Scaffold optimization in discontinuous epitope containing protein mimics of gp120 using smart libraries

2013 ◽  
Vol 11 (16) ◽  
pp. 2676 ◽  
Author(s):  
Gwenn E. Mulder ◽  
H (Linda). C. Quarles van Ufford ◽  
Jeroen van Ameijde ◽  
Arwin J. Brouwer ◽  
John A. W. Kruijtzer ◽  
...  
Keyword(s):  
Discontinuous Epitope ◽  
Protein Mimics

scholarly journals Molecular construction of HIV-gp120 discontinuous epitope mimics by assembly of cyclic peptides on an orthogonal alkyne functionalized TAC-scaffold

2016 ◽  
Vol 14 (2) ◽  
pp. 701-710 ◽  
Author(s):  
P. R. Werkhoven ◽  
M. Elwakiel ◽  
T. J. Meuleman ◽  
H. C. Quarles van Ufford ◽  
J. A. W. Kruijtzer ◽  
...  
Keyword(s):  
Cyclic Peptides ◽  
Biologically Active ◽  
Discontinuous Epitope ◽  
Protein Mimics ◽  
Gp120 Protein ◽  
Hiv Gp120

An orthogonally alkyne functionalized TAC-scaffold was used for molecular construction of biologically active gp120 protein mimics containing different peptide loops.

scholarly journals Frontispiece: Peptide-Based Molecular Hydrogels as Supramolecular Protein Mimics

2017 ◽  
Vol 23 (5) ◽  
Author(s):  
Nishant Singh ◽  
Mohit Kumar ◽  
Juan F. Miravet ◽  
Rein V. Ulijn ◽  
Beatriu Escuder
Keyword(s):  
Protein Mimics

scholarly journals Evidence for protein X binding to a discontinuous epitope on the cellular prion protein during scrapie prion propagation

1997 ◽  
Vol 94 (19) ◽  
pp. 10069-10074 ◽  
Author(s):  
K. Kaneko ◽  
L. Zulianello ◽  
M. Scott ◽  
C. M. Cooper ◽  
A. C. Wallace ◽  
...  
Keyword(s):  
Prion Protein ◽  
Cellular Prion Protein ◽  
Discontinuous Epitope ◽  
Protein X ◽  
Prion Propagation

scholarly journals An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3327 ◽  
Author(s):  
Ranjan V. Mannige
Keyword(s):  
Degrees Of Freedom ◽  
Intrinsically Disordered Proteins ◽  
Angular Displacement ◽  
Disordered Proteins ◽  
Dihedral Angles ◽  
Peptide Fragments ◽  
Ramachandran Plot ◽  
Peptide Backbone ◽  
Protein Mimics ◽  
Intrinsically Disordered

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.

scholarly journals Design, synthesis and biological evaluation of a new bridged immunosuppressor.

2001 ◽  
Vol 48 (4) ◽  
pp. 1147-1150 ◽  
Author(s):  
Z Szewczuk ◽  
A Wilczyński ◽  
I Petry ◽  
I Z Siemion ◽  
Z Wieczorek
Keyword(s):  
Immune Response ◽  
Humoral Immune Response ◽  
Biological Evaluation ◽  
Design Synthesis ◽  
Discontinuous Epitope ◽  
Humoral Immune ◽  
Hla Dq ◽  
Synthesis And Biological Evaluation

A bridged peptide with the sequence: H-Thr-Pro-Gln-Arg-Gly-Asp-Val-gamma-Abu-Asn-Asp-Gln-Glu-Glu-Thr-Thr-Gly-Val-Val-Ser-Thr-Pro-Leu-Ile-Arg-Asn-Gly-OH was designed to mimic the discontinuous epitope of the HLA-DQ molecule that might interact with CD4. The bridged peptide revealed distinct suppressory effect in the humoral immune response. This result supports our suggestion that the 164-172 region of the HLA-DQ molecule may enhance its interactions with coreceptors, possibly with CD4.

scholarly journals Optimal Hydrophobicity in Ring-Opening Metathesis Polymerization-Based Protein Mimics Required for siRNA Internalization

2016 ◽  
Vol 17 (6) ◽  
pp. 1969-1977 ◽  
Author(s):  
Brittany M. deRonde ◽  
Nicholas D. Posey ◽  
Ronja Otter ◽  
Leah M. Caffrey ◽  
Lisa M. Minter ◽  
...  
Keyword(s):  
Ring Opening ◽  
Ring Opening Metathesis Polymerization ◽  
Metathesis Polymerization ◽  
Protein Mimics

The design and synthesis of protein mimics

Peptides ◽  
1994 ◽  
pp. 310-312
Author(s):  
M. L. Smythe ◽  
M. von Itzstein
Keyword(s):  
Protein Mimics ◽  
Design And Synthesis
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