scholarly journals Substrate Affinity and Specificity of the ScSth1p Bromodomain Are Fine-Tuned for Versatile Histone Recognition

2019 ◽  
Author(s):  
Bartlomiej J. Blus ◽  
Hideharu Hashimoto ◽  
Hyuk-Soo Seo ◽  
Aleksandra Krolak ◽  
Erik W. Debler
Keyword(s):  
Binding Sites ◽  
Biological Function ◽  
Point Mutations ◽  
Substrate Affinity ◽  
List Type ◽  
Wild Type ◽  
Wide Range ◽  
Lysine Residues ◽  
Loop Regions ◽  
Peptide Binding Affinity

SummaryBromodomains recognize a wide range of acetylated lysine residues in histones and other nuclear proteins. Substrate specificity is critical for their biological function and arises from unique acetyl-lysine binding sites formed by variable loop regions. Here, we analyzed substrate affinity and specificity of the yeast ScSth1p bromodomain, an essential component of the “Remodels the Structure of Chromatin” complex, and found that the wild-type bromodomain preferentially recognizes H3K14ac and H4K20ac peptides. Mutagenesis studies—guided by our crystal structure determined at 2.7 Å resolution—revealed loop residues Ser1276 and Trp1338 as key determinants for such interactions. Strikingly, point mutations of each of these residues substantially increased peptide binding affinity and selectivity, respectively. Our data demonstrate that the ScSth1p bromodomain is not optimized for binding to an individual acetylation mark, but fine-tuned for interactions with several such modifications, consistent with the versatile and multivalent nature of histone recognition by reader modules such as bromodomains.HighlightsThe ScSth1p bromodomain preferentially recognizes H3K14ac and H4K20ac peptidesSer1276 and Trp1338 are key determinants of substrate affinity and specificityMutations of these residues drastically increase substrate affinity and specificityThe ScSth1p bromodomain is fine-tuned for promiscuous histone tail recognitionGraphical Abstract

Abstract 1042: Viral Chemokine Modulating Protein, M-T7, Interrupts Chemokine : Glycosaminoglycan (GAG) Interaction: M-T7 Inhibitory Activity is Dependent upon Y46 and V210 aminoacid residues

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Erbin Dai ◽  
Dana McIvor ◽  
Liying Liu ◽  
Ganesh Munaswamy-Ramanujam ◽  
Yunming Sun ◽  
...  
Keyword(s):  
Cell Migration ◽  
Cell Invasion ◽  
Inhibitory Activity ◽  
Active Sites ◽  
Point Mutations ◽  
List Type ◽  
Wild Type ◽  
Monocyte Activation ◽  
Cc Chemokine ◽  
Plaque Growth

Background: Chemokines bind to glycosaminoglycans (GAGs) forming gradients that direct inflammatory cell invasion. The viral chemokine modulating protein (CMP), MT-7 binds the C terminal, GAG-binding domain of chemokines and has been previously reported to significantly reduce cell invasion and plaque growth in rat aortic and renal transplant models. Two other viral CMPs, M-T1 and M3 CMPs bind the N terminal domain of chemokines that bind to cell surface receptors. To determine the role of CC chemokine receptor 2 (CCR2) and GAGs for M-T7 anti-inflammatory activity, effects of M-T7 on plaque growth were assessed after mouse CCR2 deficient (CCR2−/−) or GAG deficient (NDST1−/−) aortic allograft transplant. Mononuclear cell migration in response to MCP-1 or RANTES into mouse ascites was also tested. Active sites necessary for M-T7 inhibition of chemokine function and monocyte activation, were assessed by infusion of in the mouse cell migration and human monocyte membrane fluidity assays. Results: M-T7 significantly reduced cell migration and intimal hyperplasia in wild type CCR2+/+ (p<0.009), and CCR2−/− aortic transplants (p<0.026). M-T1 and M3 inhibited cell invasion and plaque in CCR2+/+, but not CCR2−/− mice. M-T7 inhibited plaque growth and CC chemokine (MCP-1 and RANTES)-induced cell migration in wild type mice (P<0.01), but not in NDST1−/− mice (P=0.34). Selected M-T7 point mutations Ty (Y)46A, and Val (V) 210A no longer block chemokine-induced cell migration nor monocyte activation, whereas Asn (N) 40, Asn (N) 63 and Val (V)129 retain inhibitory activity. Conclusions: M-T7 but not M-T1 nor M3, blocks cell migration and plaque growth in CCR2 deficient (CCR2−/−) mouse aortic transplant models. M-T7 loses the ability to block cell migration and plaque growth in NDST1−/−, GAG (heparan sulfate) deficient mice. Point mutations Tyr46 and Val 210 lack inflammatory for mouse and human inflammatory monocyte responses indicating that these amino acid residues on the M-T7 CMP protein are required for inhibitory activity.

scholarly journals IDH1 and IDH2 mutants identified in cancer lose inhibition by isocitrate because of a change in their binding sites

2018 ◽  
Author(s):  
Juan P. Bascur ◽  
Melissa Alegría-Arcos ◽  
Ingrid Araya-Durán ◽  
Ezequiel I. Juritz ◽  
Fernando D. González-Nilo ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Sites ◽  
Competitive Inhibition ◽  
Binding Energies ◽  
Substrate Affinity ◽  
Wild Type ◽  
Similarity Estimation ◽  
In The Wild ◽  
Docking Calculations ◽  
Idh1 And Idh2 Mutations

AbstractIDH1 and IDH2 are human enzymes that convert isocitrate (ICT) into α-ketoglutarate (AKG). However, mutations in positions R132 of IDH1 and R140 and R172 of IDH2 cause these enzymes to convert AKG into 2-hydroxyglutarate (2HG). Concurrently, accumulation of 2HG in the cell is correlated with the development of cancer. This activity change is mainly due to the loss of the competitive inhibition by ICT of these enzymes, but the molecular mechanism behind this loss of inhibition is currently unknown. In this work we characterized the inhibition and loss of inhibition of IDH1 and IDH2 by means of the binding energies derived from molecular docking calculations. We characterized the substrate binding sites and how they differ among the mutant and wild type enzymes using a Jaccard similarity coefficient based on the residues involved in binding the substrates. We found that molecular docking effectively identifies the inhibition by ICT in the wild type and mutant enzymes that do not appear in tumors, and the loss of inhibition in the mutant enzymes that appear in tumors. Additionally, we found that the binding sites of the mutant enzymes are different among themselves. Finally, we found that the regulatory segment of IDH1 plays a prominent role in the change of binding sites between the mutant enzymes and the wild-type enzymes. Our findings show that the loss of inhibition is related to variations in the enzyme binding sites. Additionally, our findings show that a drug capable of targeting all IDH1 and IDH2 mutations in cancer is unlikely to be found due to significant differences among the binding sites of these paralogs. Moreover, the methodology developed here, which combines molecular docking calculations with binding site similarity estimation, can be useful for engineering enzymes, for instance, when aiming to modify the substrate affinity of an enzyme.

scholarly journals Sequence Tolerance of the Phage λ PRM Promoter: Implications for Evolution of Gene Regulatory Circuitry

2004 ◽  
Vol 186 (23) ◽  
pp. 7988-7999 ◽  
Author(s):  
Christine B. Michalowski ◽  
Megan D. Short ◽  
John W. Little
Keyword(s):  
Binding Sites ◽  
Present Form ◽  
Wild Type ◽  
Prophage Induction ◽  
Wide Range ◽  
Sequences Analysis ◽  
Gene Regulatory ◽  
Exact Sequences ◽  
Function Sequence ◽  
Regulatory Sites

ABSTRACT Much of the gene regulatory circuitry of phage λ centers on a complex region called the O R region. This ∼100-bp region is densely packed with regulatory sites, including two promoters and three repressor-binding sites. The dense packing of this region is likely to impose severe constraints on its ability to change during evolution, raising the question of how the specific arrangement of sites and their exact sequences could evolve to their present form. Here we ask whether the sequence of a cis-acting site can be widely varied while retaining its function; if it can, evolution could proceed by a larger number of paths. To help address this question, we developed aλ cloning vector that allowed us to clone fragments spanning the O R region. By using this vector, we carried out intensive mutagenesis of the P RM promoter, which drives expression of CI repressor and is activated by CI itself. We made a pool of fragments in which 8 of the 12 positions in the− 35 and −10 regions were randomized and cloned this pool into the vector, making a pool of P RM variant phage. About 10% of the P RM variants were able to lysogenize, suggesting that the λ regulatory circuitry is compatible with a wide range of P RM sequences. Analysis of several of these phages indicated a range of behaviors in prophage induction. Several isolates had induction properties similar to those of the wild type, and their promoters resembled the wild type in their responses to CI. We term this property of different sequences allowing roughly equivalent function “sequence tolerance ” and discuss its role in the evolution of gene regulatory circuitry.

scholarly journals Application of Nanotechnology for Sensitive Detection of Low-Abundance Single-Nucleotide Variations in Genomic DNA: A Review

Nanomaterials ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1384
Author(s):  
Mahwash Mukhtar ◽  
Saman Sargazi ◽  
Mahmood Barani ◽  
Henning Madry ◽  
Abbas Rahdar ◽  
...  
Keyword(s):  
Point Mutations ◽  
Ultrasensitive Detection ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Rare Mutations ◽  
Single Base Mismatch ◽  
Wide Range ◽  
Base Mismatch ◽  
Dna Variations

Single-nucleotide polymorphisms (SNPs) are the simplest and most common type of DNA variations in the human genome. This class of attractive genetic markers, along with point mutations, have been associated with the risk of developing a wide range of diseases, including cancer, cardiovascular diseases, autoimmune diseases, and neurodegenerative diseases. Several existing methods to detect SNPs and mutations in body fluids have faced limitations. Therefore, there is a need to focus on developing noninvasive future polymerase chain reaction (PCR)–free tools to detect low-abundant SNPs in such specimens. The detection of small concentrations of SNPs in the presence of a large background of wild-type genes is the biggest hurdle. Hence, the screening and detection of SNPs need efficient and straightforward strategies. Suitable amplification methods are being explored to avoid high-throughput settings and laborious efforts. Therefore, currently, DNA sensing methods are being explored for the ultrasensitive detection of SNPs based on the concept of nanotechnology. Owing to their small size and improved surface area, nanomaterials hold the extensive capacity to be used as biosensors in the genotyping and highly sensitive recognition of single-base mismatch in the presence of incomparable wild-type DNA fragments. Different nanomaterials have been combined with imaging and sensing techniques and amplification methods to facilitate the less time-consuming and easy detection of SNPs in different diseases. This review aims to highlight some of the most recent findings on the aspects of nanotechnology-based SNP sensing methods used for the specific and ultrasensitive detection of low-concentration SNPs and rare mutations.

Comparison of Deterministic and Linear Cosine Spatial Filtering of Transmission Electron Micrographs

1972 ◽  
Vol 30 ◽  
pp. 596-597
Author(s):  
David A. Ansley
Keyword(s):  
Spherical Aberration ◽  
Focal Length ◽  
Chromatic Aberration ◽  
Spatial Filter ◽  
Operating Conditions ◽  
Objective Lens ◽  
List Type ◽  
Spatial Filters ◽  
Transmission Electron ◽  
Wide Range

The coherence of the electron flux of a transmission electron microscope (TEM) limits the direct application of deconvolution techniques which have been used successfully on unmanned spacecraft programs. The theory assumes noncoherent illumination. Deconvolution of a TEM micrograph will, therefore, in general produce spurious detail rather than improved resolution.A primary goal of our research is to study the performance of several types of linear spatial filters as a function of specimen contrast, phase, and coherence. We have, therefore, developed a one-dimensional analysis and plotting program to simulate a wide 'range of operating conditions of the TEM, including adjustment of the:(1) Specimen amplitude, phase, and separation(2) Illumination wavelength, half-angle, and tilt(3) Objective lens focal length and aperture width(4) Spherical aberration, defocus, and chromatic aberration focus shift(5) Detector gamma, additive, and multiplicative noise constants(6) Type of spatial filter: linear cosine, linear sine, or deterministic

Triply-periodic nanostructures in surfactant, block copolymer, and biomembrane systems, and simulation of TEMs

1993 ◽  
Vol 51 ◽  
pp. 884-885
Author(s):  
David M. Anderson ◽  
Tomas Landh
Keyword(s):  
Liquid Crystalline ◽  
Diblock Copolymers ◽  
Cubic Phase ◽  
List Type ◽  
Interpenetrating Networks ◽  
Triply Periodic ◽  
Wide Range ◽  
Bicontinuous Cubic ◽  
Phase Liquid ◽  
Dividing Surface

First discovered in surfactant-water liquid crystalline systems, so-called ‘bicontinuous cubic phases’ have the property that hydropnilic and lipophilic microdomains form interpenetrating networks conforming to cubic lattices on the scale of nanometers. Later these same structures were found in star diblock copolymers, where the simultaneous continuity of elastomeric and glassy domains gives rise to unique physical properties. Today it is well-established that the symmetry and topology of such a morphology are accurately described by one of several triply-periodic minimal surfaces, and that the interface between hydrophilic and hydrophobic, or immiscible polymer, domains is described by a triply-periodic surface of constant, nonzero mean curvature. One example of such a dividing surface is shown in figure 5.The study of these structures has become of increasing importance in the past five years for two reasons:1)Bicontinuous cubic phase liquid crystals are now being polymerized to create microporous materials with monodispersed pores and readily functionalizable porewalls; figure 3 shows a TEM from a polymerized surfactant / methylmethacrylate / water cubic phase; and2)Compelling evidence has been found that these same morphologies describe biomembrane systems in a wide range of cells.

scholarly journals 332 The diagnostic role of shunt series radiographs (SSR) in children presenting to the children’s emergency department (CED) with suspected ventriculoperitoneal (VP) shunt failure

2020 ◽  
Vol 37 (12) ◽  
pp. 852.3-853
Author(s):  
Angharad Griffiths ◽  
Ikechukwu Okafor ◽  
Thomas Beattie
Keyword(s):  
Clinical Outcome ◽  
Sensitivity And Specificity ◽  
Clinical Information ◽  
Flow Diagram ◽  
List Type ◽  
Shunt Failure ◽  
Vp Shunt ◽  
Wide Range ◽  
Diagnostic Role

Aims/Objectives/BackgroundVP shunts are used to drain CSF from the cranial vault because of a wide range of pathologies and, like any piece of hardware, can fail. Traditionally investigations include SSR and CT. This project examines the role of SSR in evaluating children with suspected VP shunt failure.Primary outcome: Sensitivity and specificity of SSR in children presenting to the CED with concern for shunt failure.Methods/DesignConducted in a single centre, tertiary CED of the national Irish Neurosurgical(NS) referral centre (ED attendance:>50,000 patients/year). 100 sequential SSR requested by the CED were reviewed. Clinical information was extracted from electronic requests. Shunt failure was defined by the need for NS intervention(Revision).Abstract 332 Figure 1Abstract 332 Figure 2Results/ConclusionsSensitivity and specificity is presented in figure 1 (two by two table).100 radiographs performed in 84 children.22% shunts revised (see flow diagram).7 SSR’s were abnormal.85% (n=6) shunts revised. [5 following abnormal CT].Of the normal SSR’s; 16 had abnormal CT and revised.85/100 received CT.64 of 85 CT’s (75%) were normal.□6 of the 64 had focal shunt concern.SSR’s shouldn’t be used in isolation. NPV&PPV, Sensitivity&Specificity is low.SSR’s are beneficial where there’s concern over focal shunt problems (injury/pain/swelling) or following abnormal CT.VP shunt failure is not well investigated with SSR alone.SSR’s could be omitted where there is no focal shunt concern/after normal CT (without impacting clinical outcome) reducing radiation exposure and reduce impact on CED’s.59 SSR’s could have been avoided without adverse clinical outcome.

scholarly journals CHROMOSOMAL BASIS OF THE MEROZYGOSITY IN A PARTIALLY DIPLOID MUTANT OF PNEUMOCOCCUS

Genetics ◽  
1975 ◽  
Vol 80 (4) ◽  
pp. 667-678
Author(s):  
Mary Lee S Ledbetter ◽  
Rollin D Hotchkiss
Keyword(s):  
High Efficiency ◽  
Point Mutations ◽  
Resistant Mutant ◽  
Chromosomal Marker ◽  
Structural Abnormality ◽  
C Cells ◽  
Wild Type ◽  
Chromosomal Locus ◽  
Low Efficiency ◽  
Derivatives Of

ABSTRACT A sulfonamide-resistant mutant of pneumococcus, sulr-c, displays a genetic instability, regularly segregating to wild type. DNA extracts of derivatives of the strain possess transforming activities for both the mutant and wild-type alleles, establishing that the strain is a partial diploid. The linkage of sulr-c to strr-61, a stable chromosomal marker, was established, thus defining a chromosomal locus for sulr-c. DNA isolated from sulr-c cells transforms two mutant recipient strains at the same low efficiency as it does a wild-type recipient, although the mutant property of these strains makes them capable of integrating classical "low-efficiency" donor markers equally as efficiently as "high efficiency" markers. Hence sulr-c must have a different basis for its low efficiency than do classical low efficiency point mutations. We suggest that the DNA in the region of the sulr-c mutation has a structural abnormality which leads both to its frequent segregation during growth and its difficulty in efficiently mediating genetic transformation.

scholarly journals A procedure to introduce point mutations into the Rubisco large subunit gene in wild‐type plants

2021 ◽  
Author(s):  
Myat T. Lin ◽  
Douglas J. Orr ◽  
Dawn Worrall ◽  
Martin A. J. Parry ◽  
Elizabete Carmo‐Silva ◽  
...  
Keyword(s):  
Large Subunit ◽  
Point Mutations ◽  
Subunit Gene ◽  
Wild Type

scholarly journals Using Satellite Data for CBRN (Chemical, Biological, Radiological, and Nuclear) Threat Detection, Monitoring, and Modelling

2021 ◽  
Author(s):  
Gary Sutlieff ◽  
Lucy Berthoud ◽  
Mark Stinchcombe
Keyword(s):  
Satellite Data ◽  
Meteorological Data ◽  
Atmospheric Composition ◽  
Chemical Detection ◽  
List Type ◽  
Data Types ◽  
Wide Range ◽  
Future Technologies ◽  
The Impact ◽  
Near Future

Abstract CBRN (Chemical, Biological, Radiological, and Nuclear) threats are becoming more prevalent, as more entities gain access to modern weapons and industrial technologies and chemicals. This has produced a need for improvements to modelling, detection, and monitoring of these events. While there are currently no dedicated satellites for CBRN purposes, there are a wide range of possibilities for satellite data to contribute to this field, from atmospheric composition and chemical detection to cloud cover, land mapping, and surface property measurements. This study looks at currently available satellite data, including meteorological data such as wind and cloud profiles, surface properties like temperature and humidity, chemical detection, and sounding. Results of this survey revealed several gaps in the available data, particularly concerning biological and radiological detection. The results also suggest that publicly available satellite data largely does not meet the requirements of spatial resolution, coverage, and latency that CBRN detection requires, outside of providing terrain use and building height data for constructing models. Lastly, the study evaluates upcoming instruments, platforms, and satellite technologies to gauge the impact these developments will have in the near future. Improvements in spatial and temporal resolution as well as latency are already becoming possible, and new instruments will fill in the gaps in detection by imaging a wider range of chemicals and other agents and by collecting new data types. This study shows that with developments coming within the next decade, satellites should begin to provide valuable augmentations to CBRN event detection and monitoring. Article Highlights There is a wide range of existing satellite data in fields that are of interest to CBRN detection and monitoring. The data is mostly of insufficient quality (resolution or latency) for the demanding requirements of CBRN modelling for incident control. Future technologies and platforms will improve resolution and latency, making satellite data more viable in the CBRN management field

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