I03-Macromolecular Crystallography
|
Rob
Barringer
,
Alice E.
Parnell
,
Aleix
Lafita
,
Vivian
Monzon
,
Catherine R.
Back
,
Mariusz
Madej
,
Jan
Potempa
,
Angela H.
Nobbs
,
Steven G.
Burston
,
Alex
Bateman
,
Paul R.
Race
Diamond Proposal Number(s):
[23269]
Abstract: Bacterial fibrillar adhesins are specialised extracellular polypeptides that promote the attachment of bacteria to the surfaces of other cells or materials. Adhesin-mediated interactions are critical for the establishment and persistence of stable bacterial populations within diverse environmental niches and are important determinants of virulence. The fibronectin (Fn) binding fibrillar adhesin CshA, and its paralogue CshB, play important roles in host colonisation by the oral commensal and opportunistic pathogen Streptococcus gordonii. As paralogues are often catalysts for functional diversification, we have probed the early stages of structural and functional divergence in Csh proteins by determining the X-ray crystal structure of the CshB adhesive domain NR2 and characterising its Fn binding properties in vitro. Despite sharing a common fold, CshB_NR2 displays an ~1.7-fold reduction in Fn binding affinity relative to CshA_NR2. This correlates with reduced electrostatic charge in the Fn binding cleft. Complementary bioinformatic studies reveal that homologues of CshA/B_NR2 domains are widely distributed in both Gram-positive and Gram-negative bacteria, where they are found housed within functionally cryptic multi-domain polypeptides. Our findings are consistent with the classification of Csh adhesins and their relatives as members of the recently defined Polymer Adhesin Domain (PAD) family of bacterial proteins.
|
Mar 2023
|
|
I03-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[13467]
Abstract: Bacteria are equipped with a diverse set of regulatory tools that allow them to quickly adapt to their environment. The RimK system allows for Pseudomonas spp. to adapt through post-transcriptional regulation by altering the ribosomal subunit RpsF. RimK is found in a wide range of bacteria with a conserved amino acid sequence, however the genetic context and the role of this protein is highly diverse. By solving and comparing the structures of RimK homologues from two related but functionally divergent systems, we uncovered key structural differences that likely contribute to the different activity levels of each of these homologues. Moreover, we were able to clearly resolve the active site of this protein for the first time, resolving binding of the glutamate substrate. This work advances our understanding of how subtle differences in protein sequence and structure can have profound effects on protein activity, which can in turn result in widespread mechanistic changes.
|
Sep 2022
|
|
|
|
Open Access
Abstract: Motivation: Data normalization is an essential step to reduce technical variation within and between arrays. Due to the different karyotypes and the effects of X chromosome inactivation, females and males exhibit distinct methylation patterns on sex chromosomes, thus it poses a significant challenge to normalise sex chromosome data without introducing bias. Currently, existing methods do not provide unbiased solutions to normalise sex chromosome data, usually, they just process autosomal and sex chromosomes indiscriminately.
Results: Here, we demonstrate that ignoring this sex difference will lead to introducing artificial sex bias, especially for thousands of autosomal CpGs. We present a novel two-step strategy (interpolatedXY) to address this issue, which is applicable to all quantile-based normalisation methods. By this new strategy, the autosomal CpGs are first normalised independently by conventional methods, such as funnorm or dasen; then the corrected methylation values of sex chromosome linked CpGs are estimated as the weighted average of their nearest neighbours on autosomes. The proposed two-step strategy can also be applied to other non-quantile-based normalisation methods, as well as other array-based data types. Moreover, we propose a useful concept: the sex explained fraction of variance, to quantitatively measure the normalisation effect.
Availability: The proposed methods are available by calling the function ‘adjustedDasen’ or ‘adjustedFunnorm’ in the latest wateRmelon package (https://github.com/schalkwyk/wateRmelon), with methods compatible with all the major workflows, including minfi.
|
Jun 2022
|
|
B22-Multimode InfraRed imaging And Microspectroscopy
|
Open Access
Abstract: Motivation: With continually improved instrumentation, Fourier transform infrared (FTIR) microspectroscopy can now be used to capture thousands of high-resolution spectra for chemical characterisation of a sample. The spatially resolved nature of this method lends itself well to histological profiling of complex biological specimens. However, current software can make joint analysis of multiple samples challenging and, for large datasets, computationally infeasible. Results: To overcome these limitations, we have developed Photizo – an open-source Python library enabling high-throughput spectral data pre-processing, visualisation and downstream analysis, including principal component analysis, clustering, macromolecular quantification and mapping. Photizo can be used for analysis of data without a spatial component, as well as spatially-resolved data, obtained e.g. by scanning mode IR microspectroscopy and IR imaging by focal plane array (FPA) detector. Availability: The code underlying this article is available at https://github.com/DendrouLab/Photizo with access to example data available at https://zenodo.org/record/6417982#.Yk2O9TfMI6A.
|
May 2022
|
|
I03-Macromolecular Crystallography
|
Leila T.
Alexander
,
Rosalba
Lepore
,
Andriy
Kryshtafovych
,
Athanasios
Adamopoulos
,
Markus
Alahuhta
,
Ann M.
Arvin
,
Yannick J.
Bomble
,
Bettina
Böttcher
,
Cécile
Breyton
,
Valerio
Chiarini
,
Naga Babu
Chinnam
,
Wah
Chiu
,
Krzysztof
Fidelis
,
Rhys
Grinter
,
Gagan D.
Gupta
,
Marcus D.
Hartmann
,
Christopher S.
Hayes
,
Tatjana
Heidebrecht
,
Andrea
Ilari
,
Andrzej
Joachimiak
,
Youngchang
Kim
,
Romain
Linares
,
Andrew L.
Lovering
,
Vladimir V.
Lunin
,
Andrei N.
Lupas
,
Cihan
Makbul
,
Karolina
Michalska
,
John
Moult
,
Prasun K.
Mukherjee
,
William
Nutt
,
Stefan L.
Oliver
,
Anastassis
Perrakis
,
Lucy
Stols
,
John A.
Tainer
,
Maya
Topf
,
Susan E.
Tsutakawa
,
Mauricio
Valdivia‐delgado
,
Torsten
Schwede
Open Access
Abstract: The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.
|
Dec 2021
|
|
|
|
Abstract: We report here an assessment of the model refinement category of the 14th round of Critical Assessment of Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range of starting quality. The ability of groups to accurately rank their submissions and to predict coordinate error varied widely. Overall only four groups out-performed a “naïve predictor” corresponding to resubmission of the starting model. Among the top groups there are interesting differences of approach and in the spread of improvements seen: some methods are more conservative, others more adventurous. Some targets were “double-barrelled” for which predictors were offered a high-quality AlphaFold 2 (AF2)-derived prediction alongside another of lower quality. The AF2-derived models were largely unimprovable, many of their apparent errors being found to reside at domain and, especially, crystal lattice contacts. Refinement is shown to have a mixed impact overall on structure-based function annotation methods to predict nucleic acid binding, spot catalytic sites and dock protein structures.
|
Jul 2021
|
|
|
|
Jose Ramon
Macias
,
Ruben
Sanchez-Garcia
,
Pablo
Conesa
,
Erney
Ramirez-Aportela
,
Marta
Martinez Gonzalez
,
Carlos
Wert-Carvajal
,
Alberto M.
Parra-Perez
,
Joan
Segura Mora
,
Sam
Horrell
,
Andrea
Thorn
,
Carlos O. S.
Sorzano
,
Jose Maria
Carazo
Open Access
Abstract: The web platform 3DBionotes-WS integrates multiple Web Services and an interactive Web Viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic Electron Microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions. At the same time, a plethora of new genomics and interactomics information (including fragment screening and structure-based virtual screening efforts) have been made available from different servers. In this context we have developed 3DBionotes-COVID-19 as an answer to: (1) The need to explore multi-omics data in a unified context with a special focus on structural information and (2) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryogenic Electron Microscopy.
|
May 2021
|
|
I04-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[19190, 17167]
Abstract: Symmetric proteins are currently of interest as they allow creation of larger assemblies and facilitate the incorporation of metal ions in the larger complexes. Recently this was demonstrated by the biomineralization of the cadmium‐chloride nanocrystal via the Pizza designer protein. However, the mechanism behind this formation remained unclear. Here, we set out to investigate the mechanism driving the formation of this nanocrystal via truncation, mutation, and circular permutations. In addition, the interaction of other biologically relevant metal ions with these symmetric proteins to form larger symmetric complexes was also studied. The formation of the initial nanocrystal is shown to originate from steric strain, where His 58 induces a different rotameric conformation on His 73, thereby distorting an otherwise perfect planar ring of alternating cadmium and chlorine ions, resulting in the smallest nanocrystal. Similar highly symmetric complexes were also observed for the other biological relevant metal ions. However, the flexibility of the coordinating histidine residues allows each metal ion to adopt its preferred geometry leading to either monomeric or dimeric β‐propeller units, where the metal ions are located at the interface between both propeller units. These results demonstrate that symmetric proteins are not only interesting to generate larger assemblies, but are also the perfect scaffold to create more complex metal based assemblies. Such metal protein assemblies may then find applications in bionanotechnology or biocatalysis.
|
Mar 2021
|
|
|
|
Open Access
Abstract: Covariance-based predictions of residue contacts and inter-residue distances are an increasingly popular data type in protein bioinformatics. Here we present ConPlot, a web-based application for convenient display and analysis of contact maps and distograms. Integration of predicted contact data with other predictions is often required to facilitate inference of structural features. ConPlot can therefore use the empty space near the contact map diagonal to display multiple coloured tracks representing other sequence-based predictions. Popular file formats are natively read and bespoke data can also be flexibly displayed. This novel visualisation will enable easier interpretation of predicted contact maps.
|
Jan 2021
|
|
I04-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[22637]
Abstract: Conversion of 10‐hydroxygeraniol to 10‐oxogeranial is a crucial step in iridoid biosynthesis. This reaction is catalyzed by a zinc‐dependent alcohol dehydrogenase, 10‐hydroxygeraniol dehydrogenase, belonging to the family of medium‐chain dehydrogenase/reductase (MDR). Here, we report the crystal structures of a novel 10‐hydroxygeraniol dehydrogenase from Catharanthus roseus in its apo and nicotinamide adenine dinucleotide phosphate (NADP+) bound forms. Structural analysis and docking studies reveal how subtle conformational differences of loops L1, L2, L3, and helix α9' at the orifice of the catalytic site confer differential activity of the enzyme toward various substrates, by modulating the binding pocket shape and volume. The present study, first of its kind, provides insights into the structural basis of substrate specificity of MDRs specific to linear substrates. Furthermore, comparison of apo and NADP+ bound structures suggests that the enzyme adopts open and closed states to facilitate cofactor binding.
|
Mar 2020
|
|
