Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Biomimetic conformation-specific assembly of proteins at artificial binding sites nanopatterned on silicon.

ABSTRACT: Biomolecules such as enzymes and antibodies possess binding sites where the molecular architecture and the physicochemical properties are optimum for their interaction with a particular target, in some cases even differentiating between stereoisomers. Here, we mimic this exquisite specificity via the creation of a suitable chemical environment by fabricating artificial binding sites for the protein calmodulin (CaM). By downscaling well-known surface chemical modification methodologies to the nanometer scale via silicon nanopatterning, the Ca(2+)-CaM conformer was found to selectively bind the biomimetic binding sites. The methodology could be adapted to mimic other protein-receptor interactions for sensing and catalysis.

SUBMITTER: de la Rica R

PROVIDER: S-EPMC2774499 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Biomimetic conformation-specific assembly of proteins at artificial binding sites nanopatterned on silicon.

de la Rica Roberto R Matsui Hiroshi H

Journal of the American Chemical Society 20091001 40

Biomolecules such as enzymes and antibodies possess binding sites where the molecular architecture and the physicochemical properties are optimum for their interaction with a particular target, in some cases even differentiating between stereoisomers. Here, we mimic this exquisite specificity via the creation of a suitable chemical environment by fabricating artificial binding sites for the protein calmodulin (CaM). By downscaling well-known surface chemical modification methodologies to the nan ...[more]

PMID: 19757782

Similar Datasets

GATA1 Binding Kinetics on Conformation-Specific Binding Sites Elicit Differential Transcriptional Regulation.

Project description:GATA1 organizes erythroid and megakaryocytic differentiation by orchestrating the expression of multiple genes that show diversified expression profiles. Here, we demonstrate that GATA1 monovalently binds to a single GATA motif (Single-GATA) while a monomeric GATA1 and a homodimeric GATA1 bivalently bind to two GATA motifs in palindromic (Pal-GATA) and direct-repeat (Tandem-GATA) arrangements, respectively, and form higher stoichiometric complexes on respective elements. The amino-terminal zinc (N) finger of GATA1 critically contributes to high occupancy of GATA1 on Pal-GATA. GATA1 lacking the N finger-DNA association fails to trigger a rate of target gene expression comparable to that seen with the wild-type GATA1, especially when expressed at low level. This study revealed that Pal-GATA and Tandem-GATA generate transcriptional responses from GATA1 target genes distinct from the response of Single-GATA. Our results support the notion that the distinct alignments in binding motifs are part of a critical regulatory strategy that diversifies and modulates transcriptional regulation by GATA1.

| S-EPMC4968217 | biostudies-literature

Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins.

Project description:We describe a phage display methodology for engineering synthetic antigen binders (sABs) that recognize either the apo or the ligand-bound conformation of maltose-binding protein (MBP). sABs that preferentially recognize the maltose-bound form of MBP act as positive allosteric effectors by substantially increasing the affinity for maltose. A crystal structure of a sAB bound to the closed form of MBP reveals the basis for this allosteric effect. We show that sABs that recognize the bound form of MBP can rescue the function of a binding-deficient mutant by restoring its natural affinity for maltose. Furthermore, the sABs can enhance maltose binding in vivo, as they provide a growth advantage to bacteria under low-maltose conditions. The results demonstrate that structure-specific sABs can be engineered to dynamically control ligand-binding affinities by modulating the transition between different conformations.

| S-EPMC3077571 | biostudies-literature

Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins.

Project description:Transport of small molecules across the cell membrane is a crucial biological mechanism for the maintenance of the cell activity. ABC transporter family is a huge group in the transporter membrane proteins and actively transports the substrates using the energy derived from ATP hydrolysis. In humans, there are 48 distinct genes for ABC transporters. A variation of a single amino acid in the amino acid sequence of ABC transporter has been known to be linked with certain disease. The mechanism of the onset of the disease by the variation is, however, still unclear. Recent progress in the method to measure the structures of huge membrane proteins has enabled determination of the 3D structures of ABC transporters and the accumulation of coordinate data of ABC transporter has enabled us to obtain clues for the onset of the disease caused by a single variation of amino acid residue. We compared the structures of ABC transporter in apo and ATP-binding forms and found a possible conformation shift around pivot-like residues in the transmembrane domains. When this conformation change in ABC transporter and the location of pathogenic variation were compared, we found a reasonable match between the two, explaining the onset of the disease by the variation. They likely cause impairment of the pivot-like movement, weakening of ATP binding and weakening of membrane surface interactions. These findings will give a new interpretation of the variations on ABC transporter genes and pave a way to analyse the effect of variation on protein structure and function.

| S-EPMC6435017 | biostudies-literature

Identification of specific lipid-binding sites in integral membrane proteins.

Project description:Protein-lipid interactions are increasingly recognized as central to the structure and function of membrane proteins. However, with the exception of simplified models, specific protein-lipid interactions are particularly difficult to highlight experimentally. Here, we used molecular dynamics simulations to identify a specific protein-lipid interaction in lactose permease, a prototypical model for transmembrane proteins. The interactions can be correlated with the functional dependence of the protein to specific lipid species. The technique is simple and widely applicable to other membrane proteins, and a variety of lipid matrices can be used.

| S-EPMC2856259 | biostudies-literature

Potent and specific inhibition of glycosidases by small artificial binding proteins (affitins).

Project description:Glycosidases are associated with various human diseases. The development of efficient and specific inhibitors may provide powerful tools to modulate their activity. However, achieving high selectivity is a major challenge given that glycosidases with different functions can have similar enzymatic mechanisms and active-site architectures. As an alternative approach to small-chemical compounds, proteinaceous inhibitors might provide a better specificity by involving a larger surface area of interaction. We report here the design and characterization of proteinaceous inhibitors that specifically target endoglycosidases representative of the two major mechanistic classes; retaining and inverting glycosidases. These inhibitors consist of artificial affinity proteins, Affitins, selected against the thermophilic CelD from Clostridium thermocellum and lysozyme from hen egg. They were obtained from libraries of Sac7d variants, which involve either the randomization of a surface or the randomization of a surface and an artificially-extended loop. Glycosidase binders exhibited affinities in the nanomolar range with no cross-recognition, with efficient inhibition of lysozyme (Ki = 45 nM) and CelD (Ki = 95 and 111 nM), high expression yields in Escherichia coli, solubility, and thermal stabilities up to 81.1°C. The crystal structures of glycosidase-Affitin complexes validate our library designs. We observed that Affitins prevented substrate access by two modes of binding; covering or penetrating the catalytic site via the extended loop. In addition, Affitins formed salt-bridges with residues essential for enzymatic activity. These results lead us to propose the use of Affitins as versatile selective glycosidase inhibitors and, potentially, as enzymatic inhibitors in general.

| S-EPMC4019568 | biostudies-literature

Prediction of dinucleotide-specific RNA-binding sites in proteins.

Project description:BACKGROUND: Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. Although some successful computational tools have been reported to recognize RNA binding sites in proteins, the problem of specificity remains poorly investigated. After the nucleotide base composition, the dinucleotide is the smallest unit of RNA sequence information and many RNA-binding proteins simply bind to regions enriched in one dinucleotide. Interaction preferences of protein subsequences and dinucleotides can be inferred from protein-RNA complex structures, enabling a training-based prediction approach. RESULTS: We analyzed basic statistics of amino acid-dinucleotide contacts in protein-RNA complexes and found their pairing preferences could be identified. Using a standard approach to represent protein subsequences by their evolutionary profile, we trained neural networks to predict multiclass target vectors corresponding to 16 possible contacting dinucleotide subsequences. In the cross-validation experiments, the accuracies of the optimum network, measured as areas under the curve (AUC) of the receiver operating characteristic (ROC) graphs, were in the range of 65-80%. CONCLUSIONS: Dinucleotide-specific contact predictions have also been extended to the prediction of interacting protein and RNA fragment pairs, which shows the applicability of this method to predict targets of RNA-binding proteins. A web server predicting the 16-dimensional contact probability matrix directly from a user-defined protein sequence was implemented and made available at: http://tardis.nibio.go.jp/netasa/srcpred.

| S-EPMC3278845 | biostudies-other

Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement.

Project description:Cytochrome P450 BM3 (BM3) is an important oxidoreductase that is widely used in drug synthesis, chemical synthesis, and other industries. However, as BM3 unquestionably increases costs by consuming a natural cofactor that unstably provides electrons, an alternative biomimetic cofactor with simpler structures represented by nicotinamide mononucleotide (NMNH) has been utilized. Currently, few reports exist on artificially modified BM3 enzymes using NMNH, especially regarding theoretical simulation and calculation. With the cognition of the mechanism in mind, we propose a strategy that optimizes and refines catalytic conformation. Based on constrained molecular dynamics simulation, the distance between N-5 of FAD flavin and C-4 of NMNH is used as a cue for the determination of improved conformation, and the potential positive mutants are subsequently screened virtually in accordance with binding free energy requirements. As a result, the K cat/K M values of the favorable mutant S848R increased to 205.38% compared to the wild-type BM3 with NMNH. These data indicate that our strategy can be applied for the specific utilization of biomimetic cofactors by oxidoreductases represented by BM3.

| S-EPMC8696588 | biostudies-literature

Enhanced adhesion of bioinspired nanopatterned elastomers via colloidal surface assembly.

Project description:We describe a scalable method to fabricate nanopatterned bioinspired dry adhesives using colloidal lithography. Close-packed monolayers of polystyrene particles were formed at the air/water interface, on which polydimethylsiloxane (PDMS) was applied. The order of the colloidal monolayer and the immersion depth of the particles were tuned by altering the pH and ionic strength of the water. Initially, PDMS completely wetted the air/water interface outside the monolayer, thereby compressing the monolayer as in a Langmuir trough; further application of PDMS subsequently covered the colloidal monolayers. PDMS curing and particle extraction resulted in elastomers patterned with nanodimples. Adhesion and friction of these nanopatterned surfaces with varying dimple depth were studied using a spherical probe as a counter-surface. Compared with smooth surfaces, adhesion of nanopatterned surfaces was enhanced, which is attributed to an energy-dissipating mechanism during pull-off. All nanopatterned surfaces showed a significant decrease in friction compared with smooth surfaces.

| S-EPMC4277096 | biostudies-literature

Biomimetic Nanopillar Silicon Surfaces Rupture Fungal Spores.

Project description:The mechano-bactericidal action of nanostructured surfaces is well-documented; however, synthetic nanostructured surfaces have not yet been explored for their antifungal properties toward filamentous fungal species. In this study, we developed a biomimetic nanostructured surface inspired by dragonfly wings. A high-aspect-ratio nanopillar topography was created on silicon (nano-Si) surfaces using inductively coupled plasma reactive ion etching (ICP RIE). To mimic the superhydrophobic nature of insect wings, the nano-Si was further functionalised with trichloro(1H,1H,2H,2H-perfluorooctyl)silane (PFTS). The viability of Aspergillus brasiliensis spores, in contact with either hydrophobic or hydrophilic nano-Si surfaces, was determined using a combination of standard microbiological assays, confocal laser scanning microscopy (CLSM), and focused ion beam scanning electron microscopy (FIB-SEM). Results indicated the breakdown of the fungal spore membrane upon contact with the hydrophilic nano-Si surfaces. By contrast, hydrophobised nano-Si surfaces prevented the initial attachment of the fungal conidia. Hydrophilic nano-Si surfaces exhibited both antifungal and fungicidal properties toward attached A. brasisiensis spores via a 4-fold reduction of attached spores and approximately 9-fold reduction of viable conidia from initial solution after 24 h compared to their planar Si counterparts. Thus, we reveal, for the first time, the physical rupturing of attaching fungal spores by biomimetic hydrophilic nanostructured surfaces.

| S-EPMC9864238 | biostudies-literature

Detecting cis-regulatory binding sites for cooperatively binding proteins.

Project description:Several methods are available to predict cis-regulatory modules in DNA based on position weight matrices. However, the performance of these methods generally depends on a number of additional parameters that cannot be derived from sequences and are difficult to estimate because they have no physical meaning. As the best way to detect cis-regulatory modules is the way in which the proteins recognize them, we developed a new scoring method that utilizes the underlying physical binding model. This method requires no additional parameter to account for multiple binding sites; and the only necessary parameters to model homotypic cooperative interactions are the distances between adjacent protein binding sites in basepairs, and the corresponding cooperative binding constants. The heterotypic cooperative binding model requires one more parameter per cooperatively binding protein, which is the concentration multiplied by the partition function of this protein. In a case study on the bacterial ferric uptake regulator, we show that our scoring method for homotypic cooperatively binding proteins significantly outperforms other PWM-based methods where biophysical cooperativity is not taken into account.

| S-EPMC2377448 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data