• 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)