circular dichroism sp
- The conformational studies in solution are supplemented by other experimental biophysical methods, like X-ray crystallography, isothermal titration calorimetry (ITC), circular dichroism spectroscopy (CD), as well as advanced computational approaches - molecular dynamics (MD) simulations. (edu.sa)
- It is the extension of circular dichroism spectroscopy into the infrared and near infrared ranges. (wikipedia.org)
complexes
- In plants and green algae, light is captured by the light-harvesting complexes (LHCs), a family of integral membrane proteins that coordinate chlorophylls and carotenoids. (jove.com)
- In vivo , these proteins are folded with pigments to form complexes which are inserted in the thylakoid membrane of the chloroplast. (jove.com)
- The reconstitution method is powerful for various reasons: (1) pure preparations of individual complexes can be obtained, (2) pigment composition can be controlled to assess their contribution to structure and function, (3) recombinant proteins can be mutated to study the functional role of the individual residues ( e.g., pigment binding sites) or protein domain ( e.g., protein-protein interaction, folding). (jove.com)
- The various experimental strategies available to characterize the higher-order structures of proteins and their complexes can be classified as either "direct" or "indirect" in their approach. (springer.com)
- That the ESI process itself does not significantly perturb protein structure represents an important underlying assumption in the implementation of direct ESI-MS methods to characterize the structure of proteins and protein complexes in solution or structural changes resulting from changes to solution conditions. (springer.com)
- We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect-transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water-ligand interactions observed via gradient spectroscopy experiments-with the aim of reporting recent developments and applications for the characterization of protein-ligand complexes, including affinity measurements and structural determination. (springer.com)
- while a second, diamagnetic binding partner is labeled with stable isotopes ( 15 N or 13 C). Multiple paramagnetic labeled centers or reversed labeling schemes are often necessary to obtain sufficient distance restraints to model protein-protein complexes, making this approach time consuming and expensive. (springer.com)
- In addition to reducing the cost of sample preparation and speed up PRE measurements, by detecting the intra-molecular PRE this new strategy will make it possible to measure and calibrate inter-molecular distances more accurately for both symmetric and asymmetric protein-protein complexes. (springer.com)
- In spite of spectacular progress, the determination of the three-dimensional structure of large complexes at atomic resolution by means of X-ray crystallography or nuclear magnetic resonance spectroscopy remains a difficult task. (biomedcentral.com)
- Given the deficit of structural information on these assemblies and the increasing number of available structures for isolated proteins, computational modeling tools provide a promising approach to predicting structures of protein complexes. (biomedcentral.com)
- Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. (springer.com)
- Individual domains that mediate protein-protein and protein-nucleic acid interactions are typically connected by flexible linkers, which contribute to conformational dynamics and enable the formation of complexes with distinct binding partners. (springer.com)
- Nuclear magnetic resonance spectroscopy (NMR) provides such information but often only sparse data are obtained with increasing molecular weight of the complexes. (springer.com)
- For example DEER studies deliver information on protein conformational changes on ligand binding, and enable the investigation of protein-protein complexes and oligomers in frozen solution. (edu.au)
- The assembly of multi-subunit membrane protein complexes has also been studied using spin labeling. (wikipedia.org)
- He is known for his foundational work in three-dimensional protein and nucleic acid structure determination by biomolecular NMR spectroscopy, for advancing experimental approaches to the study of large macromolecules and their complexes by NMR, and for developing NMR-based methods to study rare conformational states in protein-nucleic acid and protein-protein recognition. (wikipedia.org)
- Clore's work on complexes of all the cytoplasmic components of the bacterial phosphotransferase system (PTS) led to significant insights into how signal transduction proteins recognize multiple, structurally dissimilar partners by generating similar binding surfaces from completely different structural elements and exploiting side chain conformational plasticity. (wikipedia.org)
- To describe the types of protein-protein interactions (PPIs) it is important to consider that proteins can interact in a "transient" way (to produce some specific effect in a short time) or to interact with other proteins in a "stable" way to build multiprotein complexes that are molecular machines within the living systems. (wikipedia.org)
- A protein complex assembly can result in the formation of homo-oligomeric or hetero-oligomeric complexes. (wikipedia.org)
- Homo-oligomers are macromolecular complexes constituted by only one type of protein subunit. (wikipedia.org)
- Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. (wikipedia.org)
interactions
- Our group is focused on understanding the molecular determinants driving the protein-protein and protein-ligand interactions, thus druggability of protein targets. (edu.sa)
- With the combination of molecular biology approaches we prepare and purify the human proteins of interest and subsequently study their structures and interactions with known drugs and other small molecules - ligands - potential candidates for becoming more potent drugs. (edu.sa)
- Indirect methods typically involve ESI-MS analysis of proteolytic peptides to investigate protein conformation and interactions. (springer.com)
- Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. (springer.com)
- One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. (springer.com)
- Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein-ligand interactions. (springer.com)
- Arkin MR, Wells JA (2004) Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. (springer.com)
- Niesen FH, Berglund H, Vedadi M (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. (springer.com)
- Protein-protein interactions are pivotal to most, if not all, physiological processes, and understanding the nature of such interactions is a central step in biological research. (jove.com)
- Surface Plasmon Resonance (SPR) is a sensitive detection technique for label-free study of bio-molecular interactions in real time. (jove.com)
- Being label-free, consuming low amounts of material, and providing pre-equilibrium kinetic data, often makes SPR the method of choice when studying dynamics of protein interactions. (jove.com)
- Paramagnetic relaxation enhancement (PRE) measurements constitute a powerful approach for detecting both permanent and transient protein-protein interactions. (springer.com)
- Brutscher B et al (2015) NMR methods for the study of instrinsically disordered proteins structure, dynamics, and interactions: general overview and practical guidelines. (springer.com)
- Complex docking models - elucidating protein-protein interactions with EPR. (esr-group.org)
- Numerous studies have been dedicated to protein-protein interactions [ 1 ] and the worldwide challenge "Critical Assessment of PRedicted Interactions" (CAPRI) [ 2 - 4 ] demonstrates the interest of the scientific community in this domain. (biomedcentral.com)
- Traditional assays examining the interaction between channels and regulatory proteins require exogenous labels that can potentially alter the protein's behavior and decrease the physiological relevance of the target, while providing little information on the time course of interactions in living cells. (jove.com)
- This assay allows the detection of the relative change in mass within the bottom portion of living cells adherent to the biosensor surface resulting from ligand induced changes in cell adhesion and spreading, toxicity, proliferation, and changes in protein-protein interactions near the plasma membrane. (jove.com)
- Ligand-induced changes in ion channel-protein interactions can also be studied using this assay. (jove.com)
- Protein Interactions: 427-446. (wikipedia.org)
- His recent work has focused on developing new NMR methods (such as paramagnetic relaxation enhancement, dark state exchange saturation transfer spectroscopy and lifetime line broadening) to characterize the structure and dynamics of sparsely-populated states of macromolecules, which are important in macromolecular interactions but invisible to conventional structural and biophysical techniques. (wikipedia.org)
- and the uncovering of "dark", spectroscopically invisible states in interactions of NMR-visible proteins and polypeptides (including intrinsically disordered states) with very large megadalton macromolecular assemblies. (wikipedia.org)
- Protein-protein interactions (PPIs) are the physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by electrostatic forces including the hydrophobic effect. (wikipedia.org)
- These interactions between proteins are dependent on highly specific binding between proteins to ensure efficient electron transfer. (wikipedia.org)
- More recent work on the phylogeny of the reductase has shown that these residues involved in protein-protein interactions have been conserved througout the evolution of this enzyme. (wikipedia.org)
- Another important distinction to identify protein-protein interactions is the way they have been determined, since there are techniques that measure direct physical interactions between protein pairs, named "binary" methods, while there are other techniques that measure physical interactions among groups of proteins, without pairwise determination of protein partners, named "co-complex" methods. (wikipedia.org)
- Protein subunits assembly is guided by the establishment of non-covalent interactions in the quaternary structure of the protein. (wikipedia.org)
- The understanding of the processes in organisms, which are mainly driven by biochemical reactions and protein-protein interactions, depends to a great extent on our ability to isolate active proteins in biological samples for more detailed examination of chemical structure and physiological function. (wikipedia.org)
- This conformational change exposes a large hydrophobic pocket between helix 3, 4, and the hinge region of S100A1 that is involved in virtually all calcium-dependent target protein interactions. (wikipedia.org)
- Rational protein design dates back to the mid-1970s, although initial protein design approaches were based mostly on sequence composition and did not account for specific interactions between side-chains at the atomic level. (wikipedia.org)
- Also of interest are protein-protein interactions, cellular distribution of proteins and understanding protein activity. (wikipedia.org)
crystallography
- VDAC1's structure was solved by 3 independent labs by x-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or a combination of both. (wikipedia.org)
- Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry. (wikipedia.org)
dynamics
- The project offers the wide range of experience, from the protein biochemistry techniques that lead to preparation of biologically relevant material, followed by hands-on experience, i.e. from the design and performing the advanced nuclear magnetic resonance NMR experiments to preparation and running the comprehensive molecular dynamics MD simulations and finally integration of the results coming from the different fields of expertise. (edu.sa)
- Kay LE (2011) NMR studies of protein structure and dynamics - a look backwards and forwards. (springer.com)
- Solution techniques are therefore required for structural analysis and to characterize potential conformational dynamics. (springer.com)
- Information about the operational dynamics of ion channel proteins can be obtained by observing long stretches of current produced by a single molecule. (jove.com)
- Site-directed spin labeling (SDSL) is a technique for investigating the structure and local dynamics of proteins using electron spin resonance. (wikipedia.org)
- In the 1990s, the advent of powerful computers, libraries of amino acid conformations, and force fields developed mainly for molecular dynamics simulations enabled the development of structure-based computational protein design tools. (wikipedia.org)
Dipolar Spectroscopy
- Laser-Induced Magnetic Dipolar Spectroscopy. (esr-group.org)
- Pulse EPR Dipolar Spectroscopy with High-Spin Mn 2+ Ions. (esr-group.org)
- A powerful technique of modern EPR is dipolar spectroscopy which is utilised in structural studies of biomolecules, for example with soluble and membrane proteins and their oligomers, DNA and RNA. (edu.au)
- Here dipolar spectroscopy refers to the measurement of electron-electron couplings with techniques such as Double Electron-Electron Resonance (DEER) or synonymously pulsed electron double resonance (PELDOR), double-quantum EPR (DQ-EPR), and related EPR methods. (edu.au)
- The standard paramagnetic spin-label for dipolar spectroscopy is MTLS which is covalently attached to a protein via a disulfide bond with a cysteine residue, although there are a number of other organic labels and a number employing Cu2+ and Gd3+ ions for example. (edu.au)
- DNA and RNA studies are also readily amendable to dipolar spectroscopy technologies. (edu.au)
mass spectrometry
- Jonker N, Kool J, Irth H, Niessen WA (2011) Recent developments in protein-ligand affinity mass spectrometry. (springer.com)
Double Electron-Electron Resonance
- Utilizing the TWT linear region: Double Electron-Electron Resonance (DEER) with multiple excitation pulses and dead-time free three-pulse DEER. (esr-group.org)
site-directed mu
- In SDSL, sites for attachment of spin labels are introduced into recombinantly expressed proteins by site-directed mutagenesis. (wikipedia.org)
intrinsically disordered
- It may be mentioned that the toxic properties of Aβ also requires the cooperation of the intrinsically disordered tau protein ( 13 ), ( 14 ). (degruyter.com)
- Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions. (mdpi.com)
- α-synuclein, an intrinsically disordered protein involved in Parkinson diseases, is also a hub of the protein network. (mdpi.com)
- These proteins with intrinsically disordered regions (IDRs) are called intrinsically disordered proteins (IDPs). (mdpi.com)
ions
- Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. (jove.com)
- Metal ions in PELDOR spectroscopy. (esr-group.org)
- Proteins perform several functions in living organisms, including catalytic reactions and transport of molecules or ions within the cells, the organs or the whole body. (wikipedia.org)
- This N-terminus can serve as a scaffold for the movement of ions or attachment of proteins. (wikipedia.org)
molecules
- The following protein molecules considered here are: the Aβ 40 (PDB ID: 2LMN), Aβ 42 (PDB ID: 5KK3 and 2NAO) and the double-layered Aβ 17−42 fibril. (degruyter.com)
- Bernini A, Venditti V, Spiga O, Niccolai N (2009) Probing protein surface accessibility with solvent and paramagnetic molecules. (springer.com)
- To regulate neuronal excitability, the biophysical properties of ion channels are modified by signaling proteins and molecules, which often bind to the channels themselves to form a heteromeric channel complex 2,3 . (jove.com)
- Measurements of vibrational optical activity (VOA) have thus numerous applications, not only for small molecules, but also for large and complex biopolymers such as muscle proteins (myosin, for example) and DNA. (wikipedia.org)
- Many of these cofactors (e.g., iron, copper, or zinc) play a key role in vital enzymatic catalytic processes or stabilize globular protein molecules. (wikipedia.org)
- Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another. (wikipedia.org)
- Protein design is the rational design of new protein molecules to fold to a target protein structure, with the end goal of designing novel function and/or behavior. (wikipedia.org)
- When they possess an electron withdrawing group and an electron donating group at opposite ends of the resonance structure, they have a large shift in charge distribution across the molecule, which causes the solvent molecules to reorient to a less energetic arrangement, called solvent relaxation. (wikipedia.org)
peptides
- NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. (jove.com)
- In order to understand intrinsic acid-base properties of peptides and proteins, it is important to perform the studies in a solvent-free environment. (jove.com)
- Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. (wikipedia.org)
Structural Biology
- NMR-based Structural Biology enhanced by Dynamic Nuclear Polarization at high magnetic field. (esr-group.org)
interaction
- Local network topology in human protein interaction data predicts functional association. (genes2cognition.org)
- The use of high-throughput techniques to generate large volumes of protein-protein interaction (PPI) data has increased the need for methods that systematically and automatically suggest functional relationships among proteins. (genes2cognition.org)
- If a drug interacting with the target protein is known, and this interaction leads to therapeutic benefits of patients, then this target protein is called druggable. (edu.sa)
- These disease-associated IDPs commonly play principal roles in the disease-associated protein-protein interaction networks. (mdpi.com)
- The disease-associated IDPs may provide potential targets for drugs modulating protein-protein interaction networks. (mdpi.com)
- Metz JT, Hajduk PJ (2010) Rational approaches to targeted polypharmacology: creating and navigating protein-ligand interaction networks. (springer.com)
- Morelli X, Bourgeas R, Roche P (2011) Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I). (springer.com)
- to HER3 by surface plasmon resonance and interaction map. (jove.com)
- with surface immobilized HER3 extracellular domain by time-resolved Surface Plasmon Resonance (SPR) was so far not interpretable using any regular analysis method as the interaction was highly complex. (jove.com)
- This protocol describes an SPR experiment characterizing the kinetic properties of the interaction between a membrane protein (an ABC transporter) and a soluble protein (the transporter's cognate substrate binding protein). (jove.com)
- A number of proteins help regulate these pathways through their interaction with CaM. (jove.com)
- My main research field is Electron Paramagnetic Resonance (EPR) spectroscopy, a technique that probes the interaction of unpaired electrons with their surroundings. (edu.au)
- All this information enables the creation of large protein interaction networks - similar to metabolic or genetic/epigenetic networks - that empower the current knowledge on biochemical cascades and molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest. (wikipedia.org)
ligand
- Huang S-Y, Grinter SZ, Zou X (2010) Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. (springer.com)
- In a typical SPR experiment, one component (usually a protein, termed 'ligand') is immobilized onto a sensor chip surface, while the other (the 'analyte') is free in solution and is injected over the surface. (jove.com)
- For sensing purposes, this property is, in general, used either in combination with a biomolecule, such as a protein, which undergoes a conformational change upon ligand binding, changing the distance between the two labels on this protein, or in a competition assay, in which the analyte has to compete with a known concentration of a fixed labelled ligand for the labelled binding site of protein. (wikipedia.org)
biological
- However, as early as in the 1990s, it was reported that there is another class of proteins, which have no well-defined structures under physiological conditions, but still have biological functions [ 1 , 2 ]. (mdpi.com)
- Electron Paramagnetic Resonance (EPR) spectroscopy in biological, medical, chemical and physical sciences. (edu.au)
- Ion channel proteins are universal devices for fast communication across biological membranes. (jove.com)
- in Biological Magnetic Resonance 27 - ESR Spectroscopy in Membrane Biophysics. (wikipedia.org)
- Biological Magnetic Resonance. (wikipedia.org)
- This standardized variant of native gel electrophoresis is used by biologists to isolate active or native metalloproteins in biological samples and to resolve properly and improperly folded metal cofactor-containing proteins or protein isoforms in complex protein mixtures. (wikipedia.org)
- Due to the specific properties of the prepared gel and electrophoresis buffer solution (which is basic and contains Tris-HCl and NaN3), most proteins of a biological system (e.g. (wikipedia.org)
- Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. (wikipedia.org)
- As a discipline, proteomics has moved past rapid protein identification and has developed into a biological assay for quantitative analysis of complex protein samples by comparing protein changes in differently perturbed systems. (wikipedia.org)
sequence
- The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy. (jove.com)
- According to the traditional sequence-to-structure-to-function paradigm, active proteins have well-defined three-dimensional structures under physiological conditions. (mdpi.com)
- We showed that both proteins interact with selected glycolipids through a common loop-shaped motif exhibiting little sequence homology. (jove.com)
- A Novel Triple Resonance Correlation Sequence for Resolving and Assigning Signals in ELDOR-detected NMR Spectra. (esr-group.org)
- Roy's researches during his stint in the US was on protein folding and nuclear magnetic resonance studies of DNA and those researches identified the first hydropathy model which helped in predicting the exteriors and interiors of proteins by analyzing sequence information. (wikipedia.org)
- Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity. (wikipedia.org)
- The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. (wikipedia.org)
- The end with a free amino group is known as the N-terminus or amino terminus, whereas the end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus (the sequence of the protein is written from N-terminus to C-terminus, from left to right). (wikipedia.org)
- Helix 3, 4, and the hinge region are the most divergent areas between individual S100 proteins, and so it is likely that the sequence of these regions is pivotal in fine-tuning calcium-dependent target binding by S100 proteins. (wikipedia.org)
- Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and its sequence (termed protein redesign). (wikipedia.org)
- Rational protein design approaches make protein-sequence predictions that will fold to specific structures. (wikipedia.org)
- Protein design is then an optimization problem: using some scoring criteria, an optimized sequence that will fold to the desired structure is chosen. (wikipedia.org)
- When the first proteins were rationally designed during the 1970s and 1980s, the sequence for these was optimized manually based on analyses of other known proteins, the sequence composition, amino acid charges, and the geometry of the desired structure. (wikipedia.org)
- Richardson and coworkers designed a 79-residue protein with no sequence homology to a known protein. (wikipedia.org)
nucleic
- The published reports over the last 22 years have established VCD as a powerful technique with improved results over those previously obtained by visible/UV circular dichroism (CD) or optical rotatory dispersion (ORD) for proteins and nucleic acids. (wikipedia.org)
- For biopolymers such as proteins and nucleic acids, the difference in absorbance between the levo- and dextro- configurations is five orders of magnitude smaller than the corresponding (unpolarized) absorbance. (wikipedia.org)
electron
- Tripartite Motif Family Proteins as a Playground for Pulsed Electron Paramagnetic Resonance. (esr-group.org)
- Electron Paramagnetic Resonance Studies on Oxygen Doped CVD Diamond. (esr-group.org)
- High-Field Electron Paramagnetic Resonance Studies of Anisotropic Molecular Magnets. (esr-group.org)
- August 2007 to March 2013: Scientific Coordinator and Applications manager of the Centre of Advanced Electron Spin Resonance (CAESR) at the Oxford University, UK. (edu.au)
- I was a project leader in the electron paramagnetic resonance group of Prof. Arthur Schweiger. (edu.au)
- Owing to the large magnetic moment of the electron, the technique delivers information in the distance range from ca. 15-80 Å. (edu.au)
- In many metabolic reactions, a protein that acts as an electron carrier binds to an enzyme that acts its reductase. (wikipedia.org)
- In the case of the mitochondrial P450 systems, the specific residues involved in the binding of the electron transfer protein adrenodoxin to its reductase were identified as two basic Arg residues on the surface of the reductase and two acidic Asp residues on the adrenodoxin. (wikipedia.org)
- An additional property of fluorescence that has found a large usage is Förster resonance energy transfer (Fret) in which the energy of the excited electron of one fluorophore, called the donor, is passed on to a nearby acceptor dye, either a dark-quencher (non-emitting chromophore) or another fluorophore, which has an excitation spectrum that overlaps with the emission spectrum of the donor dye, resulting in a reduced fluorescence. (wikipedia.org)
transient
- Tracing the transient conformational signal in bacterial phototaxis using SDSL-EPR spectroscopy. (esr-group.org)
amyloid
- The crucial role of water in amyloid-β(Aβ) fibril proteins is evaluated in several ways including the water's thermodynamic and kinetic solvation effects. (degruyter.com)
- A variety of amyloid diseases begin as benign amyloid-β monomer fibril proteins which then develop into toxic amyloid dimers/oligomers ( 15 ). (degruyter.com)
- Namely, both experimental and theoretical thermodynamic stabilities of a series of amyloid fibrils proteins revealed that this structural form is likely to be the most stable one, a stability that can be acquired even under physiological conditions. (degruyter.com)
- A broad range of microbial and amyloid proteins interact with cell surface glycolipids which behave as infectivity and/or toxicity cofactors in human pathologies. (jove.com)
- In conclusion, deciphering the glycolipid code of amyloid proteins allowed us to create a universal ganglioside-binding peptide of only 12-residues with potential therapeutic applications in infectious and neurodegenerative diseases that involve cell surface gangliosides as receptors. (jove.com)
- Dr. Ralf Langen's group showed that SDSL with EPR (University of Southern California, Los Angeles) can be used to understand the structure of amyloid fibrils and the structure of membrane bound Parkinson's disease protein alpha-synuclein. (wikipedia.org)
- As about 30-40% of all known proteins contain one or more metal ion cofactors (e.g., ceruloplasmin, ferritin, amyloid precursor protein, matrix metalloproteinase), especially native metalloproteins have to be isolated, identified and quantified after liquid biopsy. (wikipedia.org)
covalently
- These proteins covalently modify flexible tails of histones by attaching or removing the -CH 3 groups to the side-chains of lysines and arginines. (edu.sa)
- iTRAQ, Tandem mass tags (TMT) and Isotope-coded affinity tag (ICAT) are protein mass-tags that consist of a covalently attaching group, a mass (isobaric or isotopic) encoded linker and a handle for isolation. (wikipedia.org)
soluble
- Therefore, the high-precision electrophoresis and other native separation techniques are highly relevant as initial step of protein analysis and trace metal speciation followed by mass spectrometric and magnetic resonance methods for quantifying and identifying the soluble proteins of interest. (wikipedia.org)
cysteine-rich
- Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. (embl-heidelberg.de)
- Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. (embl-heidelberg.de)
- Development of new radical labelling strategies for cysteine rich proteins. (esr-group.org)
residues
- Amino acid residues located at different positions in folded proteins often exhibit different degrees of acidities. (jove.com)
- Proteins (/ˈproʊˌtiːnz/ or /ˈproʊti.ɪnz/) are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. (wikipedia.org)
- Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. (wikipedia.org)
- These can be positioned on specific residues that either change their spatial arrangement due to a conformational change induced by glucose or reside in the glucose-binding pocket whereby the displacement of the water present by glucose decreases the polarity. (wikipedia.org)
groups of proteins
- We focus our attention on the closely related groups of proteins involved in the gene regulation processes, like histone methyltransferases and demethylases. (edu.sa)
heteronuclear
- Battiste JL, Wagner G (2000) Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. (springer.com)
transcriptional regulatory
- Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. (embl-heidelberg.de)
- Several enzymes, carrier proteins, scaffolding proteins, and transcriptional regulatory factors carry out their functions as homo-oligomers. (wikipedia.org)
interact
- Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. (embl-heidelberg.de)
- As of now only 2% of human proteins interact with the currently approved drugs. (edu.sa)
- Altogether, this provides a valuable tool to explore Ca 2+ /CaM signaling and proteins that interact with CaM. (jove.com)
- Distinct protein subunits interact in hetero-oligomers, which are essential to control several cellular functions. (wikipedia.org)
biochemistry
- how to efficiently work in the state-of-the-art protein biochemistry lab, prepare own protein(s) for the biophysical and spectroscopic (e.g. (edu.sa)
- He is a joint editor of Subcellular Biochemistry, volume on Proteins: Structure, Function, and Engineering published by Plenum Press, New York, USA. (wikipedia.org)
- The Assembly of a Multisubunit Photosynthetic Membrane Protein Complex: A Site-Specific Spin Labeling EPR Spectroscopic Study of the PsaC Subunit in Photosystem I". Biochemistry. (wikipedia.org)
- QPNC-PAGE, or quantitative preparative native continuous polyacrylamide gel electrophoresis, is a high-resolution and a highly accurate technique applied in biochemistry and bioinorganic chemistry to separate proteins quantitatively by isoelectric point. (wikipedia.org)
oligomers
- The assembly of amyloidogenic proteins into toxic oligomers is a seminal event in the pathogenesis of protein misfolding diseases, including Alzheimer's, Parkinson's, and Huntington's diseases, hereditary amyotrophic lateral sclerosis, and type 2 diabetes. (jove.com)
specificity
- These sensors contain, in addition to the fluorophore(s), a molecule that confers glucose specificity, in general, a protein. (wikipedia.org)
dependent
- The effects of these proteins on cellular function are often dependent on their ability to bind to CaM in a Ca 2+ -dependent manner. (jove.com)
- Voltage-dependent anion-selective channel 1 (VDAC-1) is a beta barrel protein that in humans is encoded by the VDAC1 gene located on chromosome 5. (wikipedia.org)
- This protein is a voltage-dependent anion channel and shares high structural homology with the other VDAC isoforms (VDAC2 and VDAC3), which are involved in the regulation of cell metabolism, mitochondrial apoptosis, and spermatogenesis. (wikipedia.org)
- Its permeability is dependent on VDAC1's conformational state which is determined by voltage. (wikipedia.org)
- Protein function is heavily dependent on protein structure, and rational protein design uses this relationship to design function by designing proteins that have a target structure or fold. (wikipedia.org)
measurements
- Based on chemical shift perturbations we have mapped protein-protein and protein-RNA interfaces and complemented this NMR-derived information with SAXS data, as well as SANS measurements on subunit-selectively deuterated samples of the ternary complex. (springer.com)
genes
- Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. (embl-heidelberg.de)
- This way they modulate the accessibility of the DNA double strand - genes - toward transcription factor proteins and RNA polymerase. (edu.sa)
stable
- They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. (embl-heidelberg.de)
- Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (embl-heidelberg.de)
amino-acid
- At neutral pH, protein thiol groups specifically react with the functional groups methanethiosulfonate, maleimide, and iodoacetamide, creating a covalent bond with the amino acid Cys. (wikipedia.org)
- it is the combined effect of all of the amino acid side chains in a protein that ultimately determines its three-dimensional structure and its chemical reactivity. (wikipedia.org)
- Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone. (wikipedia.org)
- Recently, however, improvements in molecular force fields, protein design algorithms, and structural bioinformatics, such as libraries of amino acid conformations, have enabled the development of advanced computational protein design tools. (wikipedia.org)
- The goal in rational protein design is to predict amino acid sequences that will fold to a specific protein structure. (wikipedia.org)
myosin
- Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. (wikipedia.org)
bacterial
- This opened the way to the use of bacterial expressed recombinant proteins for in vitro reconstitution. (jove.com)
gene
- Vertebrate insulin gene enhancer binding protein isl-1. (embl-heidelberg.de)
- Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. (embl-heidelberg.de)
- We have further studied the expression of this gene at the transcript and protein levels. (jove.com)
- Furthermore, members of the skeletal muscle lipid droplet-associated proteins family associate with other proteins, as activator of adipose triglyceride lipase and its coactivator comparative gene identification-58, to regulate lipolysis in skeletal muscle. (wikipedia.org)
- S100A1, also known as S100 calcium-binding protein A1 is a protein which in humans is encoded by the S100A1 gene. (wikipedia.org)
Cellular
- S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. (wikipedia.org)
cofactors
- Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. (wikipedia.org)
membrane-bound
- In nature, these membranes are heterogeneous mixtures of many types of lipids, contain membrane-bound proteins and are decorated with carbohydrates. (jove.com)
peptide
- The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar. (wikipedia.org)
- The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone. (wikipedia.org)
- Its applications to protein analysis was only possible in the late 1980s with the development of protein and peptide ionization with minimal fragmentation. (wikipedia.org)
characterization of protein
- Chemical biologists are poised to impact proteomics through the development of techniques, probes and assays with synthetic chemistry for the characterization of protein samples of high complexity. (wikipedia.org)
bind
- Some LIM domains bind protein partners via tyrosine-containing motifs. (embl-heidelberg.de)
- While most target proteins bind Ca 2+ -CaM, certain proteins only bind to ApoCaM. (jove.com)
- In contrast, many proteins only bind Ca 2+ -CaM and require this binding for their activation. (jove.com)
- Here, we present a method for testing the ability of proteins to bind to CaM in the presence or absence of Ca 2+ , using CaMKII and Ng as examples. (jove.com)
- It uses CaM-Sepharose beads to test proteins that bind to CaM and the influence of Ca 2+ on this binding. (jove.com)
- Optical biosensors, such as the X-BODY Biosciences BIND Scanner system, use a novel label-free technology, resonance wavelength grating (RWG) optical biosensors, to detect changes in resonant reflected light near the biosensor. (jove.com)
- Varying mass-tags bind to different proteins as a sort of footprint such that when analyzing cells of differing perturbations, the levels of each protein can be compared relatively after enrichment by the introduced handle. (wikipedia.org)
biochemical reactions
- Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. (wikipedia.org)
solvent
- In fact, most of the active sites in proteins are located near the interior region where solvent effects have been minimized 9,10 . (jove.com)
computationally
- In 2010, one of the most powerful broadly neutralizing antibodies was isolated from patient serum using a computationally designed protein probe. (wikipedia.org)
rarely
- Proteins rarely act alone as their functions tend to be regulated. (wikipedia.org)
studies
- However, in such studies, it is essential to demonstrate that the mutated proteins have the expected altered binding to CaM. (jove.com)
- Widely known for his studies on bacteriophage lambda and protein synthesis, he is an elected fellow of the Indian Academy of Sciences and the Indian National Science Academy. (wikipedia.org)
- Structural studies on transmembrane proteins. (wikipedia.org)
structure
- Concerning flexibility, conformational adjustment induced upon association can lead to complete remodeling of the partner interfaces, thus making surface recognition inefficient when starting from the structure of the isolated partners. (biomedcentral.com)
- A spin label's built-in protein structure can be detected by EPR spectroscopy. (wikipedia.org)
- The most accurate high-resolution solution structure of human apo-S100A1 protein (PDB accession code: 2L0P) has been determined by means of NMR spectroscopy in 2011. (wikipedia.org)
- Thus, protein design is the search for sequences that have the chosen structure as a free energy minimum. (wikipedia.org)
- In a sense, it is the reverse of protein structure prediction. (wikipedia.org)
- Although protein design programs vary greatly, they have to address four main modeling questions: What is the target structure of the design, what flexibility is allowed on the target structure, which sequences are included in the search, and which force field will be used to score sequences and structures. (wikipedia.org)
computational
- In conclusion, with the combination of experimental and computational data for selected families of disease related proteins, we try to understand the molecular determinants that make closely related proteins druggable or not druggable. (edu.sa)
- These computational tools can make complex calculations on protein energetics and flexibility, and perform searches over vast configuration spaces, which would be unfeasible to perform manually. (wikipedia.org)
- Due to the development of computational protein design programs, and important successes in the field (see examples below), rational protein design has become one of the most important tools in protein engineering. (wikipedia.org)
- Following the development of these computational tools, great success has been achieved over the last 30 years in protein design. (wikipedia.org)
biophysical properties
- These biophysical properties seem to be well conserved across the S100 family of proteins. (wikipedia.org)
biosensors
- RWG optical biosensors have been used to detect changes in mass near the plasma membrane of cells following activation of G protein-coupled receptors (GPCRs), receptor tyrosine kinases, and other cell surface receptors. (jove.com)
- Fluorescent glucose biosensors are devices that measure the concentration of glucose in diabetic patients by means of sensitive protein that relays the concentration by means of fluorescence, an alternative to amperometric sension of glucose. (wikipedia.org)
complex
- Direct methods rely on the analysis of the intact protein or protein complex in the gas phase by ESI-MS alone or in combination with other gas phase techniques. (springer.com)
- Our findings contribute to the general understanding that a major conformational change of HER3 during its activation is induced by a complex sequential HRG1? (jove.com)
- The approach is demonstrated with the ternary protein-protein-RNA complex involving two RNA recognition motif (RRM) domains of Sex-lethal, the N-terminal cold shock domain of Upstream-to-N-Ras, and msl-2 mRNA. (springer.com)
- Our results show that, while the use of SAXS data is beneficial, the additional combination with contrast variation in SANS data resolves remaining ambiguities and improves the docking based on chemical shift perturbations of the ternary protein-RNA complex. (springer.com)
skeletal muscle
- S100A1 is a member of the S100 family of proteins expressed in cardiac muscle, skeletal muscle and brain, with highest density at Z-lines and sarcoplasmic reticulum. (wikipedia.org)