Cargando…

Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation

Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein–DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions...

Descripción completa

Detalles Bibliográficos
Autores principales:	Faltejsková, Kateřina, Jakubec, David, Vondrášek, Jiří
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2020
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7312683/ https://www.ncbi.nlm.nih.gov/pubmed/32498246 http://dx.doi.org/10.3390/ijms21113986

Ejemplares similares

Amino Acid Interaction (INTAA) web server
por: Galgonek, Jakub, et al.
Publicado: (2017)

Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures
por: Vymětal, Jiří, et al.
Publicado: (2021)

Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis
por: Jakubec, David, et al.
Publicado: (2016)

Modern and prebiotic amino acids support distinct structural profiles in proteins
por: Tretyachenko, Vyacheslav, et al.
Publicado: (2022)

Is the hydrophobic core a universal structural element in proteins?
por: Kalinowska, Barbara, et al.
Publicado: (2017)

Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins
por: Jakubec, David, et al.
Publicado: (2018)

3DPatch: fast 3D structure visualization with residue conservation
por: Jakubec, David, et al.
Publicado: (2019)

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures
por: van Dijk, Erik, et al.
Publicado: (2015)

Refining amino acid hydrophobicity for dynamics simulation of membrane proteins
por: Hills, Jr, Ronald D.
Publicado: (2018)

Mutation of exposed hydrophobic amino acids to arginine to increase protein stability
por: Strub, Caroline, et al.
Publicado: (2004)

Experimental Measures of Amino Acid Hydrophobicity and the Topology of Transmembrane and Globular Proteins
por: Wolfenden, Richard
Publicado: (2007)

The Importance of 6-Aminohexanoic Acid as a Hydrophobic, Flexible Structural Element
por: Markowska, Agnieszka, et al.
Publicado: (2021)

Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x‐ray reference structures as a prediction benchmark
por: Vymětal, Jiří, et al.
Publicado: (2022)

Rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity
por: Matsui, Daisuke, et al.
Publicado: (2017)

Perspectives on Membrane Protein Insertion, Protein–Bilayer Interactions, and Amino Acid Side Hydrophobicity
por: Andersen, Olaf Sparre
Publicado: (2007)

Self-Structuring in Water of Polyamidoamino Acids with Hydrophobic Side Chains Deriving from Natural α-Amino Acids
por: Lazzari, Federica, et al.
Publicado: (2018)

Production of hydrophobic amino acids from biobased resources: wheat gluten and rubber seed proteins
por: Widyarani, et al.
Publicado: (2016)

Exploring the dark foldable proteome by considering hydrophobic amino acids topology
por: Bitard-Feildel, Tristan, et al.
Publicado: (2017)

Study of the Structure-Function-Stability Relationships in Yeast D-amino Acid Oxidase: Hydrophobization of Alpha-Helices
por: Golubev, I. V., et al.
Publicado: (2014)

Amino Acid Transporters and Release of Hydrophobic Amino Acids in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120
por: Pernil, Rafael, et al.
Publicado: (2015)

Random protein sequences can form defined secondary structures and are well-tolerated in vivo
por: Tretyachenko, Vyacheslav, et al.
Publicado: (2017)

Universality in RNA and DNA deformations induced by salt, temperature change, stretching force, and protein binding
por: Tian, Fu-Jia, et al.
Publicado: (2023)

Investigation of the Role of Hydrophobic Amino Acids on the Structure-Activity Relationship in the Antimicrobial Venom Peptide Ponericin L1
por: Schifano, Nicholas P., et al.
Publicado: (2022)

Identification of Channel-lining Amino Acid Residues in the Hydrophobic Segment of Colicin Ia
por: Kienker, Paul K., et al.
Publicado: (2008)

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study
por: Song, Lingshuang, et al.
Publicado: (2016)

An exceptional series of phase transitions in hydrophobic amino acids with linear side chains
por: Görbitz, Carl Henrik, et al.
Publicado: (2016)

50 years of amino acid hydrophobicity scales: revisiting the capacity for peptide classification
por: Simm, Stefan, et al.
Publicado: (2016)

Interoperable chemical structure search service
por: Kratochvíl, Miroslav, et al.
Publicado: (2019)

An Ensemble Classifier for Eukaryotic Protein Subcellular Location Prediction Using Gene Ontology Categories and Amino Acid Hydrophobicity
por: Li, Liqi, et al.
Publicado: (2012)

Correction to: Interoperable chemical structure search service
por: Kratochvíl, Miroslav, et al.
Publicado: (2020)

NPPD: A Protein-Protein Docking Scoring Function Based on Dyadic Differences in Networks of Hydrophobic and Hydrophilic Amino Acid Residues
por: Shih, Edward S. C., et al.
Publicado: (2015)

TRPM7 N-terminal region forms complexes with calcium binding proteins CaM and S100A1
por: Bousova, Kristyna, et al.
Publicado: (2021)

Generalized EmbedSOM on quadtree-structured self-organizing maps
por: Kratochvíl, Miroslav, et al.
Publicado: (2020)

Binaphthyl-anchored antibacterial tripeptide derivatives with hydrophobic C-terminal amino acid variations
por: Bremner, John B, et al.
Publicado: (2012)

Hydrophobicity and Aromaticity Are Primary Factors Shaping Variation in Amino Acid Usage of Chicken Proteome
por: Rao, Yousheng, et al.
Publicado: (2014)

Hydrophobic amino acids as a new class of kinetic inhibitors for gas hydrate formation
por: Sa, Jeong-Hoon, et al.
Publicado: (2013)

External lysis of Escherichia coli by a bacteriophage endolysin modified with hydrophobic amino acids
por: Yan, Guangmou, et al.
Publicado: (2019)

TRPV1 temperature activation is specifically sensitive to strong decreases in amino acid hydrophobicity
por: Sosa-Pagán, Jason O., et al.
Publicado: (2017)

Electrospinning and Post-Spun Chain Conformations of Synthetic, Hydrophobic Poly(α-amino acid)s
por: Devarayan, Kesavan, et al.
Publicado: (2020)

Poly(hydrophobic Amino Acids) and Liposomes for Delivery of Vaccine against Group A Streptococcus
por: Azuar, Armira, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_dhf006u9l3gn8vo04f3e283lak