scholarly journals Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor

2004 ◽  
Vol 32 (13) ◽  
pp. 4026-4032 ◽  
Author(s):  
T.-K. Man
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Binding Specificity ◽  
Quantitative Modeling ◽  
Amino Acid Substitutions ◽  
Mnt Repressor ◽  
Dna Protein Interactions

scholarly journals Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space

2015 ◽  
Vol 113 (2) ◽  
pp. 326-331 ◽  
Author(s):  
William H. Hudson ◽  
Bradley R. Kossmann ◽  
Ian Mitchelle S. de Vera ◽  
Shih-Wei Chuo ◽  
Emily R. Weikum ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Binding Specificity ◽  
Conformational Space ◽  
Amino Acid Substitutions ◽  
Ancestral Gene ◽  
Response Elements ◽  
Binding Interface

Many genomes contain families of paralogs—proteins with divergent function that evolved from a common ancestral gene after a duplication event. To understand how paralogous transcription factors evolve divergent DNA specificities, we examined how the glucocorticoid receptor and its paralogs evolved to bind activating response elements [(+)GREs] and negative glucocorticoid response elements (nGREs). We show that binding to nGREs is a property of the glucocorticoid receptor (GR) DNA-binding domain (DBD) not shared by other members of the steroid receptor family. Using phylogenetic, structural, biochemical, and molecular dynamics techniques, we show that the ancestral DBD from which GR and its paralogs evolved was capable of binding both nGRE and (+)GRE sequences because of the ancestral DBD’s ability to assume multiple DNA-bound conformations. Subsequent amino acid substitutions in duplicated daughter genes selectively restricted protein conformational space, causing this dual DNA-binding specificity to be selectively enhanced in the GR lineage and lost in all others. Key substitutions that determined the receptors’ response element-binding specificity were far from the proteins’ DNA-binding interface and interacted epistatically to change the DBD’s function through DNA-induced allosteric mechanisms. These amino acid substitutions subdivided both the conformational and functional space of the ancestral DBD among the present-day receptors, allowing a paralogous family of transcription factors to control disparate transcriptional programs despite high sequence identity.

Single amino acid substitutions in influenza haemagglutinin change receptor binding specificity

Nature ◽  
1983 ◽  
Vol 304 (5921) ◽  
pp. 76-78 ◽  
Author(s):  
G. N. Rogers ◽  
J. C. Paulson ◽  
R. S. Daniels ◽  
J. J. Skehel ◽  
I. A. Wilson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Receptor Binding ◽  
Binding Specificity ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
Receptor Binding Specificity

Defining Amino Acid Residues Involved in DNA−Protein Interactions and Revelation of 3‘-Exonuclease Activity in Endonuclease V†

Biochemistry ◽  
2005 ◽  
Vol 44 (34) ◽  
pp. 11486-11495 ◽  
Author(s):  
Hong Feng ◽  
Liang Dong ◽  
Athena M. Klutz ◽  
Nima Aghaebrahim ◽  
Weiguo Cao
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Exonuclease Activity ◽  
Amino Acid Residues ◽  
Endonuclease V ◽  
Dna Protein Interactions

scholarly journals Amino acid substitutions contributing to α2,6-sialic acid linkage binding specificity of human parainfluenza virus type 3 hemagglutinin-neuraminidase

FEBS Letters ◽  
2015 ◽  
Vol 589 (11) ◽  
pp. 1278-1282 ◽  
Author(s):  
Keijo Fukushima ◽  
Tadanobu Takahashi ◽  
Hiroo Ueyama ◽  
Masahiro Takaguchi ◽  
Seigo Ito ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Amino Acid ◽  
Virus Type ◽  
Binding Specificity ◽  
Parainfluenza Virus ◽  
Amino Acid Substitutions ◽  
Human Parainfluenza Virus ◽  
Type 3 ◽  
Sialic Acid Linkage

scholarly journals DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments

2019 ◽  
Vol 36 (7) ◽  
pp. 2286-2287
Author(s):  
Krisztian Adam ◽  
Zoltan Gyorgypal ◽  
Zoltan Hegedus
Keyword(s):  
Protein Interactions ◽  
Dna Recognition ◽  
Binding Specificity ◽  
Regulatory Proteins ◽  
Supplementary Information ◽  
Nucleotide Level ◽  
Interacting Surfaces ◽  
Depth View ◽  
Dna Protein Interactions

Abstract Summary The sequence specific recognition of DNA by regulatory proteins typically occurs by establishing hydrogen bonds and non-bonded contacts between chemical sub-structures of nucleotides and amino acids forming the compatible interacting surfaces. The recognition process is also influenced by the physicochemical and conformational character of the target oligonucleotide motif. Although the role of these mechanisms in DNA-protein interactions is well-established, bioinformatical methods rarely address them directly, instead binding specificity is mostly assessed at nucleotide level. DNA Readout Viewer (DRV) aims to provide a novel DNA representation, facilitating in-depth view into these mechanisms by the concurrent visualization of functional groups and a diverse collection of DNA descriptors. By applying its intuitive representation concept for various DNA recognition related visualization tasks, DRV can contribute to unravelling the binding specificity factors of DNA-protein interactions. Availability and implementation DRV is freely available at https://drv.brc.hu. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Packaging of the Influenza Virus Genome Is Governed by a Plastic Network of RNA- and Nucleoprotein-Mediated Interactions

2018 ◽  
Vol 93 (4) ◽  
Author(s):  
Hardin Bolte ◽  
Miruna E. Rosu ◽  
Elena Hagelauer ◽  
Adolfo García-Sastre ◽  
Martin Schwemmle
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Influenza A Virus ◽  
Protein Interactions ◽  
Influenza A ◽  
Interaction Network ◽  
Virus Genome ◽  
Amino Acid Substitutions ◽  
Rna Packaging ◽  
Genome Packaging

ABSTRACTThe genome of influenza A virus is organized into eight ribonucleoproteins, each composed of a distinct RNA segment bound by the viral polymerase and oligomeric viral nucleoprotein. Packaging sequences unique to each RNA segment together with specific nucleoprotein amino acids are thought to ensure the precise incorporation of these eight ribonucleoproteins into single virus particles, and yet the underlying interaction network remains largely unexplored. We show here that the genome packaging mechanism of an H7N7 subtype influenza A virus widely tolerates the mutation of individual packaging sequences in three different RNA segments. However, combinations of these modified RNA segments cause distinct genome packaging defects, marked by the absence of specific RNA segment subsets from the viral particles. Furthermore, we find that combining a single mutated packaging sequence with sets of specific nucleoprotein amino acid substitutions greatly impairs the viral genome packaging process. Along with previous reports, our data propose that influenza A virus uses a redundant and plastic network of RNA-RNA and potentially RNA-nucleoprotein interactions to coordinately incorporate its segmented genome into virions.IMPORTANCEThe genome of influenza A virus is organized into eight viral ribonucleoproteins (vRNPs); this provides evolutionary advantages but complicates genome packaging. Although it has been shown that RNA packaging sequences and specific amino acids in the viral nucleoprotein (NP), both components of each vRNP, ensure selective packaging of one copy of each vRNP per virus particle, the required RNA-RNA and RNA-NP interactions remain largely elusive. We identified that the genome packaging mechanism tolerates the mutation of certain individual RNA packaging sequences, while their combined mutation provokes distinct genome packaging defects. Moreover, we found that seven specific amino acid substitutions in NP impair the function of RNA packaging sequences and that this defect is partially restored by another NP amino acid change. Collectively, our data indicate that packaging of the influenza A virus genome is controlled by a redundant and plastic network of RNA/protein interactions, which may facilitate natural reassortment processes.

scholarly journals Substitutional landscape of a split fluorescent protein fragment using high-density peptide microarrays

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0241461
Author(s):  
Oana N. Antonescu ◽  
Andreas Rasmussen ◽  
Nicole A. M. Damm ◽  
Ditte F. Heidemann ◽  
Roman Popov ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Super Resolution ◽  
Protein Detection ◽  
High Density ◽  
Amino Acid Substitutions ◽  
Peptide Microarrays ◽  
Green Fluorescent

Split fluorescent proteins have wide applicability as biosensors for protein-protein interactions, genetically encoded tags for protein detection and localization, as well as fusion partners in super-resolution microscopy. We have here established and validated a novel platform for functional analysis of leave-one-out split fluorescent proteins (LOO-FPs) in high throughput and with rapid turnover. We have screened more than 12,000 variants of the beta-strand split fragment using high-density peptide microarrays for binding and functional complementation in Green Fluorescent Protein. We studied the effect of peptide length and the effect of different linkers to the solid support. We further mapped the effect of all possible amino acid substitutions on each position as well as in the context of some single and double amino acid substitutions. As all peptides were tested in 12 duplicates, the analysis rests on a firm statistical basis allowing for confirmation of the robustness and precision of the method. Based on experiments in solution, we conclude that under the given conditions, the signal intensity on the peptide microarray faithfully reflects the binding affinity between the split fragments. With this, we are able to identify a peptide with 9-fold higher affinity than the starting peptide.

scholarly journals Substitutional landscape of a split fluorescent protein fragment using high-density peptide microarrays

2020 ◽  
Author(s):  
Oana N. Antonescu ◽  
Andreas Rasmussen ◽  
Nicole A.M. Damm ◽  
Ditte F. Heidemann ◽  
Roman Popov ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Super Resolution ◽  
Protein Detection ◽  
High Density ◽  
Amino Acid Substitutions ◽  
Peptide Microarrays ◽  
Green Fluorescent

ABSTRACTSplit fluorescent proteins have wide applicability as biosensors for protein-protein interactions, genetically encoded tags for protein detection and localization, as well as fusion partners in super-resolution microscopy. We have established and validated a novel platform for functional analysis of leave-one-out split fluorescent proteins (LOO-FPs) in high throughput and with rapid turnover. We have screened more than 12,000 strand 10 variants using high-density peptide microarrays for binding and functional complementation in Green Fluorescent Protein. We studied the effect of peptide length and the effect of different linkers to the solid support and mapped the effect of all possible amino acid substitutions on each position as well as in the context of some single and double amino acid substitutions. As all peptides were tested in 12 duplicates, the analysis rests on a firm statistical basis allowing determination of robustness and precision of the method. We showed that the microarray fluorescence correlated with the affinity in solution between the LOO-FP and peptides. A double substitution yielded a peptide with 9-fold higher affinity than the starting peptide.

Recombinant Variants of Tissue-Type Plasminogen Activator Containing Amino Acid Substitutions in the Finger Domain

1992 ◽  
Vol 68 (06) ◽  
pp. 672-677 ◽  
Author(s):  
Hitoshi Yahara ◽  
Keiji Matsumoto ◽  
Hiroyuki Maruyama ◽  
Tetsuya Nagaoka ◽  
Yasuhiro Ikenaka ◽  
...  
Keyword(s):  
Amino Acid ◽  
Plasminogen Activator ◽  
Half Life ◽  
Tissue Type ◽  
Clot Lysis ◽  
Amino Acid Substitutions ◽  
Wild Type ◽  
Plasma Clot ◽  
Tissue Type Plasminogen Activator ◽  
Type Plasminogen Activator

SummaryTissue-type plasminogen activator (t-PA) is a fibrin-specific agent which has been used to treat acute myocardial infarction. In an attempt to clarify the determinants for its rapid clearance in vivo and high affinity for fibrin clots, we produced five variants containing amino acid substitutions in the finger domain, at amino acid residues 7–9, 10–14, 15–19, 28–33, and 37–42. All the variants had a prolonged half-life and a decreased affinity for fibrin of various degrees. The 37–42 variant demonstrated about a 6-fold longer half-life with a lower affinity for fibrin. Human plasma clot lysis assay estimated the fibrinolytic activity of the 37–42 variant to be 1.4-fold less effective than that of the wild-type rt-PA. In a rabbit jugular vein clot lysis model, doses of 1.0 and 0.15 mg/kg were required for about 70% lysis in the wild-type and 37–42 variant, respectively. Fibrinogen was degraded only when the wild-type rt-PA was administered at a dose of 1.0 mg/kg. These findings suggest that the 37–42 variant can be employed at a lower dosage and that it is a more fibrin-specific thrombolytic agent than the wild-type rt-PA.

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