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A novel likely pathogenic CLCN5 variant in Dent's disease. BMC Nephrol 2023; 24:256. [PMID: 37641036 PMCID: PMC10463507 DOI: 10.1186/s12882-023-03292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/07/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND The majority of cases of Dent's disease are caused by pathogenic variants in the CLCN5 gene, which encodes a voltage-gated chloride ion channel (ClC-5), resulting in proximal tubular dysfunction. We present three members of the same family and one unrelated paediatric patient with the same insertion-deletion CLCN5 variant. The identification of these patients and positive familial segregation led to the re-classification of this variant from one of unknown significance to one of likely pathogenicity. CASE PRESENTATION A 41 year old male presented with end stage kidney failure, proteinuria and haematuria. Whole genome sequencing identified an insertion-deletion variant in CLCN5, resulting in a missense change (c.1744_1745delinsAA p.(Ala582Lys)). His brother and nephew, who both exhibited renal impairment, haematuria, proteinuria, glycosuria and nephrocalcinosis, were found to have the same variant. In addition, genetic testing of an unrelated paediatric patient who presented with proteinuria and hypercalciuria, demonstrated the same variant. CONCLUSIONS The identification of this novel variant in four individuals with features of Dent's disease, has led to the re-classification of the variant to one of likely pathogenicity. As a result, our patients and any future patients with the same variant can be offered a likely diagnosis, without the need for kidney biopsy, and their family members can be offered genetic screening.
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A Retrospective on the Development of Methods for the Analysis of Protein Conformational Ensembles. Protein J 2023:10.1007/s10930-023-10113-9. [PMID: 37072659 DOI: 10.1007/s10930-023-10113-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 04/20/2023]
Abstract
Analysing protein conformational ensembles whether from molecular dynamics (MD) simulation or other sources for functionally relevant conformational changes can be very challenging. In the nineteen nineties dimensional reduction methods were developed primarily for analysing MD trajectories to determine dominant motions with the aim of understanding their relationship to function. Coarse-graining methods were also developed so the conformational change between two structures could be described in terms of the relative motion of a small number of quasi-rigid regions rather than in terms of a large number of atoms. When these methods are combined, they can characterize the large-scale motions inherent in a conformational ensemble providing insight into possible functional mechanism. The dimensional reduction methods first applied to protein conformational ensembles were referred to as Quasi-Harmonic Analysis, Principal Component Analysis and Essential Dynamics Analysis. A retrospective on the origin of these methods is presented, the relationships between them explained, and more recent developments reviewed.
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Tspan6 stimulates the chemoattractive potential of breast cancer cells for B cells in an EV- and LXR-dependent manner. Cell Rep 2023; 42:112207. [PMID: 36867531 DOI: 10.1016/j.celrep.2023.112207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/11/2023] [Accepted: 02/15/2023] [Indexed: 03/04/2023] Open
Abstract
The immune microenvironment in breast cancer (BCa) is controlled by a complex network of communication between various cell types. Here, we find that recruitment of B lymphocytes to BCa tissues is controlled via mechanisms associated with cancer cell-derived extracellular vesicles (CCD-EVs). Gene expression profiling identifies the Liver X receptor (LXR)-dependent transcriptional network as a key pathway that controls both CCD-EVs-induced migration of B cells and accumulation of B cells in BCa tissues. The increased accumulation oxysterol ligands for LXR (i.e., 25-hydroxycholesterol and 27-hydroxycholesterol) in CCD-EVs is regulated by the tetraspanin 6 (Tspan6). Tspan6 stimulates the chemoattractive potential of BCa cells for B cells in an EV- and LXR-dependent manner. These results demonstrate that tetraspanins control intercellular trafficking of oxysterols via CCD-EVs. Furthermore, tetraspanin-dependent changes in the oxysterol composition of CCD-EVs and the LXR signaling axis play a key role in specific changes in the tumor immune microenvironment.
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Interactive Flexible-Receptor Molecular Docking in Virtual Reality Using DockIT. J Chem Inf Model 2022; 62:5855-5861. [PMID: 36398912 DOI: 10.1021/acs.jcim.2c01274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Interactive docking enables the user to guide and control the docking of two biomolecules into a binding pose. It is of particular use when the binding site is known and is thought to be applicable to structure-based drug design (SBDD) and educating students about biomolecular interactions. For SBDD, it enables expertise and intuition to be brought to bear in the drug design process. In education, it can teach students about the most basic level of biomolecular function. Here, we introduce DockIT for virtual reality (VR) that uses a VR headset and hand-held controllers. Using the method of linear response on explicit solvent molecular dynamics simulations, DockIT can model both global and local conformational changes within the receptor due to forces of interaction with the ligand. It has real-time flexible molecular surface rendering and can show the real-time formation and breaking of hydrogen bonds, both between the ligand and receptor and within the receptor itself as it smoothly changes conformation.
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Characterization of the Immune Microenvironment in Inflammatory Breast Cancer Using Multiplex Immunofluorescence. Pathobiology 2022; 90:31-43. [PMID: 35705026 DOI: 10.1159/000524549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/01/2022] [Indexed: 01/27/2023] Open
Abstract
INTRODUCTION Inflammatory breast cancer (IBC) is an aggressive form of breast cancer with a poorly characterized immune microenvironment. METHODS We used a five-colour multiplex immunofluorescence panel, including CD68, CD4, CD8, CD20, and FOXP3 for immune microenvironment profiling in 93 treatment-naïve IBC samples. RESULTS Lower grade tumours were characterized by decreased CD4+ cells but increased accumulation of FOXP3+ cells. Increased CD20+ cells correlated with better response to neoadjuvant chemotherapy and increased CD4+ cells infiltration correlated with better overall survival. Pairwise analysis revealed that both ER+ and triple-negative breast cancer were characterized by co-infiltration of CD20 + cells with CD68+ and CD4+ cells, whereas co-infiltration of CD8+ and CD68+ cells was only observed in HER2+ IBC. Co-infiltration of CD20+, CD8+, CD4+, and FOXP3+ cells, and co-existence of CD68+ with FOXP3+ cells correlated with better therapeutic responses, while resistant tumours were characterized by co-accumulation of CD4+, CD8+, FOXP3+, and CD68+ cells and co-expression of CD68+ and CD20+ cells. In a Cox regression model, response to therapy was the most significant factor associated with improved patient survival. CONCLUSION Those results reveal a complex unique pattern of distribution of immune cell subtypes in IBC and provide an important basis for detailed characterization of molecular pathways that govern the formation of IBC immune landscape and potential for immunotherapy.
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Implementation of a mobilisation guideline and training programme to increase mobilisation levels on a cardiothoracic intensive therapy unit (CITU). Physiotherapy 2022. [DOI: 10.1016/j.physio.2021.12.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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The novel use of lung ultrasound to reduce anxiety during weaning from mechanical ventilation: A case report. Physiotherapy 2022. [DOI: 10.1016/j.physio.2021.12.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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A qualitative exploration of respiratory physiotherapists experiences of lung ultrasound training and its adoption in critical care. Physiotherapy 2022. [DOI: 10.1016/j.physio.2021.12.296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Digital screening tool (Health Catch-UP!) to promote multi-disease screening in migrants. Eur J Public Health 2021. [DOI: 10.1093/eurpub/ckab165.358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
The ECDC has called for innovative strategies to deliver multi-disease screening (TB, LTBI, HIV, hepatitis B/C, Chagas, Strongyloidiasis and schistosomiasis) and catch-up vaccination (MMR, DTP) to adult migrants within the primary care context. We did a UK i qualitative study to explore current practice and seek views on a novel integrated digital tool to support delivery of screening recommendations for migrants https://emishealth.vids.io/videos/a49ad1bb1a18e4c72c/health-catch-up-with-requested-edits-mp4).
Methods
Phase 1 was conducted via telephone with clinical primary care practitioners (PCPs) (phase 1) and informed data collection and analysis for phase 2 with administrative staff. Data were analysed iteratively, informed by thematic analysis (Ethics no.20/HRA/1674).
Results
64 participants were recruited in Phase 1 (25 general practitioners [GPs], 15 nurses, 7 healthcare assistants, 1 pharmacist); Phase 2 comprised administrative staff (11 Practice-Managers, 5 receptionists). There was lack of consistency in delivery of screening and vaccination. Most GP practices adopted a practice-specific approach, or had no system in place; screening only for HIV and hepatitis B/C. Barriers to screening were perceived lack of knowledge/training and limited financial resources. Facilitators included having an infectious disease/migrant-health champion, incentivisation, and clear protocols. Participants responded positively to the integrated Health Catch-UP! tool, confirming that it would increase screening and vaccination, reduce missed opportunities for preventative healthcare, and raise awareness of migrant health.
Conclusions
Infectious disease screening and catch-up vaccination is not currently delivered well in primary care in high-migrant receiving European countries. Innovative digital tools like Health Catch-UP! could aid clinical decision-making and facilitating improved health outcomes for migrants. Further work is needed to evaluate this intervention.
Key messages
Infectious disease screening and catch-up vaccination is not currently delivered well in primary care in high-migrant receiving European countries. Innovative digital tools could aid clinical decision-making and facilitating improved health outcomes for migrants.
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Determination of amino acids that favour the α L region using Ramachandran propensity plots. Implications for α-sheet as the possible amyloid intermediate. J Struct Biol 2021; 213:107738. [PMID: 33838226 DOI: 10.1016/j.jsb.2021.107738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/28/2022]
Abstract
In amyloid diseases an insoluble amyloid fibril forms via a soluble oligomeric intermediate. It is this intermediate that mediates toxicity and it has been suggested, somewhat controversially, that it has the α-sheet structure. Nests and α-strands are similar peptide motifs in that alternate residues lie in the αR and γL regions of the Ramachandran plot for nests, or αR and αL regions for α-strands. In nests a concavity is formed by the main chain NH atoms whereas in α-strands the main chain is almost straight. Using "Ramachandran propensity plots" to focus on the αL/γL region, it is shown that glycine favours γL (82% of amino acids are glycine), but disfavours αL (3% are glycine). Most charged and polar amino acids favour αL with asparagine having by far the highest propensity. Thus, glycine favours nests but, contrary to common expectation, should not favour α-sheet. By contrast most charged or polar amino acids should favour α-sheet by their propensity for the αL conformation, which is more discriminating amongst amino acids than the αR conformation. Thus, these results suggest the composition of sequences that favour α-sheet formation and point towards effective prediction of α-sheet from sequence.
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DockIT: a tool for interactive molecular docking and molecular complex construction. Bioinformatics 2020; 36:5698-5700. [PMID: 33367508 DOI: 10.1093/bioinformatics/btaa1059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/30/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY DockIT is a tool that has a unique set of physical and graphical features for interactive molecular docking. It enables the user to bring a ligand and a receptor into a docking pose by controlling relative position and orientation, either with a mouse and keyboard, or with a haptic device. Atomic interactions are modelled using molecular dynamics-based force-fields with the force on the ligand being felt on a haptic device. Real-time calculation and display of intermolecular hydrogen bonds and multipoint collision detection either using maximum force or maximum atomic overlap, mean that together with the ability to monitor selected intermolecular atomic distances, the user can find physically feasible docking poses that satisfy distance constraints derived from experimental methods. With these features and the ability to output and reload docked structures it can be used to accurately build up large multi-component molecular systems in preparation for molecular dynamics simulation. AVAILABILITY AND IMPLEMENTATION DockIT is available free of charge for non-commercial use at http://www.haptimol.co.uk/downloads.htm. It requires a windows computer with GPU that supports OpenCL 1.2 and OpenGL 4.0. It may be used with a mouse and keyboard, or a haptic device from 3DSystems.
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Migration and outbreaks of vaccine-preventable disease in Europe: a systematic analysis (1990-2019). Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa165.1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Migrant populations (defined as foreign-born) in the EU/EEA may be one of several under-immunised populations yet their role in outbreaks of vaccine-preventable diseases (VPDs) has been poorly defined to date.
Methods
We did both a temporal analysis to map published reports of migrant-related outbreaks against data from the ECDC's Surveillance Atlas of Infectious Disease, and a systematic review (PROSPERO CRD42019157473; 1990-2019) adhering to PRISMA guidelines, to explore whether migrants are involved in outbreaks in Europe and which particular subpopulations may be at increased risk. Studies on VPD outbreaks (measles, mumps, rubella, diphtheria, pertussis, polio, hepatitis A, N meningitidis, and H influenzae) in migrants residing in the EU/EEA were included.
Results
46 studies were included, reporting on 50 VPD outbreaks across 13 EU/EEA countries, of which 98% (n = 49) occured since January 2000. Measles had the highest number of reports of outbreaks involving migrants (n = 21; 5043 cases), followed by varicella (n = 10; 595 cases) and hepatitis A (n = 10; 1226 cases). 21 (40%) of outbreaks were reported from shelters for asylum seekers and refugees (mainly varicella or measles). Of 27 outbreaks where the index case was defined, 20 (74.1%) were migrants, including 9 (33.3%) from Eastern Europe and 6 (22.2%) from Africa. When mapped against the ECDC timeline of measles outbreaks, migrant-related outbreaks coincide with Europe-wide peaks in measles incidence (in 2006, 2010, and 2018).
Conclusions
Migrants represent one key group involved in VPD outbreaks, with refugees/asylum seekers residing in shelters or camps particularly at risk. Measles accounted for 38% of all reported outbreaks. Improved data collection on migrant status across Europe is crucial to understanding the complex relationship between migration and occurrence of VPD outbreaks to inform policy decisions on the most effective strategies to prevent future outbreaks.
Key messages
Migrants represent one key group involved in vaccine-preventable diseases outbreaks in Europe. Refugees and asylum seekers may be particularly at risk.
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The potential role of physiotherapy performed lung ultrasound during an acute adult cystic fibrosis exacerbation: A case report. Physiotherapy 2020. [DOI: 10.1016/j.physio.2020.03.293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lung ultrasound in the management of patients with cystic fibrosis: a literature review. Physiotherapy 2020. [DOI: 10.1016/j.physio.2020.03.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression. BMC Bioinformatics 2020; 21:137. [PMID: 32272894 PMCID: PMC7147021 DOI: 10.1186/s12859-020-3464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/20/2020] [Indexed: 11/12/2022] Open
Abstract
Background Hinge-bending movements in proteins comprising two or more domains form a large class of functional movements. Hinge-bending regions demarcate protein domains and collectively control the domain movement. Consequently, the ability to recognise sequence features of hinge-bending regions and to be able to predict them from sequence alone would benefit various areas of protein research. For example, an understanding of how the sequence features of these regions relate to dynamic properties in multi-domain proteins would aid in the rational design of linkers in therapeutic fusion proteins. Results The DynDom database of protein domain movements comprises sequences annotated to indicate whether the amino acid residue is located within a hinge-bending region or within an intradomain region. Using statistical methods and Kernel Logistic Regression (KLR) models, this data was used to determine sequence features that favour or disfavour hinge-bending regions. This is a difficult classification problem as the number of negative cases (intradomain residues) is much larger than the number of positive cases (hinge residues). The statistical methods and the KLR models both show that cysteine has the lowest propensity for hinge-bending regions and proline has the highest, even though it is the most rigid amino acid. As hinge-bending regions have been previously shown to occur frequently at the terminal regions of the secondary structures, the propensity for proline at these regions is likely due to its tendency to break secondary structures. The KLR models also indicate that isoleucine may act as a domain-capping residue. We have found that a quadratic KLR model outperforms a linear KLR model and that improvement in performance occurs up to very long window lengths (eighty residues) indicating long-range correlations. Conclusion In contrast to the only other approach that focused solely on interdomain hinge-bending regions, the method provides a modest and statistically significant improvement over a random classifier. An explanation of the KLR results is that in the prediction of hinge-bending regions a long-range correlation is at play between a small number amino acids that either favour or disfavour hinge-bending regions. The resulting sequence-based prediction tool, HingeSeek, is available to run through a webserver at hingeseek.cmp.uea.ac.uk.
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The CD151-midkine pathway regulates the immune microenvironment in inflammatory breast cancer. J Pathol 2020; 251:63-73. [PMID: 32129471 DOI: 10.1002/path.5415] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/27/2020] [Accepted: 02/25/2020] [Indexed: 12/19/2022]
Abstract
The immune microenvironment in inflammatory breast cancer (IBC) is poorly characterised, and molecular and cellular pathways that control accumulation of various immune cells in IBC tissues remain largely unknown. Here, we discovered a novel pathway linking the expression of the tetraspanin protein CD151 in tumour cells with increased accumulation of macrophages in cancerous tissues. It is notable that elevated expression of CD151 and a higher number of tumour-infiltrating macrophages correlated with better patient responses to chemotherapy. Accordingly, CD151-expressing IBC xenografts were characterised by the increased infiltration of macrophages. In vitro migration experiments demonstrated that CD151 stimulates the chemoattractive potential of IBC cells for monocytes via mechanisms involving midkine (a heparin-binding growth factor), integrin α6β1, and production of extracellular vesicles (EVs). Profiling of chemokines secreted by IBC cells demonstrated that CD151 increases production of midkine. Purified midkine specifically stimulated migration of monocytes, but not other immune cells. Further experiments demonstrated that the chemoattractive potential of IBC-derived EVs is blocked by anti-midkine antibodies. These results demonstrate for the first time that changes in the expression of a tetraspanin protein by tumour cells can affect the formation of the immune microenvironment by modulating recruitment of effector cells to cancerous tissues. Therefore, a CD151-midkine pathway can be considered as a novel target for controlled changes of the immune landscape in IBC. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Methodological improvements for the analysis of domain movements in large biomolecular complexes. Biophys Physicobiol 2019; 16:328-336. [PMID: 31984188 PMCID: PMC6975908 DOI: 10.2142/biophysico.16.0_328] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/03/2019] [Indexed: 12/01/2022] Open
Abstract
Domain movements play a prominent role in the function of many biomolecules such as the ribosome and F0F1-ATP synthase. As more structures of large biomolecules in different functional states become available as experimental techniques for structure determination advance, there is a need to develop methods to understand the conformational changes that occur. DynDom and DynDom3D were developed to analyse two structures of a biomolecule for domain movements. They both used an original method for domain recognition based on clustering of "rotation vectors". Here we introduce significant improvements in both the methodology and implementation of a tool for the analysis of domain movements in large multimeric biomolecules. The main improvement is in the recognition of domains by using all six degrees of freedom required to describe the movement of a rigid body. This is achieved by way of Chasles' theorem in which a rigid-body movement can be described as a screw movement about a unique axis. Thus clustering now includes, in addition to rotation vector data, screw-axis location data and axial climb data. This improves both the sensitivity of domain recognition and performance. A further improvement is the recognition and annotation of interdomain bending regions, something not done for multimeric biomolecules in DynDom3D. This is significant as it is these regions that collectively control the domain movement. The new stand-alone, platform-independent implementation, DynDom6D, can analyse biomolecules comprising protein, DNA and RNA, and employs an alignment method to automatically achieve the required equivalence of atoms in the two structures.
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Multi-strand β-sheet of Alzheimer Aβ(1–40) folds to β-strip helix: implication for protofilament formation. J Biomol Struct Dyn 2019; 37:2143-2153. [DOI: 10.1080/07391102.2018.1477626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. J Chem Inf Model 2019; 59:2900-2912. [DOI: 10.1021/acs.jcim.9b00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
Citrate synthase plays a fundamental role in the metabolic cycle of the cell. Its catalytic mechanism is complex involving the binding of two substrates that cause a domain movement. In this paper, we used classical molecular dynamics simulations and umbrella-sampling simulations to determine the potential of mean force along a reaction coordinate for the domain movement in ligand-free citrate synthase from pig ( Sus scrofa). The results show that, at 293 K, the closed-domain conformation has a ∼4 kb T higher energy than the open-domain conformation. In a simple two-state model, this difference means that the enzyme spends 98% of the time in the open-domain conformation ready to receive the substrate, oxaloacetate, rather than the closed-domain conformation where the binding site would be inaccessible to the substrate. Given that experimental evidence indicates that the binding of oxaloacetate induces at least partial closure, this would imply an induced-fit mechanism which we argue is applicable to all enzymes with a functional domain movement for reasons of catalytic efficiency. A barrier of 4 kb T gives an estimation of the mean first passage time in the range 1-10 μs.
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Opaque hemithorax (whiteout): a literature review exploring its causes, potential use of thoracic ultrasound and the role of physiotherapy. Physiotherapy 2019. [DOI: 10.1016/j.physio.2018.11.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Thoracic ultrasound to differentially diagnose causes of opaque hemithorax (whiteout) when patients are referred for “chest” physiotherapy. Physiotherapy 2019. [DOI: 10.1016/j.physio.2018.11.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Thoracic ultrasound can differentiate between the causes of an opaque hemithorax (whiteout) during an on-call physiotherapy assessment: a case report. Physiotherapy 2019. [DOI: 10.1016/j.physio.2018.11.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Morphing and docking visualisation of biomolecular structures using Multi-Dimensional Scaling. J Mol Graph Model 2018; 82:108-116. [PMID: 29729647 DOI: 10.1016/j.jmgm.2018.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 11/28/2022]
Abstract
Protein structures are often solved at atomic resolution in two states defining a functional movement but intervening conformations are usually unknown. Morphing methods generate intervening conformations between two known structures. When viewed as an animation using molecular graphics, a smooth, direct morph enables the eye to track changes in structure that might be otherwise missed. We present a morphing method that aims to linearly interpolate interatomic distances and which uses SMACOF (Scaling by MAjorisation of COmplicated Function) and multigrid techniques with a cut-off distance based weighting that optimizes the MolProbity score of intervening structures. The all-atom morphs are smooth, move directly between the two structures, and are shown, in general, to pass closer to a set of known intermediates than those generated using other methods. The techniques are also used for docking by putting the unbound structures in a "near-approach pose" and then morphing to the bound complex. The resulting GPU-accelerated tools are available on a webserver, Morphit_Pro, at http://morphit-pro.cmp.uea.ac.uk/ and more than 5000 domains movements available at the DynDom website can now be viewed as morphs http://morphit-pro.cmp.uea.ac.uk/dyndom/.
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Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments. Proteins 2017. [PMID: 28646497 DOI: 10.1002/prot.25341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Examples of homomeric β-helices and β-barrels have recently emerged. Here we generalize the theory for the shear number in β-barrels to encompass β-helices and homomeric structures. We introduce the concept of the "β-strip," the set of parallel or antiparallel neighboring strands, from which the whole helix can be generated giving it n-fold rotational symmetry. In this context, the shear number is interpreted as the sum around the helix of the fixed register shift between neighboring identical β-strips. Using this approach, we have derived relationships between helical width, pitch, angle between strand direction and helical axis, mass per length, register shift, and number of strands. The validity and unifying power of the method is demonstrated with known structures including α-hemolysin, T4 phage spike, cylindrin, and the HET-s(218-289) prion. From reported dimensions measured by X-ray fiber diffraction on amyloid fibrils, the relationships can be used to predict the register shift and the number of strands within amyloid protofilaments. This was used to construct models of transthyretin and Alzheimer β(40) amyloid protofilaments that comprise a single strip of in-register β-strands folded into a "β-strip helix." Results suggest both stabilization of an individual β-strip helix and growth by addition of further β-strip helices can involve the same pair of sequence segments associating with β-sheet hydrogen bonding at the same register shift. This process would be aided by a repeat sequence. Hence, understanding how the register shift (as the distance between repeat sequences) relates to helical dimensions will be useful for nanotube design.
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Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics. J Chem Inf Model 2017; 57:1142-1152. [DOI: 10.1021/acs.jcim.7b00051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Determination of locked interfaces in biomolecular complexes using Haptimol_RD. Biophys Physicobiol 2016; 13:97-103. [PMID: 27924263 PMCID: PMC5042165 DOI: 10.2142/biophysico.13.0_97] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 02/26/2016] [Indexed: 12/01/2022] Open
Abstract
Interactive haptics-assisted docking provides a virtual environment for the study of molecular complex formation. It enables the user to interact with the virtual molecules, experience the interaction forces via their sense of touch, and gain insights about the docking process itself. Here we use a recently developed haptics software tool, Haptimol_RD, for the rigid docking of protein subunits to form complexes. Dimers, both homo and hetero, are loaded into the software with their subunits separated in space for the purpose of assessing whether they can be brought back into the correct docking pose via rigid-body movements. Four dimers were classified into two types: two with an interwinding subunit interface and two with a non-interwinding subunit interface. It was found that the two with an interwinding interface could not be docked whereas the two with the non-interwinding interface could be. For the two that could be docked a “sucking” effect could be felt on the haptic device when the correct binding pose was approached which is associated with a minimum in the interaction energy. It is clear that for those that could not be docked, the conformation of one or both of the subunits must change upon docking. This leads to the steric-based concept of a locked or non-locked interface. Non-locked interfaces have shapes that allow the subunits to come together or come apart without the necessity of intra-subunit conformational change, whereas locked interfaces require a conformational change within one or both subunits for them to be able to come apart.
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Abstract
DynDom3D is a program for the analysis of domain movements in multimeric proteins. Its inputs are two structure files that indicate a possible domain movement, but the onus has been on the user to process the files so that there is the necessary one-to-one equivalence between atoms in the two atom lists. This is often a prohibitive task to carry out manually, which has limited the application of DynDom3D. Here we report on a webserver with a preprocessor that automatically creates an equivalence between atoms using sequence alignment methods. The processed structure files are passed to DynDom3D and the results are presented on a webpage that includes molecular graphics for easy visualization.
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Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics. J Mol Graph Model 2015; 61:1-12. [DOI: 10.1016/j.jmgm.2015.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 11/29/2022]
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Consultant-delivered care. Anaesthesia 2015; 70:1099-100. [DOI: 10.1111/anae.13175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Monte Carlo Sampling with Linear Inverse Kinematics for Simulation of Protein Flexible Regions. J Chem Theory Comput 2015; 11:3895-905. [DOI: 10.1021/acs.jctc.5b00215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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FP178FOLLISTATIN, AN ACTIVIN-BINDING PROTEIN, ATTENUATES RENAL ISCHAEMIA-REPERFUSION INJURY IN MICE. Nephrol Dial Transplant 2015. [DOI: 10.1093/ndt/gfv172.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Determining the biomass fraction of mixed waste fuels: A comparison of existing industry and (14)C-based methodologies. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 35:293-300. [PMID: 25318703 DOI: 10.1016/j.wasman.2014.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 08/13/2014] [Accepted: 09/01/2014] [Indexed: 06/04/2023]
Abstract
(14)C analysis of flue gas by accelerator mass spectrometry (AMS) and liquid scintillation counting (LSC) were used to determine the biomass fraction of mixed waste at an operational energy-from-waste (EfW) plant. Results were converted to bioenergy (% total) using mathematical algorithms and assessed against existing industry methodologies which involve manual sorting and selective dissolution (SD) of feedstock. Simultaneous determinations using flue gas showed excellent agreement: 44.8 ± 2.7% for AMS and 44.6 ± 12.3% for LSC. Comparable bioenergy results were obtained using a feedstock manual sort procedure (41.4%), whilst a procedure based on selective dissolution of representative waste material is reported as 75.5% (no errors quoted). (14)C techniques present significant advantages in data acquisition, precision and reliability for both electricity generator and industry regulator.
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Abstract
Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a ‘hinge’ mechanism and those with a ‘shear’ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term ‘shear’ is often interpreted to mean a relative translation of the domains. Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms. Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/. Contact:sjh@cmp.uea.ac.uk. Supplementary information:Supplementary data are available at Bioinformatics online.
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Abstract
The importance of collective motions in proteins, such as hinge-bending motions or motions involving domains, has been recognized. Occurrence of such motions and their experimental and theoretical studies are reviewed. Normal-mode analysis and principal component analysis are powerful theoretical tools for studying such motions. The former is based on the assumption of harmonicity of the dynamics, while the latter is valid even when the dynamics is highly anharmonic. The results of the latter analysis indicate that most important conformational events are taking place in a conformational subspace spanned by a rather small number of principal modes, and this important subspace is also spanned by a small number of normal modes. The normal-mode refinement method of protein X-ray crystallography, which is developed based on the concept of the above important subspace, is discussed.
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Abstract
British sheep farmers were invited to complete a questionnaire about the impact of Schmallenberg virus (SBV) on animal health, welfare and their own emotional wellbeing during the 2011–2012 lambing season, through Defra and Farming Industry websites, letters to farmers who had requested SBV laboratory tests and advertisement at Sheep 2012. The 494 responders included SBV confirmed (positive by RT-PCR) (n=76), SBV suspected by farmer (n=140) or SBV not suspected (n=278). Percentage of barren ewes was similar across SBV groups, however, lamb and ewe losses were higher on responder farms where SBV was confirmed or suspected. The median percentages of all lambs born (and lambs born deformed ) that died within one week of birth was 10.4 per cent (5.5 per cent), 7.0 per cent (2.9 per cent) and 5.3 per cent (0 per cent), respectively, on SBV confirmed, suspected and not suspected farms (P<0.001). Eight to 16 per cent of SBV confirmed or suspected farms reported lamb mortality of ≥40 per cent. Farmer perceived impact was greater where SBV was confirmed or suspected (P<0.001): 25 per cent reported a high impact on emotional wellbeing (4 per cent of SBV not suspected), 13 per cent reported a high impact on flock welfare and financial performance and 6 per cent were less likely to farm sheep next year because of SBV (<2 per cent in SBV not suspected). Overall, SBV impact has been large relative to reported sheep loss.
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A real-time proximity querying algorithm for haptic-based molecular docking. Faraday Discuss 2014; 169:359-77. [DOI: 10.1039/c3fd00123g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, force-feedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol_RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol_RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware.
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Classification of domain movements in proteins using dynamic contact graphs. PLoS One 2013; 8:e81224. [PMID: 24260562 PMCID: PMC3832408 DOI: 10.1371/journal.pone.0081224] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/09/2013] [Indexed: 12/02/2022] Open
Abstract
A new method for the classification of domain movements in proteins is described and applied to 1822 pairs of structures from the Protein Data Bank that represent a domain movement in two-domain proteins. The method is based on changes in contacts between residues from the two domains in moving from one conformation to the other. We argue that there are five types of elemental contact changes and that these relate to five model domain movements called: “free”, “open-closed”, “anchored”, “sliding-twist”, and “see-saw.” A directed graph is introduced called the “Dynamic Contact Graph” which represents the contact changes in a domain movement. In many cases a graph, or part of a graph, provides a clear visual metaphor for the movement it represents and is a motif that can be easily recognised. The Dynamic Contact Graphs are often comprised of disconnected subgraphs indicating independent regions which may play different roles in the domain movement. The Dynamic Contact Graph for each domain movement is decomposed into elemental Dynamic Contact Graphs, those that represent elemental contact changes, allowing us to count the number of instances of each type of elemental contact change in the domain movement. This naturally leads to sixteen classes into which the 1822 domain movements are classified.
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Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides. Proteins 2013; 82:230-9. [DOI: 10.1002/prot.24357] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/10/2013] [Accepted: 06/10/2013] [Indexed: 12/30/2022]
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Abstract
Chicken eggs categorised as conventional, omega-3 enriched, free range and organic were collected at grading stations in three regions of Canada between 2005 and 2006. Free run eggs, which were only available for collection from two regions, were also sampled during this time frame. Egg yolks from each of these egg types (n = 162) were analysed to determine brominated flame retardant levels, specifically polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecane (HBCD). PBDEs were detected in 100% of the 162 samples tested, while HBCD was observed in 85% of the egg yolks. Total PBDE concentrations in egg yolks ranged from 0.018 to 20.9 ng g(-1) lipid (median = 3.03 ng g(-1) lipid), with PBDE 209 identified as being the major contributor to ΣPBDE concentrations. In addition to PBDE 209, PBDE 99, 47, 100, 183 and 153 were important contributors to ΣPBDE concentrations. Total HBCD concentrations ranged from below the limit of detection to a maximum concentration of 71.9 ng g(-1) lipid (median = 0.053 ng g(-1) lipid). The α-isomer was the dominant contributor to ΣHBCD levels in Canadian egg yolks and was the most frequently detected HBCD isomer. ΣPBDE levels exhibited large differences in variability between combinations of region and type. ΣHBCD concentrations were not significantly different among regions, although differences were observed between the different types of egg yolks analysed in the present study.
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Simulation of the β- to α-sheet transition results in a twisted sheet for antiparallel and an α-nanotube for parallel strands: Implications for amyloid formation. Proteins 2011; 79:3193-207. [DOI: 10.1002/prot.23154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 07/19/2011] [Accepted: 07/27/2011] [Indexed: 01/16/2023]
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The effect of end constraints on protein loop kinematics. Biophys J 2010; 98:1976-85. [PMID: 20441762 DOI: 10.1016/j.bpj.2010.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 01/08/2010] [Accepted: 01/11/2010] [Indexed: 11/17/2022] Open
Abstract
Despite the prevalent involvement of loops in function little is known about how the constraining of end groups influences their kinematics. Using a linear inverse-kinematics approach and assuming fixed bond lengths, bond angles, and peptide bond torsions, as well as ignoring molecular interactions to assess the effect of the end-constraint only, it is shown that the constraint creates a closed surface in torsion angle space. For pentapeptides, the constraint gives rise to inaccessible regions in a Ramachandran plot. This complex and tightly curved surface produces interesting effects that may play a functional role. For example, a small change in one torsion angle can radically change the behavior of the whole loop. The constraint also produces long-range correlations, and structures exist where the correlation coefficient is 1.0 or -1.0 between rotations about bonds separated by >30 A. Another application allows some torsion angles to be targeted to specified values while others are constrained. When this application was used on key torsions in lactate dehydrogenase, it was found that the functional loop first folds forward and then moves sideways. For horse liver alcohol dehydrogenase, it was confirmed that the functional loop's Pro-Pro motif creates a rigid arm in an NAD-activated switch for domain closure.
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Antioxidant capacity of potato chips and snapshot trends in acrylamide content in potato chips and cereals on the Canadian market. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2010; 27:1193-8. [PMID: 20582779 DOI: 10.1080/19440049.2010.483692] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The concentration of acrylamide was measured in selected varieties of five brands of potato chips and breakfast cereals over a 5-year period. Most of the products were purchased in one locality in Canada. Samples were analysed by an isotope dilution ((13)C(3)) acrylamide method. They were extracted with water, partitioned with dichloromethane, filtered through a 5 kDa centrifuge filter, cleaned-up on HLB Oasis polymeric and Accucat mixed mode anion and cation exchange SPE columns, and analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The acrylamide concentration in potato chips varied from 106 to 4630 ng g(-1), while values in cereals varied from 50 to 347 ng g(-1). Wide variations were observed between brands, within brands over time, and between lots of the same brand. A subset of potato chip samples was analysed for in vitro antioxidant activity. No relationship was found between antioxidative capacity of potato chips and their acrylamide content.
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Development of an analytical method and survey of foods for furan, 2-methylfuran and 3-methylfuran with estimated exposure. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2010; 27:764-75. [DOI: 10.1080/19440040903473332] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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47
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Health risk assessment of ochratoxin A for all age-sex strata in a market economy. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2010; 27:212-40. [PMID: 20013446 PMCID: PMC3474135 DOI: 10.1080/02652030903013278] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 03/27/2009] [Indexed: 11/30/2022]
Abstract
In order to manage risk of ochratoxin A (OTA) in foods, we re-evaluated the tolerable daily intake (TDI), derived the negligible cancer risk intake (NCRI), and conducted a probabilistic risk assessment. A new approach was developed to derive 'usual' probabilistic exposure in the presence of highly variable occurrence data, such as encountered with low levels of OTA. Canadian occurrence data were used for various raw food commodities or finished foods and were combined with US Department of Agriculture (USDA) food consumption data, which included data on infants and young children. Both variability and uncertainty in input data were considered in the resulting exposure estimates for various age/sex strata. Most people were exposed to OTA on a daily basis. Mean adjusted exposures for all age-sex groups were generally below the NCRI of 4 ng OTA kg bw(-1), except for 1-4-year-olds as a result of their lower body weight. For children, the major contributors of OTA were wheat-based foods followed by oats, rice, and raisins. Beer, coffee, and wine also contributed to total OTA exposure in older individuals. Predicted exposure to OTA decreased when European Commission maximum limits were applied to the occurrence data. The impact on risk for regular eaters of specific commodities was also examined.
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Interacting with the biomolecular solvent accessible surface via a haptic feedback device. BMC STRUCTURAL BIOLOGY 2009; 9:69. [PMID: 19860901 PMCID: PMC2774689 DOI: 10.1186/1472-6807-9-69] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 10/27/2009] [Indexed: 11/23/2022]
Abstract
Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from ), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software.
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The interwinding nature of protein-protein interfaces and its implication for protein complex formation. ACTA ACUST UNITED AC 2009; 25:3108-13. [PMID: 19789269 PMCID: PMC2778332 DOI: 10.1093/bioinformatics/btp563] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motivation: Structural features at protein–protein interfaces can be studied to understand protein–protein interactions. It was noticed that in a dataset of 45 multimeric proteins the interface could either be described as flat against flat or protruding/interwound. In the latter, residues within one chain were surrounded by those in other chains, whereas in the former they were not. Results: A simple method was developed that could distinguish between these two types with results that matched those made by a human annotator. Applying this automatic method to a large dataset of 888 structures, chains at interfaces were categorized as non-surrounded or surrounded. It was found that the surrounded set had a significantly lower folding tendency using a sequence based measure, than the non-surrounded set. This suggests that before complexation, surrounded chains are relatively unstable and may be involved in ‘fly-casting’. This is supported by the finding that terminal regions are overrepresented in the surrounded set. Availability:http://cib.cf.ocha.ac.jp/DACSIS/ Contact:yura.kei@ocha.ac.jp; sjh@cmp.uea.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Abstract
A new method for the analysis of domain movements in large, multichain, biomolecular complexes is presented. The method is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. The method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA, or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a "rotation space" and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have colocated points. Thus a domain can be identified from the clustering of points from blocks that span it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. Here, we report on the application of the method to biomolecules covering a considerable size range: hemoglobin, liver alcohol dehydrogenase, S-Adenosylhomocysteine hydrolase, aspartate transcarbamylase, and the 70S ribosome. The results provide a depiction of the conformational change within each molecule that is easily understood, giving a perspective that is expected to lead to new insights. Of particular interest is the allosteric mechanism in some of these molecules. Results indicate that common boundaries between subunits and domains are good regions to focus on as movement in one subunit can be transmitted to another subunit through such interfaces.
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