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Garib N Murshudov

Publications and source records attributed to Garib N Murshudov.

13 recordsLinked to original sources
PubMed2005

Intensity statistics in twinned crystals with examples from the PDB.

Entries deposited in the Protein Data Bank as of February 2004 for which both model and X-ray data were available were analysed to identify cases of twinning using such simple statistics as the R factor between potential twin-related reflections. Careful consideration of all identified twins showed that in many cases twinning was ignored during structure solution and refinement. Manual analysis of the models showed that twinning often occurs in association with rotational pseudosymmetry parallel to the twinning operator. The coexistence of these two phenomena complicates the detection and diagnostics of twinning using currently available twinning tests. It was concluded that a twinning-detection step should be incorporated in every stage of structure analysis from data acquisition to refinement and validation.

Algorithms↗
PubMed2005

Variable role of ions in two drug intercalation complexes of DNA.

The crystal structures of the hexamer duplex d(CGTACG)(2) complexed with the intercalating anthraquinone derivative 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione and the acridine derivative 9-acridinyl tetralysine have been solved at 2.0- and 1.4-A resolution, respectively. In both cases, the drugs adopt multiple orientations within a large DNA cavity constituted by two groups of four approximately coplanar bases. Cations play a pivotal role in the crystal structure. Both complexes crystallise in the presence of Co(2+), Ba(2+) and Na(+) ions. They reveal at least two different types of coordination environments: (1) specific sites for Co(2+) interacting with N7 of guanine; (2) a central ionic site formed by four phosphate groups, which can be occupied by different ions. One more ionic site that is not always occupied by ions is also visible in the electron density map. All of them play a role in the crystal structure.

Acridines↗
PubMed2005

Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine.

Purine metabolism in the parasite Plasmodium has been identified as a promising target for antimalarial therapies. Purine nucleoside phosphorylase (PNP) is part of a salvage pathway for the biosynthesis of purines, which are essential for parasite survival. Two crystal structures of PNP from Plasmodium falciparum (PfPNP) in two space groups, each with a single subunit in the asymmetric unit, are described here. One structure, refined to 2.4 A, has an empty nucleoside-binding site and a sulfate ion bound in the phosphate-binding pocket. The second structure, refined to 2.0 A, has the substrate inosine bound to the active centre. Structure comparison reveals alterations in the active site upon ligand binding. The new structures presented here specifically highlight the likely roles of Asp206 and two loops flanking the active site: the beta7-alpha6 loop (residues approximately 161-169) and the beta9-alpha8 loop (residues approximately 208-223). Comparison with PNP in complex with transition-state inhibitors suggests that the purine substrate moves towards the phosphate substrate, rather than vice versa, upon forming the transition state. The single-substrate-containing PfPNP structures also appear to be more flexible than PfPNP bound to inhibitors. Together, these structures serve as a basis for better understanding of ligand binding and mechanism that can be further exploited to optimize the specificity of anti-PfPNP drugs.

Animals↗
PubMed2004

Direct incorporation of experimental phase information in model refinement.

The incorporation of prior phase information into a maximum-likelihood formalism has been shown to strengthen model refinement. However, the currently available likelihood refinement target using prior phase information has shortcomings; the 'phased' refinement target considers experimental phase information indirectly and statically in the form of Hendrickson-Lattman coefficients. Furthermore, the current refinement target implicitly assumes that the prior phase information is independent of the calculated model structure factor. This paper describes the derivation of a multivariate likelihood function that overcomes these shortcomings and directly incorporates experimental phase information from a single-wavelength anomalous diffraction (SAD) experiment. This function, which simultaneously refines heavy-atom and model parameters, has been implemented in the refinement program REFMAC5. The SAD function used in conjunction with the automated model-building procedures of ARP/wARP leads to a successful solution when current likelihood functions fail in a test case shown.

Algorithms↗
PubMed2004

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.

Chemical Phenomena↗
PubMed2004

Developments in the CCP4 molecular-graphics project.

Progress towards structure determination that is both high-throughput and high-value is dependent on the development of integrated and automatic tools for electron-density map interpretation and for the analysis of the resulting atomic models. Advances in map-interpretation algorithms are extending the resolution regime in which fully automatic tools can work reliably, but at present human intervention is required to interpret poor regions of macromolecular electron density, particularly where crystallographic data is only available to modest resolution [for example, I/sigma(I) < 2.0 for minimum resolution 2.5 A]. In such cases, a set of manual and semi-manual model-building molecular-graphics tools is needed. At the same time, converting the knowledge encapsulated in a molecular structure into understanding is dependent upon visualization tools, which must be able to communicate that understanding to others by means of both static and dynamic representations. CCP4 mg is a program designed to meet these needs in a way that is closely integrated with the ongoing development of CCP4 as a program suite suitable for both low- and high-intervention computational structural biology. As well as providing a carefully designed user interface to advanced algorithms of model building and analysis, CCP4 mg is intended to present a graphical toolkit to developers of novel algorithms in these fields.

Algorithms↗
PubMed2004

Crystallization and preliminary X-ray diffraction studies of a fungal hydrolase from Ophiostoma novo-ulmi.

Dutch elm disease fungus Ophiostoma novo-ulmi contains a hydrolase activity which catalyses the resolution of racemic ethyl naproxen to the corresponding acid. The recombinant enzyme has been crystallized by the vapour-diffusion method in two crystal forms. The crystals of the first form belong to space group P2(1)2(1)2, with unit-cell parameters a = 115.9, b = 174.4, c = 62.1 A. The enzyme also crystallizes in space group P2(1)2(1)2, with unit-cell parameters a = 72.9, b = 212.7, c = 61.7 A. Synchrotron data have been collected for both crystal forms to 2.6 and 2.3 A, respectively. A molecular-replacement solution has been found using a remote starting model of a bacterial esterase (23% sequence identity) for both crystal forms. Multicrystal averaging has resulted in interpretable electron-density maps.

Ascomycota↗
PubMed2004

DNA variability in five crystal structures of d(CGCAATTGCG).

The deoxyoligonucleotide d(CGCAATTGCG) has previously been crystallized in four different space groups. The crystals diffract to moderate resolution (2.3-2.9 A). Here, a fifth crystal form that diffracts to higher resolution (1.6 A) is presented which was obtained thanks to the use of Co2+ and cryogenic temperatures. The availability of five different crystal structures allows a thorough analysis of the conformational variability of this DNA sequence. It is concluded that the central hexamer sequence CAATTG has a practically constant conformation under all conditions, whilst the terminal base pairs at both ends vary considerably as a result of differing interactions in the crystals. The new crystal structure presented here is stabilized by guanine-Co2+-guanine interactions and the formation of C1+ -G8.C3 triplexes between neighbouring duplexes. As a result of the higher resolution of the crystal structure, a more regular structure was obtained and a clear definition of the spine of hydration was observed which was not visible in the four previous structures.

Base Pairing↗
PubMed2003

Fisher's information in maximum-likelihood macromolecular crystallographic refinement.

Fisher's information is a statistical quantity related to maximum-likelihood theory. It is a matrix defined as the expected value of the squared gradient of minus the log-likelihood function. This matrix is positive semidefinite for any parameter value. Fisher's information is used in the quasi-Newton scoring method of minimization to calculate the shift vectors of model parameters. If the matrix is non-singular, the scoring-minimization step is always downhill. In this article, it is shown how the scoring method can be applied to macromolecular crystallographic refinement. It is also shown how the computational costs involved in calculation of the Fisher's matrix can be efficiently reduced. Speed is achieved by assuming a continuous distribution of reciprocal-lattice points. Matrix elements calculated with this method agree very well with those calculated analytically. The scoring algorithm has been implemented in the program REFMAC5 of the CCP4 suite. The Fisher's matrix is used in its sparse approximation. Tests indicate that the algorithm performs satisfactorily.

Algorithms↗
PubMed2002

The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.

The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.

Amino Acid Sequence↗
PubMed2002

Structural origins of the functional divergence of human insulin-like growth factor-I and insulin.

Human insulin-like growth factors I and II (hIGF-I, hIGF-II) are potent stimulators of cell and growth processes. They display high sequence similarity to both the A and B chains of insulin but contain an additional connecting C-domain, which reflects their secretion without specific packaging or precursor conversion. IGFs also have an extension at the C-terminus known as the D-domain. This paper describes four homologous hIGF-1 structures, obtained from crystals grown in the presence of the detergent SB12, which reveal additional detail in the C- and D-domains. Two different detergent binding modes observed in the crystals may reflect different hIGF-I biological properties such as the interaction with IGF binding proteins and self-aggregation. While the helical core of hIGF-I is very similar to that in insulin, there are distinct differences in the region of hIGF-I corresponding to the insulin B chain C-terminus, residues B25-B30. In hIGF-I, these residues (24-29) and the following C-domain form an extensive loop protruding 20 A from the core, which results in a substantially different conformation for the receptor binding epitope in hIGF-I compared to insulin. One notable feature of the structures presented here is demonstration of peptide-bond cleavage between Ser35 and Arg36 resulting in an apparent gap between residues 35 and 39. The equivalent region of proinsulin is involved in hormone processing demanding a reassessment of the structural integrity of hIGF-I in relation to its biological function.

Amino Acid Sequence↗