Binding Residues and Motifs
Sequence-Based Prediction of RNA-Binding Residues in Proteins
... individual residues in the interfaces of protein–RNA complexes is important for understanding the molecular determinants of protein–RNA recognition and has many potential ...RNA-binding residues in ...
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Cell Surface-Binding Motifs of L2 That Facilitate Papillomavirus Infection
... of residues 91 to 128 of BPV1 L2 from the surface of BPV1 virions eliminates ...L2 residues 1 to 88 binds to cells and blocks infection by BPV1, the BPV L2 peptide comprising residues 45 to 173 ...
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Structure of Pumilio Reveals Similarity between RNA and Peptide Binding Motifs
... conserved residues (Figure 4C) projecting into the solvent are reminiscent of the asparagine and tryptophan arrays on the H3 sur- face of karyopherin- ␣ (Conti et ...basic residues neutralize the ...
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Identification of caspase 3 motifs and critical aspartate residues in human Phospholipase D1b and Phopsholipase D2a
... PKC binding and phosphorylation sites within PLD1b and located in the extreme N-terminus [17], the mechanism by which this mutation prevents phosphatidylcholine hydrolysis is not ...
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Structures and metal-ion-binding properties of the Ca 2 + -binding helix–loop–helix EF-hand motifs
... the binding of Ca 2+ to the unbound form stabilizes certain substates at the expense of others, as it results in structural changes in the EF-hands which decrease the frequency with which the closed substates are ...
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Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation
... Conserved residues in eIF3 subunits a and c control HCV IRES binding To determine the regions of eIF3 subunits a and c that bind the HCV IRES IIIabc domain, the sequences of these two subunits were analyzed ...
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Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites
... acid residues that are found in α-helices, β-strands, or loops in the Mg2+-proteins according to the secondary structure infor- mation in the Protein Data Bank [16] (PDB) files were computed (see Figure ...all ...
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Two RNA-binding motifs in eif3 direct HCV IRES-dependent translation
... Conserved residues in eIF3 subunits a and c control HCV IRES binding To determine the regions of eIF3 subunits a and c that bind the HCV IRES IIIabc domain, the sequences of these two subunits were analyzed ...
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Identification of HI-Like Loop in CELO Adenovirus Fiber for Incorporation of Receptor Binding Motifs
... acid residues 661 to ...integrin- binding motif RGD (5, 6, 15, 17, 21, 36) as a heterologous receptor binding sequence within the identified HI-like loop, as well as at the C terminus of the fiber 1 ...
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Pretargeted Imaging with Gallium-68 Improving the Binding Capability by Increasing the Number of Tetrazine Motifs
... the binding capacity and may lead to enhanced PET imaging with ...protein binding, stability, binding towards TCO modified rituximab (RTX)) and in vivo (biodistribution- and imaging studies in normal ...
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Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs
... acid residues (Figure ...mutating residues that are located distant from the binding sites and not involved in RNA binding justi- fied the ...among binding site residues, and ...
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Effects of Secondary Binding Motifs in Arylethynyl Anion Receptors
... anion-binding motifs in supramolecular structures effectively—and perhaps still necessary in the recent past to convince skeptics that this attractive interaction rises to the level of inclusion as a ...
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Identifying combinatorial regulation of transcription factors and binding motifs
... 'over-represented motifs' with 'over-represented TFs' (see Materials and meth- ...and motifs that are specific to a functional gene ...9-mer motifs as well as combina- tions of ...known ...
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Variable structure motifs for transcription factor binding sites
... factors, both of which are known to affect binding pre- ferences [70,71]. Model limited to one gap A natural extension to our model would be to allow the optional characters to span more than one base. For ...
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Variable structure motifs for transcription factor binding sites
... factors, both of which are known to affect binding pre- ferences [70,71]. Model limited to one gap A natural extension to our model would be to allow the optional characters to span more than one base. For ...
20
Different gene regulation strategies revealed by analysis of binding motifs
... spurious binding events was estimated by using an information-theoretical bound provided by the classical result of Berg and von Hippel [44], by simulations where the frequency of a motif with a given length and ...
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PREDICTION OF CALMODULIN-BINDING PROTEINS USING SHORT LINEAR MOTIFS
... Because of their importance in development and disease identification and curation, prediction of protein interactions has been the object of intense research for many years. It has emerged from these studies that nature ...
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Identification of novel sphingolipid-binding motifs in mammalian membrane proteins
... move motifs that do not generate a statistically signi ficant over- representation of hits in the database being ...tify motifs that are signi ficantly over-represented in the original data ...
5
ATPsite: sequence-based prediction of ATP-binding residues
... finds binding residues for other ligand types, cata- lytic residues, and key residues that are critical for pro- tein ...ATP-binding residues are in conserved sequence segments, ...
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A Plasmodium falciparum copper binding membrane protein with copper transport motifs
... coli is thought to be regulated by the actions of the DNA-binding metal sensor CueR, which controls the ex- pression of genes encoding proteins involved in metal homeostasis [50]. A copper-requiring protein is ...
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