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  • Scaffold
  • De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities. (ucsf.edu)
  • The modularity in NPC architecture is reflected in its hierarchical and symmetrical organization that partitions the predicted nup folds into three groups: the transmembrane group containing transmembrane helices and a cadherin fold, the central scaffold group containing β-propeller and α-solenoid folds, and the peripheral FG group containing predominantly the FG repeats and the coiled-coil fold. (pnas.org)
  • molecular
  • By combining molecular dynamics simulations with cryo-electron microscopy data, we recently resolved the first structure of a membrane-protein-insertion intermediate state of SecY bound to a translating ribosome, with a transmembrane (TM) segment. (gatech.edu)
  • Other methods such as MembStruk [ 12 ] and PREDICT [ 13 ] start from ideal helices that are later subjected to "coarse" and "fine" optimization steps by energy minimization and molecular dynamics simulations. (biomedcentral.com)
  • amphipathic
  • As the common feature Bcl-2 Inhibitor of these domains is the presence of membrane-inserting amphipathic helices at their N termini we hypothesize that this structural module might be the key element necessary and likely adequate for membrane fission. (conferencecallsworld.com)
  • However, DHNs contain at least one copy of a consensus 15-amino acid sequence, the "K segment," which resembles a class A2 amphipathic α-helical, lipid-binding domain found in other proteins such as apolipoproteins and α-synuclein. (plantphysiol.org)
  • B, Helical wheel plot of the predicted amphipathic helix-forming consensus K segment peptide of maize DHN1 (KGIMDKIKEKLPG). (plantphysiol.org)
  • Conformational
  • The highly dynamic nature of LacY is consistent with an alternating access mechanism involving a global conformational change in which sugar and H + binding sites are alternatively exposed to either side of the membrane (reviewed in ref. 6 ). (pnas.org)
  • thermodynamic
  • The simulations reveal spontaneous motion of the TM segment, either inserting into the membrane or toward the channel interior, depending on its sequence, in agreement with a thermodynamic partitioning proposed previously. (gatech.edu)
  • Thermodynamic analysis of membrane proteins has been hampered by the experimental difficulties imposed by their insolubility in water and great stability in membranes. (pnas.org)
  • Thus, to understand folding of membrane proteins it is essential to discover systems in which folding is in thermodynamic equilibrium and to develop methods to quantitatively assess this equilibrium in membrane-like environments. (pnas.org)
  • small molecule
  • My research focuses on small molecule and protein design as an approach to understanding macromolecule structure and function. (ucsf.edu)
  • For wider applicability, top-down mass spectrometry must address the entire proteome including the membrane proteins that constitute 20 to 30% of the open reading frames (ORF's) in fully sequenced genomes [ 3 ], with their important functions ranging from photosynthesis, respiration and cellular communication to small molecule transport. (pubmedcentralcanada.ca)
  • insertion
  • Now, using novel free-energy calculations and by carefully matching the context of the simulations to experiment, I will demonstrate a significantly improved agreement for multiple membrane-protein-insertion assays. (gatech.edu)
  • This analysis expected that proteins comprising shallow insertion domains promote membrane scission whereas a protein whose membrane connection face is definitely crescent-like such?as crescent Pub domains (without insertions or Bcl-2 Inhibitor twists) which bend. (conferencecallsworld.com)
  • We also tested for the presence of translocation signals that enable insertion of these proteins into rough endoplasmic reticulum (RER) membranes. (jneurosci.org)
  • 1999
  • Russ WP, Engelman DM (1999) TOXCAT: a measure of transmembrane helix association in a biological membrane. (springer.com)
  • Li M, Reddy LG, Bennett R et al (1999) A fluorescence energy transfer method for analyzing protein oligomeric structure: application to phospholamban. (springer.com)
  • An alternative hypothesis is that DHNs are akin to many other "intrinsically unstructured" proteins ( Wright and Dyson, 1999 ) in that their lack of intrinsic structure is relieved when bound to target molecules, and that their function is related to their membrane targets. (plantphysiol.org)
  • structure
  • 1987). While electron microscopy (EM) has provided the overall shape of a protein including the number of helix strands, detailed information regarding secondary structure is not likely to be easily obtained from EM. (springer.com)
  • The rod-shaped tetraspanin structure allows it to serve as stable pilings in the lipid sea, ideal for docking partner proteins to form structural/signaling networks. (rupress.org)
  • The small number of predicted fold types in the NPC and their internal symmetries suggest that the bulk of the NPC structure has evolved through extensive motif and gene duplication from a simple precursor set of only a few proteins. (pnas.org)
  • 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)
  • The three-dimensional structure of a protein defines not only its size and shape, but also its function. (learner.org)
  • One characteristic that affects function is the hydrophobicity of a protein, which is determined by the primary and secondary structure. (learner.org)
  • Top-down proteomics is dependent upon high resolution and accurate mass measurements for analysis of intact proteins and their dissociation-derived product ions and can provide complete primary structure and post-translational modification assignment [ 1 , 2 ]. (pubmedcentralcanada.ca)
  • Each of the 10 helices of the Na/K-ATPase is unique, as well as being highly conserved, both in terms of amino acid sequence, and in 3D structure. (pubmedcentralcanada.ca)
  • Typically
  • FIP pathology is characterized typically by severe systemic inflammatory damage of serosal membranes and widespread pyogranulomatous lesions, which occurs in the lungs, liver, lymph tissue, and brain ( 8 ). (cdc.gov)
  • structural
  • Even solid-state NMR, such as cross-polarization magic angle spin NMR, to compensate the anisotropy, has limited success in obtaining structural information about prosthetic groups in membrane proteins, such as retinal in bacteriorhodopsin (Harbison et al . (springer.com)
  • 2005. Structural mechanism for sterol sensing and transport by OSBP-related proteins. (umich.edu)
  • However, the structural basis of how the tetraspanins bind to their partner proteins and how they form the tetraspanin web has not yet been elucidated. (rupress.org)
  • coli
  • The envelope stress sensor, CpxA and its interaction with E. coli membranes were studied. (diva-portal.org)
  • To identify YpdB-regulated genes, we compared the transcriptomes of E. coli cells overproducing either YpdB or a control protein. (asm.org)
  • transmembrane protein
  • Tetraspanin uroplakins (UPs) Ia and Ib, together with their single-spanning transmembrane protein partners UP II and IIIa, form a unique crystalline 2D array of 16-nm particles covering almost the entire urothelial surface. (rupress.org)
  • Recently, we have reported a disulfide-coupled folding approach to measure the energetics of transmembrane protein association in detergent micelles ( 16 ). (pnas.org)
  • ligand
  • In the latter systems, signaling is initiated either by the direct binding of chemoeffectors or chemoeffector-loaded periplasmic binding proteins to the ligand binding domain (LBD) of chemoreceptors ( Matilla and Krell, 2017 ). (frontiersin.org)
  • In a similar manner, certain sites in cell receptor proteins bind to specific ligand molecules that the receptor recognizes. (learner.org)
  • periplasmic
  • Trp replacements for conserved Gly-Gly pairs between the N- and C-terminal six-helix bundles on the periplasmic side of lactose permease (LacY) cause complete loss of transport activity with little or no effect on sugar binding. (pnas.org)
  • analysis
  • The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins. (omictools.com)
  • Proteomic analysis indicated that the FAO and FADH proteins can be detected on wax bodies, but they localized to the endoplasmic reticulum when they were expressed as amino-terminal green fluorescent protein fusions in tobacco ( Nicotiana tabacum ) leaves. (plantphysiol.org)
  • fatty
  • Recombinant jojoba FAO and FADH proteins are active on very-long-chain fatty alcohol and fatty aldehyde substrates, respectively, and have biochemical properties consistent with those previously reported in jojoba cotyledons. (plantphysiol.org)