• target proteins
  • While most target proteins bind Ca 2+ -CaM, certain proteins only bind to ApoCaM. (jove.com)
  • The sample workflow presented here is robust, efficient, and eliminates the need for in-line HPLC clean-up prior to MS. Gel pieces containing target proteins are washed in acetonitrile, water, and ethyl acetate to remove contaminants, including polymeric acrylamide fragments. (jove.com)
  • O-linked glycans are released from target proteins by in-gel reductive β-elimination and recovered through robust, simple clean-up procedures. (jove.com)
  • Incorporation of a "docking station peptide" into the hydrogel building block enables convenient incorporation of "docking protein"-tagged target proteins. (jove.com)
  • dynamics
  • Kay LE (2011) NMR studies of protein structure and dynamics - a look backwards and forwards. (springer.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)
  • 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)
  • The targets are moving, and as predictions become more sophisticated with each passing tournament, so does our appreciation of the intricacies of protein structure, function, and dynamics. (mdpi.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)
  • 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)
  • 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)
  • Sequence
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • Biochemistry
  • 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)
  • polypeptides
  • Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. (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)
  • Several enzymes, carrier proteins, scaffolding proteins, and transcriptional regulatory factors carry out their functions as homo-oligomers. (wikipedia.org)
  • Distinct protein subunits interact in hetero-oligomers, which are essential to control several cellular functions. (wikipedia.org)
  • molecular
  • Surface Plasmon Resonance (SPR) is a sensitive detection technique for label-free study of bio-molecular interactions in real time. (jove.com)
  • Finally we demonstrate that the CaM KMT interacts with the middle portion of the Hsp90 molecular chaperon and is probably a client protein since it is degraded upon treatment of cells with the Hsp90 inhibitor geldanamycin. (jove.com)
  • Many molecular processes within a cell are carried out by molecular machines that are built from a large number of protein components organized by their PPIs. (wikipedia.org)
  • Protein design programs use computer models of the molecular forces that drive proteins in in vivo environments. (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)
  • 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)
  • 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)
  • stable
  • We present the synthesis of a highly stable protein hydrogel mediated by a split-intein-catalyzed protein trans -splicing reaction. (jove.com)
  • sequences
  • And finally, there are papers that continue to address the fundamental unresolved problem of how protein sequences encode for the three-dimensional structures of proteins. (mdpi.com)
  • The goal in rational protein design is to predict amino acid sequences that will fold to a specific protein structure. (wikipedia.org)
  • Although the number of possible protein sequences is vast, growing exponentially with the size of the protein chain, only a subset of them will fold reliably and quickly to one native state. (wikipedia.org)
  • Protein design involves identifying novel sequences within this subset. (wikipedia.org)
  • Thus, protein design is the search for sequences that have the chosen structure as a free energy minimum. (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)
  • Current goals in proteomics include determining protein sequences, abundance and any post-translational modifications. (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)
  • Dear Colleagues, In recent years protein folding often seems to have become synonymous with protein structure prediction. (mdpi.com)
  • A spin label's built-in protein structure can be detected by EPR spectroscopy. (wikipedia.org)
  • Protein subunits assembly is guided by the establishment of non-covalent interactions in the quaternary structure of the protein. (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)
  • 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)
  • In a sense, it is the reverse of protein structure prediction. (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)
  • 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)
  • structures
  • The first designed proteins are attributed to Bernd Gutte, who designed a reduced version of a known catalyst, bovine ribonuclease, and tertiary structures consisting of beta-sheets and alpha-helices, including a binder of DDT. (wikipedia.org)
  • calmodulin
  • These findings suggest that the CaM KMT is the major, possibly the single, methyltransferase of calmodulin in human cells with a wide tissue distribution and is a novel Hsp90 client protein. (jove.com)
  • Much of Ca 2+ signaling is mediated through the calcium-binding protein known as calmodulin (CaM) 1,2 . (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)
  • covalently
  • 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)
  • subunit
  • The building blocks of this hydrogel are two protein block-copolymers each containing a subunit of a trimeric protein that serves as a crosslinker and one half of a split intein. (jove.com)
  • separation
  • Chemometrics tools for the separation of chemical contributions in EPR spectroscopy. (esr-group.org)
  • A high reproducibility in gel pore size and a high-yield electroelution of proteins performed by this highly reliable technique strongly correlate with the polymerization time of the acrylamide gels representing an inherent stability constant of the separation system. (wikipedia.org)
  • synthesis
  • 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)
  • 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)
  • 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)
  • biosensors
  • 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)
  • 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)
  • skeletal muscle
  • 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 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)
  • yielding a polypeptide
  • Mixing of the two protein block copolymers triggers an intein trans -splicing reaction, yielding a polypeptide unit with crosslinkers at either end that rapidly self-assembles into a hydrogel. (jove.com)
  • interact
  • Altogether, this provides a valuable tool to explore Ca 2+ /CaM signaling and proteins that interact with CaM. (jove.com)