Madison Kennedy
YOU?
Author Swipe
View article: Design of intrinsically disordered region binding proteins
Design of intrinsically disordered region binding proteins Open
Intrinsically disordered proteins and peptides play key roles in biology, but a lack of defined structures and high variability in sequence and conformational preferences have made targeting such systems challenging. We describe a general …
View article: Four-component protein nanocages designed by programmed symmetry breaking
Four-component protein nanocages designed by programmed symmetry breaking Open
Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures1,2. Viruses access more complex higher triangulation number icosahe…
View article: Design of pseudosymmetric protein hetero-oligomers
Design of pseudosymmetric protein hetero-oligomers Open
Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins de novo would provide new routes to c…
View article: Design of intrinsically disordered region binding proteins
Design of intrinsically disordered region binding proteins Open
Intrinsically disordered proteins and peptides play key roles in biology, but the lack of defined structures and the high variability in sequence and conformational preferences has made targeting such systems challenging. We describe a gen…
View article: De novo design of proteins housing excitonically coupled chlorophyll special pairs
De novo design of proteins housing excitonically coupled chlorophyll special pairs Open
Natural photosystems couple light harvesting to charge separation using a ‘special pair’ of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics o…
View article: Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking
Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking Open
Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral (T-sym), octahedral (O-sym) or icosahedral (I-sym) point group symmetry to generate closed cage-like structures 1,2 . Generating more complex closed struct…
View article: De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs
De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs Open
Natural photosystems couple light harvesting to charge separation using a “special pair” of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics o…
View article: Stepwise design of pseudosymmetric protein hetero-oligomers
Stepwise design of pseudosymmetric protein hetero-oligomers Open
Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins de novo would provide new routes to c…
View article: Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI
Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI Open
Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, i…
View article: Figure 8 Time-dependent digestion of plasmids with four PaqCI target sites indicate a sequential cleavage at individual sites
Figure 8 Time-dependent digestion of plasmids with four PaqCI target sites indicate a sequential cleavage at individual sites Open
Panel a. Cleavage of a head-to-head four-site substrate with and without an activator added in trans. The no activator reaction contained 1 ug substrate DNA (37 nM sites) and 2 units (17.2 nM) of PaqCI per ug DNA in 50 ul rCutSmart buffer …
View article: Figure 9 DNA pre-bound at all four sites in the PaqCI tetramer is cut sequentially
Figure 9 DNA pre-bound at all four sites in the PaqCI tetramer is cut sequentially Open
Panel a. Cleavage of a four-site plasmid substrate either pre-bound or not pre-bound with a 1:1 enzyme-binding-site to DNA-sites ratio. The pre-bound reaction contained 1 ug substrate DNA (37 nM sites) and 4.3 units (37 nM) of PaqCI per ug…
View article: Figure 2 Time-dependent digestion of plasmids with two PaqCI target sites indicate a sequential cleavage profile
Figure 2 Time-dependent digestion of plasmids with two PaqCI target sites indicate a sequential cleavage profile Open
The reaction contained 1 ug substrate DNA and 2 units/ug PaqCI endonuclease in rCutSmart buffer at 37C. Digest time points were quenched at 0.25 min, 0.5 min, 1 min, 3 min, 5 min, 10 min, 30 min, and 60 minutes with 1 ug dual site substrat…
View article: Figure S1 Purification and solution behavior of PaqCI
Figure S1 Purification and solution behavior of PaqCI Open
Panel a: SDS-PAGE gel of induced cell lysate and purification via metal affinity chromatography. Panel b: Size exclusion chromatographic elution of final purified PaqCI used for subsequent structural analyses. The protein elution profile i…
View article: Figure S5 Plasmids with two PaqCI target sites show potential sequential cleavage when trans oligo enhancer is added
Figure S5 Plasmids with two PaqCI target sites show potential sequential cleavage when trans oligo enhancer is added Open
The reaction contained 1 ug substrate DNA, 2 units/ug PaqCI endonuclease and 40 nM/unit activating oligonucleotide in rCutSmart buffer at 37C. Reactions were quenched at the time points indicated above each lane. The mobilities of the supe…
View article: Figure 1 Biochemical analyses of PaqCI cleavage activity
Figure 1 Biochemical analyses of PaqCI cleavage activity Open
Panel a: PaqCI demonstrates substrate turnover when acting on a stoichiometric excess of DNA targets. Digest time points are quenched at 10 minutes and 60 minutes with protein concentration ranging from 0.3-8.0 units with the DNA concentra…
View article: Figure S3 CryoEM analysis of PaqCI DNA-bound enzyme, Panel a
Figure S3 CryoEM analysis of PaqCI DNA-bound enzyme, Panel a Open
Size exclusion chromatographic elution behavior of PaqCI enzyme in the presence of a stoichiometric excess of double strand DNA (see Figure 3a) indicates formation of a stable DNA-bound enzyme complex. The elution profiles for free protein…
View article: Structures and mechanism of a type IIS restriction endonuclease: PaqCI
Structures and mechanism of a type IIS restriction endonuclease: PaqCI Open
Restriction endonucleases are an essential component of innate, 'preprogrammed' phage restriction systems that protect bacteria from foreign DNA.Type II restriction endonucleases are invaluable tools in research because of their ability to…
View article: De novo design of protein homodimers containing tunable symmetric protein pockets
De novo design of protein homodimers containing tunable symmetric protein pockets Open
Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantage…
View article: Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces
Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces Open
Circular tandem repeat proteins (‘cTRPs’) are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that contain repeated protein sequences and structural motifs and form closed circular st…
View article: Structural basis for isoform-specific inhibition of human CTPS1
Structural basis for isoform-specific inhibition of human CTPS1 Open
Significance An effective immune response depends on the proliferation of T cells, a process that requires the enzyme CTP synthase 1 (CTPS1). Individuals lacking CTPS1 due to a rare genetic disorder exhibit severe immunodeficiencies but la…