• kinase
  • For replication to ensue, two protein kinases, cyclin-dependent kinase (Cdk)1p (also known as Cdc28p) and Cdc7p, must be activated. (genetics.org)
  • The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. (mdpi.com)
  • We used a structurally consistent model on kinase‐docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under‐explored part of the human proteome and applied experimental tools specifically tailored to detect low‐affinity protein-protein interactions for their validation in vitro and in cell‐based assays. (embopress.org)
  • This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase‐mediated partnerships evolved over time. (embopress.org)
  • Myotonin-protein kinase (MT-PK) also known as myotonic dystrophy protein kinase (MDPK) or dystrophia myotonica protein kinase (DMK) is an enzyme that in humans is encoded by the DMPK gene. (wikipedia.org)
  • The dmpk gene product is a Ser/Thr protein kinase homologous to the MRCK p21-activated kinases and the Rho family of kinases. (wikipedia.org)
  • Myotonin-protein kinase is a serine-threonine kinase that is closely related to other kinases that interact with members of the Rho family of small GTPases. (wikipedia.org)
  • For example, myotonic dystrophy protein kinase has been shown to turn off (inhibit) part of a muscle protein called myosin phosphatase. (wikipedia.org)
  • Dystrophia myotonica protein kinase (DMPK) is a serine/threonine kinase composed of a kinase domain and a coiled-coil domain involved in the multimerization. (wikipedia.org)
  • The affinity of dimerisation suggested that the kinase domain alone is insufficient for dimerisation in vivo and that the coiled-coil domains are required for stable dimer formation. (wikipedia.org)
  • Myotonic dystrophy protein kinase has been shown to interact with HSPB2 and RAC1. (wikipedia.org)
  • In this model, transient activation of kinase activity would occur in response to G protein second messengers, while longterm activation of DMPK could be mediated by a membrane associated protease that cleaves DMPK-1 to release cytosolic DMPK-2 in a persistently activated form. (wikipedia.org)
  • Protein phosphorylation is a post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. (wikipedia.org)
  • In the early 1980, the amino-acid sequence of the first protein kinase was determined which helped geneticists understand the functions of regulatory genes. (wikipedia.org)
  • In the late 1980s and early 1990s, the first protein tyrosine phosphatase (PTP1B) was purified and the discovery, as well as, cloning of JAK kinases was accomplished which led to many in the scientific community to name the 1990s as the decade of protein kinase cascades. (wikipedia.org)
  • Energetics
  • Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. (garlandscience.com)
  • 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)
  • beta-hairpin
  • Blanco FJ, Rivas G, Serrano L. A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. (springer.com)
  • A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native beta-hairpin. (springer.com)
  • As substitutions are the most common amino acid mutations, a protein could potentially undergo a conversion without affecting the functionality of the beta hairpin. (wikipedia.org)
  • In the folding of overall proteins, the turn may originate not in the native turn region but in the C-strand of the beta-hairpin. (wikipedia.org)
  • Sequences
  • However, the precise conformations of DM-20 and PLP may differ, because they each respond differently to many identical missense mutations in their primary sequences. (jneurosci.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)
  • affinity
  • It has been found that the affinity of peptide fragments of the human Pin1 WW domain for Cu(II) ions depends on its conformation. (springer.com)
  • Notably, some PAS domains control the binding affinity of this interface via changes in the conformation or occupancy of environmentally sensitive cofactors bound on the opposite, internal side of the sheet. (pnas.org)
  • Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less‐characterized disordered regions. (embopress.org)
  • Folding
  • This information can be relevant for understanding important areas of biology such as protein folding, protein aggregation and amyloid formation. (pubmedcentralcanada.ca)
  • Kinetical accessibility: means that the path in the free energy surface from the unfolded to the folded state must be reasonably smooth or, in other words, that the folding of the chain must not involve highly complex changes in the shape (like knots or other high order conformations). (wikipedia.org)
  • How the protein reaches this structure is the subject of the field of protein folding, which has a related concept called Levinthal's paradox. (wikipedia.org)
  • Prions are stable conformations of proteins which differ from the native folding state. (wikipedia.org)
  • Correct protein folding is integral to proper functionality within biological systems. (wikipedia.org)
  • This is because protein folding requires entropic cost. (wikipedia.org)
  • Via several techniques, the mechanism of protein folding is currently being studied. (wikipedia.org)
  • Levinthal's paradox is a thought experiment, also constituting a self-reference in the theory of protein folding. (wikipedia.org)
  • If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3198 different conformations (including any possible folding redundancy). (wikipedia.org)
  • Indeed, the protein folding intermediates and the partially folded transition states were experimentally detected, which explains the fast protein folding. (wikipedia.org)
  • This is also described as protein folding directed within funnel-like energy landscapes Some computational approaches to protein structure prediction have sought to identify and simulate the mechanism of protein folding. (wikipedia.org)
  • Chaperone - proteins that assist other proteins in folding or unfolding Folding funnel Anfinsen's dogma Levinthal, Cyrus (1969). (wikipedia.org)
  • Folding of molecules, where some shapes are stable and functional, but others are not. (wikipedia.org)
  • The most important factor governing the folding of a protein into 3D structure is the distribution of polar and non-polar side chains. (wikipedia.org)
  • have used protein NMR to show that beta-hairpins can be formed from isolated short peptides in aqueous solution, suggesting that hairpins could form nucleation sites for protein folding. (wikipedia.org)
  • Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner. (wikipedia.org)
  • The essential fact of folding, however, remains that the amino acid sequence of each protein contains the information that specifies both the native structure and the pathway to attain that state. (wikipedia.org)
  • Formation of a secondary structure is the first step in the folding process that a protein takes to assume its native structure. (wikipedia.org)
  • Collagen
  • In this work, we analyzed by atomic force microscopy (AFM) the distribution and conformation of type I collagen on plasma-treated surfaces before and after silanization. (gla.ac.uk)
  • Subsequently, we investigated the effect of the different collagen conformations on fibroblasts adhesion and fibronectin secretion by immunofluorescence analyses. (gla.ac.uk)
  • AFM studies revealed different conformations of type I collagen depending on the silane employed. (gla.ac.uk)
  • Collagen was organized in fibrillar networks over very hydrophilic (plasma treated titanium) or hydrophobic (silanized with CPTES) surfaces, the latter forming little globules with a beads-on-a-string appearance, whereas over surfaces presenting an intermediate hydrophobic character (silanized with GPTES), collagen was organized into clusters with a size increasing at higher protein concentration in solution. (gla.ac.uk)
  • Cell response was strongly affected by collagen conformation, especially at low collagen density. (gla.ac.uk)
  • In contrast, when a certain protein concentration was reached at the material surface, the effect of collagen conformation was masked, and similar fibroblast response was observed in all samples. (gla.ac.uk)
  • Functions
  • It is known that G-protein-coupled receptors exhibit several distinct low-energy conformations, each of which might favor binding to different ligands and/or lead to different downstream functions. (pnas.org)
  • Since being recognized in these three eukaryotic transcription factors, PAS domains have been found in proteins from all three kingdoms of life that perform functions as diverse as DNA binding, phosphorylation, ion conduction, and others ( , 1 ). (pnas.org)
  • Membrane proteins mediate critical functions in biological systems and are important drug targets for a number of diseases. (mit.edu)
  • Proteins perform extremely specific functions which are dependent on their structure. (wikipedia.org)
  • transmembrane
  • We earlier reported the BiHelix method for efficiently sampling the (12) 7 = 35 million conformations resulting from 30° rotations about the axis (η) of all seven transmembrane helices (TMHs), showing that the experimental structure is reliably selected as the best conformation from this ensemble. (pnas.org)
  • We find that the topologies of DM-20 and PLP are identical, with both proteins possessing four transmembrane domains and N and C termini exposed to the cytoplasm. (jneurosci.org)
  • We find that the transmembrane topologies of DM-20 and PLP are identical, with both proteins possessing four transmembrane domains and both N and C termini located within the cytoplasmic compartment. (jneurosci.org)
  • SNAREs are small, abundant, sometimes tail-anchored proteins which are often post-translationally inserted into membranes via a C-terminal transmembrane domain. (wikipedia.org)
  • computational
  • The book ends with a synopsis the roles of computational biology and bioinformatics in protein science. (garlandscience.com)
  • The combined computational and experimental approach enabled the identification of many novel MAPK‐docking motifs that were elusive for other large‐scale protein-protein interaction screens. (embopress.org)
  • The solution to this paradox has been established by computational approaches to protein structure prediction. (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)
  • structure
  • The book begins by introducing the basic principles of protein structure and function. (garlandscience.com)
  • We have validated this method by predicting known crystal structure conformations starting from the template of a different protein structure. (pnas.org)
  • 3d structure of protein is determined by? (memorize.com)
  • Subsequent to the elucidation of the primary structure of PLP, several topologies for this protein have been proposed based on mathematical modeling, chemical labeling, limited protease digestion, and immunolabeling. (jneurosci.org)
  • A high-resolution solution structure of a mutant ARNT PAS-B domain stabilized in the new conformation revealed a 3-residue slip in register and accompanying inversion of the central Iβ-strand. (pnas.org)
  • This β-sheet plays a particularly critical role in PAS structure and function because its solvent-exposed side is the binding site for a wide range of PAS-bound protein targets ( , 3 ). (pnas.org)
  • Proteins are stable enough to maintain a three-dimensional structure, but flexible enough for biological function. (wikipedia.org)
  • This maintains the stability of the structure within localized segments of the protein. (wikipedia.org)
  • Each domain forms a compact three-dimensional structure and often can be independently stable and folded. (wikipedia.org)
  • One study has suggested that a single ancestral enzyme could have diverged into several families, while another suggests that a stable TIM-barrel structure has evolved through convergent evolution. (wikipedia.org)
  • The primary structure (string of amino acids) of a protein ultimately encodes its uniquely folded three-dimensional (3D) conformation. (wikipedia.org)
  • Some simple combinations of secondary structure elements have been found to frequently occur in protein structure and are referred to as supersecondary structure or motifs. (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)
  • In a sense, it is the reverse of protein structure prediction. (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)
  • Ensembles are models consisting of a set of conformations that together attempt to describe the structure of a flexible protein. (wikipedia.org)
  • The main purpose of these models is to gain insights regarding the function of the flexible protein, extending the structure-function paradigm from folded proteins to intrinsically disordered proteins. (wikipedia.org)
  • This polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). (wikipedia.org)
  • Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), known as the native state. (wikipedia.org)
  • Experiments beginning in the 1980s indicate the codon for an amino acid can also influence protein structure. (wikipedia.org)
  • The primary structure of a protein, its linear amino-acid sequence, determines its native conformation. (wikipedia.org)
  • Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. (wikipedia.org)
  • There are four distinct levels of protein structure. (wikipedia.org)
  • The primary structure of a protein refers to the sequence of amino acids in the polypeptide chain. (wikipedia.org)
  • The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis. (wikipedia.org)
  • The primary structure of a protein is determined by the gene corresponding to the protein. (wikipedia.org)
  • The sequence of a protein is unique to that protein, and defines the structure and function of the protein. (wikipedia.org)
  • polypeptide
  • The polypeptide interacts with water, thus placing thermodynamic pressures on these regions which then aggregate or "collapse" into a tertiary conformation with a hydrophobic core. (wikipedia.org)
  • In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. (wikipedia.org)
  • centers
  • The current work on membrane proteins centers on bacterial mechanosensitive channels and ATP dependent bacterial transporters mediating translocation of transition metals and nutrients. (k-state.edu)
  • amyloid fibrils
  • The formation of amyloid fibrils, insoluble aggregates of hydrophobic protein can lead to a myriad of diseases including Parkinson's and Alzheimer's disease. (wikipedia.org)
  • Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. (wikipedia.org)
  • function
  • Understanding the function of such proteins requires knowledge of the ensemble of low-energy configurations that might play a role in this pleiotropic functionality. (pnas.org)
  • The function of a protein depends on its? (memorize.com)
  • In a multidomain protein, each domain may fulfill its own function independently, or in a concerted manner with its neighbours. (wikipedia.org)
  • SNAREs are thought to be the core required components of the fusion machinery and can function independently of additional cytosolic accessory proteins. (wikipedia.org)
  • Although the specific function of this protein is unknown, it appears to play an important role in muscle, heart, and brain cells. (wikipedia.org)
  • Protein kinases and phosphatases work independently and in a balance to regulate the function of proteins. (wikipedia.org)
  • regulatory
  • MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C -terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. (mdpi.com)
  • We propose that short MAPK‐binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles. (embopress.org)
  • These simple proteinprotein recruitment sites represent a major resource for ancient signaling enzymes to acquire new regulatory roles. (embopress.org)
  • Domains can either serve as modules for building up large assemblies such as virus particles or muscle fibres, or can provide specific catalytic or binding sites as found in enzymes or regulatory proteins. (wikipedia.org)
  • secretion
  • Recent emergence of oseltamivir and zanamivir resistant human influenza A(H1N1) H274Y has emphasized the need for suitable expression systems to obtain large quantities of highly pure and stable, recombinant neuraminidase through two separate artificial tetramerization domains that facilitate the formation of catalytically active neuraminidase homotetramers from yeast and Staphylothermus marinus, which allow for secretion of FLAG-tagged proteins and further purification. (wikipedia.org)
  • small
  • There is great hope that the design of new proteins, small and large, will have uses in biomedicine and bioengineering. (wikipedia.org)
  • The close relationship of DMPK to the Rho-kinases has led to speculation whether DMPK activity may be regulated in vivo by small G proteins, particularly of the Rho family. (wikipedia.org)
  • different
  • Those visible light photons give just enough energy to kick an electron into the higher energy state, which transforms the retinal molecule into a different, more stable shape, which triggers a protein conformation that triggers an electrical pulse to the brain. (physicsforums.com)
  • See protein electrophoresis for more information on the different globulins. (wikipedia.org)
  • Note that the two eclipsed conformations have different energies: at 0° the two methyl groups are eclipsed, resulting in higher energy (≈ 5 kcal/mol) than at 120°, where the methyl groups are eclipsed with hydrogens (≈ 3.5 kcal/mol). (wikipedia.org)
  • One domain may appear in a variety of different proteins. (wikipedia.org)
  • Broadly
  • Mitogen‐activated protein kinases (MAPK) are broadly used regulators of cellular signaling. (embopress.org)
  • In 2010, one of the most powerful broadly neutralizing antibodies was isolated from patient serum using a computationally designed protein probe. (wikipedia.org)
  • molecule
  • if the energy barrier is high enough that there is restricted rotation, a molecule may exist for a relatively long time period as a stable rotational isomer or rotamer. (wikipedia.org)