Wyniki wyszukiwania dla: Volkhard Helms

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Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in Mammalian Cells and Mice (Small 38/2024)

Alexandra A.M. Fischer, Hanah B. Robertson, Deqiang Kong, Merlin M. Grimm, więcej

Small > 20 > 38 > n/a - n/a

Controlling Gene Expression In article number 2311834, Wilfried Weber and co‐workers demonstrate that the material properties of transcription factor condensates impact their activity on target promoters. While liquid (spherical) condensates induce increased transcriptional activity, gel‐like (non‐spherical) condensates correlate with strongly decreased gene expression.

artykuł

Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in Mammalian Cells and Mice

Alexandra A.M. Fischer, Hanah B. Robertson, Deqiang Kong, Merlin M. Grimm, więcej

Small > 20 > 38 > n/a - n/a

Phase separation of biomolecules into condensates is a key mechanism in the spatiotemporal organization of biochemical processes in cells. However, the impact of the material properties of biomolecular condensates on important processes, such as the control of gene expression, remains largely elusive. Here, the material properties of optogenetically induced transcription factor condensates are systematically...

artykuł

Is the proteomic composition of the salivary pellicle dependent on the substrate material?

Simone Trautmann, Nicolas Künzel, Claudia Fecher‐Trost, Ahmad Barghash, więcej

PROTEOMICS – Clinical Applications > 16 > 3 > n/a - n/a

Purpose The use of dental restorative materials is a routine task in clinical dentistry. Upon exposure to the oral cavity, continuous adsorption of salivary proteins and other macromolecules to all surfaces occurs, representing the first step in dental biofilm formation. Different physico‐chemical properties of substrate materials potentially influence the composition of the initial biofilm, termed...

artykuł

How phosphorylation of peptides affects their interaction with 14‐3‐3η domains

Nicolas Künzel, Volkhard Helms

Proteins: Structure, Function, and Bioinformatics > 90 > 2 > 351 - 362

Members of the 14‐3‐3 domain family have important functions as adapter domains. Via an amphipathic groove on their protein surface they typically bind to disordered C‐terminals of other proteins. Importantly, binding partners of 14‐3‐3 domains usually contain a phosphorylated serine or threonine residue at their binding interface and possess one of three different sequence motifs. Binding of the...

artykuł

Deep Proteomic Insights into the Individual Short‐Term Pellicle Formation on Enamel—An In Situ Pilot Study

Simone Trautmann, Nicolas Künzel, Claudia Fecher‐Trost, Ahmad Barghash, więcej

PROTEOMICS – Clinical Applications > 14 > 6 > n/a - n/a

artykuł

Identification of signal peptide features for substrate specificity in human Sec62/Sec63‐dependent ER protein import

Stefan Schorr, Duy Nguyen, Sarah Haßdenteufel, Nagarjuna Nagaraj, więcej

The FEBS Journal > 287 > 21 > 4612 - 4640

In mammalian cells, one‐third of all polypeptides are integrated into the membrane or translocated into the lumen of the endoplasmic reticulum (ER) via the Sec61 channel. While the Sec61 complex facilitates ER import of most precursor polypeptides, the Sec61‐associated Sec62/Sec63 complex supports ER import in a substrate‐specific manner. So far, mainly posttranslationally imported precursors and...

artykuł

Deep Proteomic Insights into the Individual Short‐Term Pellicle Formation on Enamel—An In Situ Pilot Study

Simone Trautmann, Nicolas Künzel, Claudia Fecher‐Trost, Ahmad Barghash, więcej

PROTEOMICS – Clinical Applications > 14 > 3 > n/a - n/a

Purpose Dental pellicle formation starts instantaneously after oral hygiene due to the adsorption of salivary proteins to all orally exposed surfaces. The pellicle acts as a physiological mediator, protects the tooth surface from mechanical damages and reduces acid‐induced enamel demineralization. The aim of this pilot study is to identify and characterize individual proteomic profiles of the initial...

artykuł

Topology Consistency of Disease-specific Differential Co-regulatory Networks

Maryam Nazarieh, Hema Sekhar Reddy Rajula, Volkhard Helms

BMC Bioinformatics > 2019 > 20 > 1 > 1-10

Background Sets of differentially expressed genes often contain driver genes that induce disease processes. However, various methods for identifying differentially expressed genes yield quite different results. Thus, we investigated whether this affects the identification of key players in regulatory networks derived by downstream analysis from lists of differentially expressed genes. Results While...

artykuł

ER import of small human presecretory proteins: components and mechanisms

Sarah Haßdenteufel, Duy Nguyen, Volkhard Helms, Sven Lang, więcej

FEBS Letters > 593 > 18 > 2506 - 2524

Protein transport into the mammalian endoplasmic reticulum (ER) used to be seen as strictly cotranslational, that is temporarily and mechanistically coupled to protein synthesis. In the course of the last decades, however, several classes of precursors of soluble and membrane proteins were found to be post‐translationally imported into the ER, without any involvement of the ribosome. The first such...

artykuł

Proteomic Analysis of the Initial Oral Pellicle in Caries‐Active and Caries‐Free Individuals

Simone Trautmann, Ahmad Barghash, Claudia Fecher‐Trost, Pascal Schalkowsky, więcej

PROTEOMICS – Clinical Applications > 13 > 4 > n/a - n/a

Purpose To 1) elucidate individual proteomic profiles of the 3‐min biofilm of caries‐active and caries‐free individuals and 2) compare these proteomic profiles against the background of caries. Experimental design The initial oral pellicle of 12 caries‐active and 12 caries‐free individuals is generated in situ on ceramics specimens. The individual, host‐specific proteomic profiles of this basic...

artykuł

Differential analysis of combinatorial protein complexes with CompleXChange

Thorsten Will, Volkhard Helms

BMC Bioinformatics > 2019 > 20 > 1 > 1-14

Background Although a considerable number of proteins operate as multiprotein complexes and not on their own, organism-wide studies so far are only able to quantify individual proteins or protein-coding genes in a condition-specific manner for a sizeable number of samples, but not their assemblies. Consequently, there exist large amounts of transcriptomic data and an increasing amount of data on proteome...

artykuł

ALLO: A tool to discriminate and prioritize allosteric pockets

Rahmad Akbar, Volkhard Helms

Chemical Biology & Drug Design > 91 > 4 > 845 - 853

Allosteric proteins make up a substantial proportion of human drug targets. Thus, rational design of small molecule binders that target these proteins requires the identification of putative allosteric pockets and an understanding of their potential activity. Here, we characterized allosteric pockets using a set of physicochemical descriptors and compared them to pockets that are found on the surface...

artykuł

Human profilin 1 is a negative regulator of CTL mediated cell‐killing and migration

Rouven Schoppmeyer, Renping Zhao, He Cheng, Mohamed Hamed, więcej

European Journal of Immunology > 47 > 9 > 1562 - 1572

The actin‐binding protein profilin1 (PFN1) plays a central role in actin dynamics, which is essential for cytotoxic T lymphocyte (CTL) functions. The functional role of PFN1 in CTLs, however still remains elusive. Here, we identify PFN1 as the only member of the profilin family expressed in primary human CD8⁺ T cells. Using in vitro assays, we find that PFN1 is a negative regulator of CTL‐mediated...

artykuł

ENRI: A tool for selecting structure‐based virtual screening target conformations

Rahmad Akbar, Siti Azma Jusoh, Rommie E. Amaro, Volkhard Helms

Chemical Biology & Drug Design > 89 > 5 > 762 - 771

Finding pharmaceutically relevant target conformations from an arbitrary set of protein conformations remains a challenge in structure‐based virtual screening (SBVS). The growth in the number of available conformations, either experimentally determined or computationally derived, obscures the situation further. While the inflated conformation space potentially contains viable druggable targets, the...

artykuł

Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare

Thorsten Will, Volkhard Helms

BMC Systems Biology > 2017 > 11 > 1 > 1-19

Background Differential analysis of cellular conditions is a key approach towards understanding the consequences and driving causes behind biological processes such as developmental transitions or diseases. The progress of whole-genome expression profiling enabled to conveniently capture the state of a cell’s transcriptome and to detect the characteristic features that distinguish cells in specific...

artykuł

Methylation-targeted specificity of the DNA binding proteins R.DpnI and MeCP2 studied by molecular dynamics simulations

Siba Shanak, Ozlem Ulucan, Volkhard Helms

Journal of Molecular Modeling > 2017 > 23 > 5 > 1-12

DNA methylation plays a major role in organismal development and the regulation of gene expression. Methylation of cytosine bases and the cellular roles of methylated cytosine in eukaryotes are well established, as well as methylation of adenine bases in bacterial genomes. Still lacking, however, is a general mechanistic understanding, in structural and thermodynamic terms, of how proteins recognize...

rozdział

Predicting the burial/exposure status of transmembrane residues in helical membrane proteins

Volkhard Helms, Sikander Hayat, Jennifer Metzger

Structural Bioinformatics of Membrane Proteins > 151-164

In multipass transmembrane proteins one face of the transmembrane helices is in contact with the aliphatic acyl chains of the phospholipids and with the polar interface region. The other face makes contacts with other helices or points into the protein interior. In larger proteins, some helices may even be buried completely. Analysis of the available three-dimensional crystal structures has shown...

artykuł

Identification of key player genes in gene regulatory networks

Maryam Nazarieh, Andreas Wiese, Thorsten Will, Mohamed Hamed, więcej

BMC Systems Biology > 2016 > 10 > 1 > 1-12

Background Identifying the gene regulatory networks governing the workings and identity of cells is one of the main challenges in understanding processes such as cellular differentiation, reprogramming or cancerogenesis. One particular challenge is to identify the main drivers and master regulatory genes that control such cell fate transitions. In this work, we reformulate this problem as the optimization...

artykuł

Whole genome sequence typing and microarray profiling of nasal and blood stream methicillin-resistant Staphylococcus aureus isolates: Clues to phylogeny and invasiveness

Mohamed Hamed, Daniel Patric Nitsche-Schmitz, Ulla Ruffing, Matthias Steglich, więcej

Infection, Genetics and Evolution > 2015 > 36 > C > 475-482

Hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) infections are frequently caused by predominant clusters of closely related isolates that cannot be discriminated by conventional diagnostic typing methods. Whole genome sequencing (WGS) and DNA microarray (MA) now allow for better discrimination within a prevalent clonal complex (CC). This single center exploratory study aims...

artykuł

Erratum to “Hepatic hepcidin expression is decreased in cirrhosis and HCC” [J Hepatol 2015;62:977–979]

Sonja M. Kessler, Ahmad Barghash, Stephan Laggai, Volkhard Helms, więcej

Journal of Hepatology > 2015 > 63 > 2 > 536

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MOLECULAR DYNAMICS SIMULATION (7)
ENDOPLASMIC RETICULUM (6)
MOLECULAR DOCKING (3)
PROTEIN TRANSLOCATION (3)
SEC61 COMPLEX (3)
BINDING POCKET (2)
BIOMOLECULAR CONDENSATES (2)
CHARGED AMINO ACIDS (2)
COULOMBIC FUNCTION (2)
DNA METHYLATION (2)
EPIGENETICS (2)
INDIVIDUAL PROTEOMIC PROFILES (2)
LENNARD-JONES FUNCTION (2)
LIQUID‐LIQUID PHASE SEPARATION (2)
MATERIAL PROPERTIES OF PROTEIN CONDENSATES (2)
MEMBRANE INSERTION (2)
MINIMUM CONNECTED DOMINATING SET (2)
MINIMUM DOMINATING SET (2)
MOLECULAR DYNAMICS (2)
OPTOGENETICS (2)
PROTEIN–PROTEIN INTERACTIONS (2)
PROTON TRANSFER (2)
SEC61 CHANNEL (2)
SILICA NANOPARTICLE (2)
SYNTHETIC BIOLOGY (2)
TRANSMEMBRANE BETA BARREL PROTEINS (2)
3‐MIN PELLICLE (1)
3‐MIN PELLICLE AND SALIVA (1)
ABSORPTION SPECTRUM (1)
ACETYLCHOLINESTERASE (1)
ACTIN DYNAMICS (1)
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FREE ENERGY CALCULATION (1)
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Biophysical Journal (14)
Journal of Molecular Modeling (4)
PROTEOMICS – Clinical Applications (4)
Proteins: Structure, Function, and Bioinformatics (4)
The Journal of Physical Chemistry B (4)
Journal of Inorganic Biochemistry (3)
Angewandte Chemie (2)
Angewandte Chemie International Edition (2)
BBA - Biomembranes (2)
BBA - Proteins and Proteomics (2)
BMC Bioinformatics (2)
BMC Systems Biology (2)
Chemical Biology & Drug Design (2)
FEBS Letters (2)
Journal of Chemical Theory and Computation (2)
Journal of Computational Chemistry (2)
Journal of Hepatology (2)
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BMC Genomics (1)
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Current Opinion in Structural Biology (1)
European Journal of Immunology (1)
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Infection, Genetics and Evolution (1)
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Journal of Computer-Aided Molecular Design (1)
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Journal of the American Chemical Society (1)
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