabilized within a normal sequence. The conformation of the modified base relative to the sugar residue depends on many local interactions not accessible to the isolated nucleoside. We have also studied the essential dynamics of both normal and modified sequences and show that there are only subtle changes to the dynamics on inclusion of such a modification.

Base Pairing↗
PubMed1997

Modelling protein unfolding: hen egg-white lysozyme.

A novel modelling procedure, which rapidly unfolds a protein by enhancing solvent penetration of its core, was used to investigate the unfolding pathway of hen egg-white lysozyme. Early on the unfolding pathway there is a dramatic disruption of the tertiary contacts within the protein, which decouples its domains. Subsequently, the helical domain slowly loses its compactness and the helices fluctuate rapidly. The protein then adopts a 'molten globule-like' structure in which the native beta-sheet is essentially intact. The modelled structures have properties similar to those of lysozyme's experimentally characterized partially folded states and provide insight into its complex (un)folding process. The sequence of unfolding events shows how the unfolding pathway of a multidomain protein may be most similar to its fastest, but not necessarily its dominant, folding pathway.

Animals↗
PubMed1996

Hydrophobic solvation in aqueous trifluoroethanol solution.

The titration of an aqueous solution of a de novo designed peptide with trifluoroethanol (TFE) shows complete helix formation with the addition of only 30% TFE. A molecular simulation of the peptide, in which a single shell of TFE molecules initially surrounds the peptide, reveals preferred sites of solvent interaction. The TFE molecules show greater preference for the hydrophobic compared with hydrophilic side chains. The helix-enhancing ability of TFE in aqueous solution may be rationalized in terms of stabilizing the hydrophobic collapse of apolar side chains of the formed helix.

Amino Acid Sequence↗
PubMed1995

Competing interactions contributing to alpha-helical stability in aqueous solution.

The stability of a 15-residue peptide has been investigated using CD spectroscopy and molecular simulation techniques. The sequence of the peptide was designed to include key features that are known to stabilize alpha-helices, including ion pairs, helix dipole capping, peptide bond capping, and aromatic interactions. The degree of helicity has been determined experimentally by CD in three solvents (aqueous buffer, methanol, and trifluoroethanol) and at two temperatures. Simulations of the peptide in the aqueous system have been performed over 500 ps at the same two temperatures using a fully explicit solvent model. Consistent with the CD data, the degree of helicity is decreased at the higher temperature. Our analysis of the simulation results has focused on competition between different side-chain/side-chain and side-chain/main-chain interactions, which can, in principle, stabilize the helix. The unfolding in aqueous solution occurs at the amino terminus because the side-chain interactions are insufficient to stabilize both the helix dipole and the peptide hydrogen bonds. Loss of capping of the peptide backbone leads to water insertion within the first peptide hydrogen bond and hence unfolding. In contrast, the carboxy terminus of the alpha-helix is stable in both simulations because the C-terminal lysine residue stabilizes the helix dipole, but at the expense of an ion pair.

Amino Acid Sequence↗
PubMed1995

A knowledge-based model of DNA hydration.

The aqueous hydration of DNA is an important aspect of its structure, which is of direct relevance to mechanisms of radiation damage. We have made a quantitative analysis of solvent interactions within hydrogen bonding distance of polar atoms of oligonucleotides using 12 B-DNA oligonucleotide crystal structures. The distribution of water molecules around the four bases, the sugar residues and the phosphate groups were generated and analysed both qualitatively and quantitatively. These data have then been used in a knowledge-based method to generate the likely hydration sites around a canonical B-DNA conformation in order to generate models of use in track studies of radiation damage.

Base Sequence↗
PubMed1995

Solvent interactions with pi ring systems in proteins.

The interaction of water molecules with apolar amino acids is an important aspect of the hydrophobic effect and hence of protein folding. Our distributed multiple electrostatic model for water interacting with phenylalanine dipeptides shows that minimum energy sites exist above the aromatic ring such that a solvent molecule can interact with the pi electrons, but only when this site is not blocked by main-chain atoms or disturbed by main-chain polar atoms. This is consistent with the experimental evidence of others that water can hydrogen bond to aromatic pi electrons. In contrast, our analysis of solvent interactions with phenylalanine residues based on 48 high-resolution, well-refined protein structures shows that the dominant interaction of solvent molecules is with the edge of the ring and not with the pi elections. As the faces of phenylalanine rings tend to be buried, and solvent interactions with neighbouring polar atoms are more favourable, the interaction of water molecules with the faces of aromatic pi rings appears not to occur frequently in proteins.

Crystallography↗
PubMed1994

Adenine.methylthymine base-pairs enhance non-uniformity in DNA helices.

Nitroso compounds are known to induce mutations and cancer. Here we study the effect of methylation of O4 of thymine by nitroso compounds on the structure and dynamics of DNA helices. Four dodecamers, for which there exist experimental data obtained by NMR techniques, are studied using very long (approximately 1 ns) molecular dynamics simulations. The conformations obtained are in good agreement with the NMR data. A statistical analysis indicates that DNA in solution adopts conformations which are intermediate between those of the ideal DNA families, such as A and B-DNA. Also, the structures obtained in these molecular dynamics simulations possess a greater degree of non-uniformity than the crystal structures. Most importantly, the helices containing adenine.methylthymine base-pairs show a further enhancement in non-uniformity. A biological role for the enhanced nonuniformity is suggested.

Adenine↗
PubMed1994

Buried waters and internal cavities in monomeric proteins.

We have analyzed the buried water molecules and internal cavities in a set of 75 high-resolution, nonhomologous, monomeric protein structures. The number of hydrogen bonds formed between each water molecule and the protein varies from 0 to 4, with 3 being most common. Nearly half of the water molecules are found in pairs or larger clusters. Approximately 90% are shown to be associated with large cavities within the protein, as determined by a novel program, PRO_ACT. The total volume of a protein's large cavities is proportional to its molecular weight and is not dependent on structural class. The largest cavities in proteins are generally elongated rather than globular. There are many more empty cavities than hydrated cavities. The likelihood of a cavity being occupied by a water molecule increases with cavity size and the number of available hydrogen bond partners, with each additional partner typically stabilizing the occupied state by 0.6 kcal/mol.

Camphor 5-Monooxygenase↗
PubMed1994

Molecular dynamics simulations of oligonucleotides in solution: visualization of intrinsic curvature.

We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG).d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman and NMR spectroscopy and cyclization kinetics. Our method of analysis allows us to visualise the curvature of the helix as a function of time during the simulation. We find that the major distortions of the helix axis path occur at the junctions between the (essentially straight) A-tract and the CG- and GC-tracts, although at one junction this is due to hyperflexibility (i.e., regions of high flexibility with no preferred direction of curvature), while at the other junction a static curvature is found (i.e., a preferred, sustained direction of curvature).

Base Sequence↗
PubMed1994

DNA structure, hydration and dynamics.

Although the double helical model of DNA structure is now 40 years old, there is still considerable effort being made to elucidate the range of conformations that can be adopted by this flexible molecule. We review the current state of our knowledge of DNA structure which is available from both experimental and computational approaches.

DNA↗
PubMed1994

Flexibility and curvature of DNA duplexes containing O4-methylthymine: implications for DNA repair.

Nitroso compounds are known to induce mutations and cancer. We study the effect of one of their products, O4-methylthymine, on the structure and flexibility of DNA sequences. In particular, we focus on aspects of DNA that are relevant for the interaction with the repair protein, O6-alkylguanine-DNA alkyltransferase. In general, sequences that contain O4-methylthymine have greater local curvatures. Sequences in which O4-methylthymine is paired with adenine have larger regions of increased flexibility, a consistent bend in the direction of the major groove and strong oscillations in the major groove widths. On the other hand, sequences in which O4-methylthymine is paired with guanine have only sites of increased flexibility, short regions bent towards the major groove alternating with sites bent toward the minor groove and larger major groove widths than those of canonical B-DNA. These features may possibly lead to the difference in the efficiency with which repair proteins correct the lesions in the two base pairs. Further experimental data are needed to make more definitive conclusions.

Alkylation↗
PubMed1993

Distribution of solvent molecules around apolar side-chains in protein crystals.

We have analysed the distribution of solvent sites within 5.0 A of the apolar side-chains alanine, valine, leucine, isoleucine and phenylalanine based on experimental data from 24 high-resolution protein structures. Clustering of solvent molecules into specific regions can be seen superimposed on a broad background of sites. The non-random nature of these distributions is confirmed by quantitative analysis of the solvent sites according to a spherical polar (r, theta and phi) co-ordinate system with the apolar atom of interest at the centre. One of the general features of these solvent sites is that they peak at around 4.0 A from an apolar protein carbon atom. Preferences in orientation (theta and phi) are also seen in the solvent distributions especially around the alanine CB atom and the phenylalanine ring. Most (around 75%) of the solvent sites around apolar groups are also within hydrogen bonding distance of protein (main chain) polar groups which leads to a distribution dependent on the local secondary structure. The remaining 25% of solvent sites are referred to as "non-polar" water molecules and their crystallographic temperature factors are higher than average by between 15% to 28%. For alanine and phenylalanine there are enough data to show that water molecules not within hydrogen bonding distance of protein polar atoms also cluster into specific regions. However, the main conclusion appears to be that the hydrophobic hydration in protein crystals is correlated with hydration of polar groups and thus depends on the local environment as well as on the stereochemistry of the apolar atoms.

Alanine↗
PubMed1993

The pore dimensions of gramicidin A.

The ion channel forming peptide gramicidin A adopts a number of distinct conformations in different environments. We have developed a new method to analyze and display the pore dimensions of ion channels. The procedure is applied to two x-ray crystal structures of gramicidin that adopt distinct antiparallel double helical dimer conformations and a nuclear magnetic resonance (NMR) structure for the beta6.3 NH2-terminal to NH2-terminal dimer. The results are discussed with reference to ion conductance properties and dependence of pore dimensions on the environment.

Amino Acid Sequence↗