1,721,003 research outputs found
Self-Assembled Templates for Polypeptide Synthesis
No full textThe chemical synthesis of polypeptide chains >50 amino acids with prescribed sequences is
challenging. In one approach, native chemical ligation (NCL), short, unprotected peptides are connected
through peptide bonds to render proteins in water. Here we combine chemical ligation with peptide self-assembly to deliver extremely long polypeptide chains with stipulated, repeated sequences. We use a
self-assembling fiber (SAF) system to form structures tens of micrometers long. In these assemblies, tens
of thousands of peptides align with their N- and C-termini abutting. This arrangement facilitates chemical
ligation without the usual requirement for a catalytic cysteine residue at the reactive N-terminus. We
introduced peptides with C-terminal thioester moieties into the SAFs. Subsequent ligation and disassembly
of the noncovalent components produced extended chains ≥10 μm long and estimated at ≥3 MDa in
mass. These extremely long molecules were characterized by a combination of biophysical, hydrodynamic,
and microscopic measurements
De Novo-Designed α-Helical Barrels as Receptors for Small Molecules
Get PDFWe describe de novo-designed α-helical barrels (αHBs) that bind and discriminate between lipophilic biologically active molecules. αHBs have five or more α-helices arranged around central hydrophobic channels the diameters of which scale with oligomer state. We show that pentameric, hexameric, and heptameric αHBs bind the environmentally sensitive dye 1,6-diphenylhexatriene (DPH) in the micromolar range and fluoresce. Displacement of the dye is used to report the binding of nonfluorescent molecules: palmitic acid and retinol bind to all three αHBs with submicromolar inhibitor constants; farnesol binds the hexamer and heptamer; but β-carotene binds only the heptamer. A co-crystal structure of the hexamer with farnesol reveals oriented binding in the center of the hydrophobic channel. Charged side chains engineered into the lumen of the heptamer facilitate binding of polar ligands: a glutamate variant binds a cationic variant of DPH, and introducing lysine allows binding of the biosynthetically important farnesol diphosphate.</p
Fiber Recruiting Peptides: Noncovalent Decoration of an Engineered Protein Scaffold
No full textFiber Recruiting (FiRe) peptides are described. These are derivatives of self-assembling fiber (SAF) forming peptides that are conjugated with small molecules (in our case, biotin or a FLAG-tag octapeptide). The FiRe peptides are co-assembled into fibers and used as bait to recruit folded and functional proteins to the fiber surfaces. This was demonstrated using two molecular recognition models: namely, a protein−ligand interaction (biotin-streptavidin) and an antigen−antibody (FLAG octapeptide−anti-FLAG-antibody) interaction. This concept offers an approach to mimicking in natural fibrillar systems, such as collagen or fibrin, that communicate specifically with their environments via incorporated or decorated active peptide and protein components
Interplay of Hydrogen Bonds and <i>n</i>→π* Interactions in Proteins
No full textProtein structures are stabilized
by multiple weak interactions,
including the hydrophobic effect, hydrogen bonds, electrostatic effects,
and van der Waals interactions. Among these interactions, the hydrogen
bond is distinct in having its origins in electron delocalization.
Recently, another type of electron delocalization, the n→π* interaction between carbonyl groups, has been shown
to play a role in stabilizing protein structure. Here we examine the
interplay between hydrogen bonding and n→π*
interactions. To address this issue, we used data available from high-resolution
protein crystal structures to interrogate asparagine side-chain oxygen
atoms that are both acceptors of a hydrogen bond and donors of an n→π* interaction. Then we employed natural
bond orbital analysis to determine the relative energetic contributions
of the hydrogen bonds and n→π* interactions
in these systems. We found that an n→π*
interaction is worth ∼5–25% of a hydrogen bond and that
stronger hydrogen bonds tend to attenuate or obscure n→π* interactions. Conversely, weaker hydrogen bonds
correlate with stronger n→π* interactions
and demixing of the orbitals occupied by the oxygen lone pairs. Thus,
these two interactions conspire to stabilize local backbone–side-chain
contacts, which argues for the inclusion of n→π*
interactions in the inventory of non-covalent forces that contribute
to protein stability and thus in force fields for biomolecular modeling
Interplay of Hydrogen Bonds and <i>n</i>→π* Interactions in Proteins
No full textProtein structures are stabilized
by multiple weak interactions,
including the hydrophobic effect, hydrogen bonds, electrostatic effects,
and van der Waals interactions. Among these interactions, the hydrogen
bond is distinct in having its origins in electron delocalization.
Recently, another type of electron delocalization, the n→π* interaction between carbonyl groups, has been shown
to play a role in stabilizing protein structure. Here we examine the
interplay between hydrogen bonding and n→π*
interactions. To address this issue, we used data available from high-resolution
protein crystal structures to interrogate asparagine side-chain oxygen
atoms that are both acceptors of a hydrogen bond and donors of an n→π* interaction. Then we employed natural
bond orbital analysis to determine the relative energetic contributions
of the hydrogen bonds and n→π* interactions
in these systems. We found that an n→π*
interaction is worth ∼5–25% of a hydrogen bond and that
stronger hydrogen bonds tend to attenuate or obscure n→π* interactions. Conversely, weaker hydrogen bonds
correlate with stronger n→π* interactions
and demixing of the orbitals occupied by the oxygen lone pairs. Thus,
these two interactions conspire to stabilize local backbone–side-chain
contacts, which argues for the inclusion of n→π*
interactions in the inventory of non-covalent forces that contribute
to protein stability and thus in force fields for biomolecular modeling
Interplay of Hydrogen Bonds and <i>n</i>→π* Interactions in Proteins
No full textProtein structures are stabilized
by multiple weak interactions,
including the hydrophobic effect, hydrogen bonds, electrostatic effects,
and van der Waals interactions. Among these interactions, the hydrogen
bond is distinct in having its origins in electron delocalization.
Recently, another type of electron delocalization, the n→π* interaction between carbonyl groups, has been shown
to play a role in stabilizing protein structure. Here we examine the
interplay between hydrogen bonding and n→π*
interactions. To address this issue, we used data available from high-resolution
protein crystal structures to interrogate asparagine side-chain oxygen
atoms that are both acceptors of a hydrogen bond and donors of an n→π* interaction. Then we employed natural
bond orbital analysis to determine the relative energetic contributions
of the hydrogen bonds and n→π* interactions
in these systems. We found that an n→π*
interaction is worth ∼5–25% of a hydrogen bond and that
stronger hydrogen bonds tend to attenuate or obscure n→π* interactions. Conversely, weaker hydrogen bonds
correlate with stronger n→π* interactions
and demixing of the orbitals occupied by the oxygen lone pairs. Thus,
these two interactions conspire to stabilize local backbone–side-chain
contacts, which argues for the inclusion of n→π*
interactions in the inventory of non-covalent forces that contribute
to protein stability and thus in force fields for biomolecular modeling
Interplay of Hydrogen Bonds and <i>n</i>→π* Interactions in Proteins
No full textProtein structures are stabilized
by multiple weak interactions,
including the hydrophobic effect, hydrogen bonds, electrostatic effects,
and van der Waals interactions. Among these interactions, the hydrogen
bond is distinct in having its origins in electron delocalization.
Recently, another type of electron delocalization, the n→π* interaction between carbonyl groups, has been shown
to play a role in stabilizing protein structure. Here we examine the
interplay between hydrogen bonding and n→π*
interactions. To address this issue, we used data available from high-resolution
protein crystal structures to interrogate asparagine side-chain oxygen
atoms that are both acceptors of a hydrogen bond and donors of an n→π* interaction. Then we employed natural
bond orbital analysis to determine the relative energetic contributions
of the hydrogen bonds and n→π* interactions
in these systems. We found that an n→π*
interaction is worth ∼5–25% of a hydrogen bond and that
stronger hydrogen bonds tend to attenuate or obscure n→π* interactions. Conversely, weaker hydrogen bonds
correlate with stronger n→π* interactions
and demixing of the orbitals occupied by the oxygen lone pairs. Thus,
these two interactions conspire to stabilize local backbone–side-chain
contacts, which argues for the inclusion of n→π*
interactions in the inventory of non-covalent forces that contribute
to protein stability and thus in force fields for biomolecular modeling
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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