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Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?

Publications by Adrian Schreyer - Mon, 19/06/2017 - 10:01
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Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?

J Chem Inf Model. 2014 Mar 24;54(3):944-55

Authors: Ballester PJ, Schreyer A, Blundell TL

Abstract
Predicting the binding affinities of large sets of diverse molecules against a range of macromolecular targets is an extremely challenging task. The scoring functions that attempt such computational prediction are essential for exploiting and analyzing the outputs of docking, which is in turn an important tool in problems such as structure-based drug design. Classical scoring functions assume a predetermined theory-inspired functional form for the relationship between the variables that describe an experimentally determined or modeled structure of a protein-ligand complex and its binding affinity. The inherent problem of this approach is in the difficulty of explicitly modeling the various contributions of intermolecular interactions to binding affinity. New scoring functions based on machine-learning regression models, which are able to exploit effectively much larger amounts of experimental data and circumvent the need for a predetermined functional form, have already been shown to outperform a broad range of state-of-the-art scoring functions in a widely used benchmark. Here, we investigate the impact of the chemical description of the complex on the predictive power of the resulting scoring function using a systematic battery of numerical experiments. The latter resulted in the most accurate scoring function to date on the benchmark. Strikingly, we also found that a more precise chemical description of the protein-ligand complex does not generally lead to a more accurate prediction of binding affinity. We discuss four factors that may contribute to this result: modeling assumptions, codependence of representation and regression, data restricted to the bound state, and conformational heterogeneity in data.

PMID: 24528282 [PubMed - indexed for MEDLINE]

Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency.

Publications by the Blundell group - Mon, 19/06/2017 - 10:01
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Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency.

J Biol Chem. 2016 Nov 18;291(47):24377-24389

Authors: Chang HH, Watanabe G, Gerodimos CA, Ochi T, Blundell TL, Jackson SP, Lieber MR

Abstract
The nonhomologous DNA end-joining (NHEJ) pathway is a key mechanism for repairing dsDNA breaks that occur often in eukaryotic cells. In the simplest model, these breaks are first recognized by Ku, which then interacts with other NHEJ proteins to improve their affinity at DNA ends. These include DNA-PKcs and Artemis for trimming the DNA ends; DNA polymerase μ and λ to add nucleotides; and the DNA ligase IV complex to ligate the ends with the additional factors, XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor/Cernunos), and PAXX (paralog of XRCC4 and XLF). In vivo studies have demonstrated the degrees of importance of these NHEJ proteins in the mechanism of repair of dsDNA breaks, but interpretations can be confounded by other cellular processes. In vitro studies with NHEJ proteins have been performed to evaluate the nucleolytic resection, polymerization, and ligation steps, but a complete system has been elusive. Here we have developed a NHEJ reconstitution system that includes the nuclease, polymerase, and ligase components to evaluate relative NHEJ efficiency and analyze ligated junctional sequences for various types of DNA ends, including blunt, 5' overhangs, and 3' overhangs. We find that different dsDNA end structures have differential dependence on these enzymatic components. The dependence of some end joining on only Ku and XRCC4·DNA ligase IV allows us to formulate a physical model that incorporates nuclease and polymerase components as needed.

PMID: 27703001 [PubMed - indexed for MEDLINE]

Categories: Publications

Structure-activity relationship of the peptide binding-motif mediating the BRCA2:RAD51 protein-protein interaction.

Publications by the Blundell group - Mon, 19/06/2017 - 10:01
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Structure-activity relationship of the peptide binding-motif mediating the BRCA2:RAD51 protein-protein interaction.

FEBS Lett. 2016 Apr;590(8):1094-102

Authors: Scott DE, Marsh M, Blundell TL, Abell C, Hyvönen M

Abstract
RAD51 is a recombinase involved in the homologous recombination of double-strand breaks in DNA. RAD51 forms oligomers by binding to another molecule of RAD51 via an 'FxxA' motif, and the same recognition sequence is similarly utilised to bind BRCA2. We have tabulated the effects of mutation of this sequence, across a variety of experimental methods and from relevant mutations observed in the clinic. We use mutants of a tetrapeptide sequence to probe the binding interaction, using both isothermal titration calorimetry and X-ray crystallography. Where possible, comparison between our tetrapeptide mutational study and the previously reported mutations is made, discrepancies are discussed and the importance of secondary structure in interpreting alanine scanning and mutational data of this nature is considered.

PMID: 26992456 [PubMed - indexed for MEDLINE]

Categories: Publications

SDM: a server for predicting effects of mutations on protein stability.

Publications by the Blundell group - Mon, 22/05/2017 - 21:16
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SDM: a server for predicting effects of mutations on protein stability.

Nucleic Acids Res. 2017 May 19;:

Authors: Pandurangan AP, Ochoa-Montaño B, Ascher DB, Blundell TL

Abstract
Here, we report a webserver for the improved SDM, used for predicting the effects of mutations on protein stability. As a pioneering knowledge-based approach, SDM has been highlighted as the most appropriate method to use in combination with many other approaches. We have updated the environment-specific amino-acid substitution tables based on the current expanded PDB (a 5-fold increase in information), and introduced new residue-conformation and interaction parameters, including packing density and residue depth. The updated server has been extensively tested using a benchmark containing 2690 point mutations from 132 different protein structures. The revised method correlates well against the hypothetical reverse mutations, better than comparable methods built using machine-learning approaches, highlighting the strength of our knowledge-based approach for identifying stabilising mutations. Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of the protein atoms), and a point mutation, the server calculates the stability difference score between the wildtype and mutant protein. The server is available at http://structure.bioc.cam.ac.uk/sdm2.

PMID: 28525590 [PubMed - as supplied by publisher]

Categories: Publications

Fragment screening against the EthR-DNA interaction by native mass spectrometry.

Publications by the Blundell group - Mon, 22/05/2017 - 21:16
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Fragment screening against the EthR-DNA interaction by native mass spectrometry.

Angew Chem Int Ed Engl. 2017 May 17;:

Authors: Chan DS, Mendes V, Thomas SE, McConnell BN, Matak-Vinković D, Coyne AG, Blundell TL, Abell C

Abstract
Native nanoelectrospray ionization mass spectrometry is an underutilized technique for fragment screening. In this study, the first demonstration is provided of the use of native mass spectrometry for screening fragments against a protein-DNA interaction. EthR is a transcriptional repressor of EthA expression in Mycobacterium tuberculosis (Mtb) that reduces the efficacy of ethionamide, a second-line anti-tubercular drug used to combat multidrug resistant Mtb strains. A small-scale fragment screening campaign was conducted against the EthR-DNA interaction using native mass spectrometry, and results were compared with those from differential scanning fluorimetry, a commonly used primary screening technique. Hits were validated using surface plasmon resonance and X-ray crystallography. The screening campaign identified two new fragments that disrupt the EthR-DNA interaction in vitro (IC50 = 460 μM to 610 μM) and that bind to the hydrophobic channel of the EthR dimer.

PMID: 28513917 [PubMed - as supplied by publisher]

Categories: Publications

XSuLT: a web server for structural annotation and representation of sequence-structure alignments.

Publications by the Blundell group - Mon, 22/05/2017 - 21:16
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XSuLT: a web server for structural annotation and representation of sequence-structure alignments.

Nucleic Acids Res. 2017 May 16;:

Authors: Ochoa-Montaño B, Blundell TL

Abstract
The web server XSuLT, an enhanced version of the protein alignment annotation program JoY, formats a submitted multiple-sequence alignment using three-dimensional (3D) structural information in order to assist in the comparative analysis of protein evolution and in the optimization of alignments for comparative modelling and construct design. In addition to the features analysed by JoY, which include secondary structure, solvent accessibility and sidechain hydrogen bonds, XSuLT annotates each amino acid residue with residue depth, chain and ligand interactions, inter-residue contacts, sequence entropy, root mean square deviation and secondary structure and disorder prediction. It is also now integrated with built-in 3D visualization which interacts with the formatted alignment to facilitate inspection and understanding. Results can be downloaded as stand-alone HTML for the formatted alignment and as XML with the underlying annotation data. XSuLT is freely available at http://structure.bioc.cam.ac.uk/xsult/.

PMID: 28510698 [PubMed - as supplied by publisher]

Categories: Publications

Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance.

Publications by the Blundell group - Tue, 16/05/2017 - 22:34
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Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance.

Biochem Soc Trans. 2017 Apr 15;45(2):303-311

Authors: Pandurangan AP, Ascher DB, Thomas SE, Blundell TL

Abstract
For over four decades structural biology has been used to understand the mechanisms of disease, and structure-guided approaches have demonstrated clearly that they can contribute to many aspects of early drug discovery, both computationally and experimentally. Structure can also inform our understanding of impacts of mutations in human genetic diseases and drug resistance in cancers and infectious diseases. We discuss the ways that structural insights might be useful in both repurposing off-licence drugs and guide the design of new molecules that might be less susceptible to drug resistance in the future.

PMID: 28408471 [PubMed - indexed for MEDLINE]

Categories: Publications
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