Following evolutionary paths to protein-protein interactions with high affinity and selectivity

2009 ◽  
Vol 16 (10) ◽  
pp. 1049-1055 ◽  
Author(s):  
Kalia Bernath Levin ◽  
Orly Dym ◽  
Shira Albeck ◽  
Shlomo Magdassi ◽  
Anthony H Keeble ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
High Affinity ◽  
Evolutionary Paths

scholarly journals Structural design principles for specific ultra-high affinity interactions between colicins/pyocins and immunity proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Avital Shushan ◽  
Mickey Kosloff
Keyword(s):  
Protein Interactions ◽  
Structural Elements ◽  
Protein Protein Interactions ◽  
Immunity Protein ◽  
Rational Engineering ◽  
High Affinity ◽  
Comparative Structure ◽  
Polar Interactions ◽  
Exquisite Specificity

AbstractThe interactions of the antibiotic proteins colicins/pyocins with immunity proteins is a seminal model system for studying protein–protein interactions and specificity. Yet, a precise and quantitative determination of which structural elements and residues determine their binding affinity and specificity is still lacking. Here, we used comparative structure-based energy calculations to map residues that substantially contribute to interactions across native and engineered complexes of colicins/pyocins and immunity proteins. We show that the immunity protein α1–α2 motif is a unique structurally-dissimilar element that restricts interaction specificity towards all colicins/pyocins, in both engineered and native complexes. This motif combines with a diverse and extensive array of electrostatic/polar interactions that enable the exquisite specificity that characterizes these interactions while achieving ultra-high affinity. Surprisingly, the divergence of these contributing colicin residues is reciprocal to residue conservation in immunity proteins. The structurally-dissimilar immunity protein α1–α2 motif is recognized by divergent colicins similarly, while the conserved immunity protein α3 helix interacts with diverse colicin residues. Electrostatics thus plays a key role in setting interaction specificity across all colicins and immunity proteins. Our analysis and resulting residue-level maps illuminate the molecular basis for these protein–protein interactions, with implications for drug development and rational engineering of these interfaces.

scholarly journals Identifying protein–protein interactions in somatic hypermutation

2005 ◽  
Vol 201 (4) ◽  
pp. 493-496 ◽  
Author(s):  
Myron F. Goodman ◽  
Matthew D. Scharff
Keyword(s):  
Mouse Model ◽  
Protein Interactions ◽  
Somatic Hypermutation ◽  
Model Systems ◽  
Antigen Binding ◽  
Immunoglobulin Genes ◽  
Protein Protein Interactions ◽  
Cell Systems ◽  
High Affinity ◽  
Key Players

Somatic hypermutation (SHM) in immunoglobulin genes is required for high affinity antibody–antigen binding. Cultured cell systems, mouse model systems, and human genetic deficiencies have been the key players in identifying likely SHM pathways, whereas “pure” biochemical approaches have been far less prominent, but change appears imminent. Here we comment on how, when, and why biochemistry is likely to emerge from the shadows and into the spotlight to elucidate how the somatic mutation of antibody variable (V) regions is generated.

Functional Display of Bioactive Peptides on the vGFP Scaffold.

2021 ◽  
Author(s):  
Sharon Min Qi Chee ◽  
Jantana Wongsantichon ◽  
Sze Yi Lau ◽  
Barindra Sana ◽  
Yuri Frosi ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Bioactive Peptides ◽  
Negative Regulator ◽  
Live Cells ◽  
Structural Studies ◽  
Protein Protein Interactions ◽  
Target Interaction ◽  
High Affinity ◽  
Novel Scaffold

Abstract Grafting bioactive peptides into recipient protein scaffolds can often increase their activities by conferring enhanced stability and cellular longevity. Here, we describe use of vGFP as a novel scaffold to display peptides. vGFP comprises GFP fused to a bound high affinity Enhancer nanobody that potentiates its fluorescence. We show that peptides inserted into the linker region between GFP and the Enhancer are correctly displayed for on-target interaction, both in vitro and in live cells by pull-down, measurement of target inhibition and imaging analyses. This is further confirmed by structural studies highlighting the optimal display of a vGFP-displayed peptide bound to Mdm2, the key negative regulator of p53 that is often overexpressed in cancer. We also demonstrate a potential biosensing application of the vGFP scaffold by showing target-dependent modulation of intrinsic fluorescence. vGFP is relatively thermostable, well-expressed and inherently fluorescent. These properties make it a useful scaffold to add to the existing tool box for displaying peptides that can disrupt clinically relevant protein-protein interactions.

Engineering High Affinity Protein–Protein Interactions Using a High-Throughput Microcapillary Array Platform

2016 ◽  
Vol 12 (2) ◽  
pp. 336-341 ◽  
Author(s):  
Sungwon Lim ◽  
Bob Chen ◽  
Mihalis S. Kariolis ◽  
Ivan K. Dimov ◽  
Thomas M. Baer ◽  
...  
Keyword(s):  
High Throughput ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
High Affinity ◽  
Array Platform

scholarly journals Functional display of bioactive peptides on the vGFP scaffold

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sharon Min Qi Chee ◽  
Jantana Wongsantichon ◽  
Lau Sze Yi ◽  
Barindra Sana ◽  
Yuri Frosi ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Bioactive Peptides ◽  
Negative Regulator ◽  
Live Cells ◽  
Structural Studies ◽  
Protein Protein Interactions ◽  
Target Interaction ◽  
High Affinity ◽  
Novel Scaffold

AbstractGrafting bioactive peptides into recipient protein scaffolds can often increase their activities by conferring enhanced stability and cellular longevity. Here, we describe use of vGFP as a novel scaffold to display peptides. vGFP comprises GFP fused to a bound high affinity Enhancer nanobody that potentiates its fluorescence. We show that peptides inserted into the linker region between GFP and the Enhancer are correctly displayed for on-target interaction, both in vitro and in live cells by pull-down, measurement of target inhibition and imaging analyses. This is further confirmed by structural studies highlighting the optimal display of a vGFP-displayed peptide bound to Mdm2, the key negative regulator of p53 that is often overexpressed in cancer. We also demonstrate a potential biosensing application of the vGFP scaffold by showing target-dependent modulation of intrinsic fluorescence. vGFP is relatively thermostable, well-expressed and inherently fluorescent. These properties make it a useful scaffold to add to the existing tool box for displaying peptides that can disrupt clinically relevant protein–protein interactions.

scholarly journals Design and Synthesis of a New Orthogonally Protected Glutamic Acid Analog and Its Use in the Preparation of High Affinity Polo-like Kinase 1 Polo-box Domain – binding Peptide Macrocycles

2021 ◽  
Author(s):  
David Hymel ◽  
Kohei Tsuji ◽  
Robert A. Grant ◽  
Ramesh M. Chingle ◽  
Dominique L. Kunciw ◽  
...  
Keyword(s):  
Glutamic Acid ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Binding Peptide ◽  
Design And Synthesis ◽  
High Affinity ◽  
Acid Analog ◽  
Therapeutic Development

Targeting protein – protein interactions (PPIs) has emerged as important area of discovery for anticancer therapeutic development. In the case of phospho-dependent PPIs, such as the polo-like kinase 1 (Plk1)...

scholarly journals Integrative proteomics reveals exceptional diversity and versatility of mammalian humoral immunity

2020 ◽  
Author(s):  
Yufei Xiang ◽  
Zhe Sang ◽  
Lirane Bitton ◽  
Jianquan Xu ◽  
Yang Liu ◽  
...  
Keyword(s):  
Immune Response ◽  
Protein Interactions ◽  
Specific Antigen ◽  
Cellular Protein ◽  
Protein Protein Interactions ◽  
Humoral Immune ◽  
High Affinity ◽  
Interaction Interface ◽  
Systematic Understanding ◽  
Antigen Antibody

SummaryThe humoral immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the specific serologic antibody repertoire in response to an antigen. We developed a proteomic strategy to survey, at an unprecedented scale, the landscapes of antigen-engaged, serum-circulating repertoires of camelid heavy-chain antibodies (hcAbs). The sensitivity and robustness of this technology were validated using three antigens spanning orders of magnitude in immune response; thousands of divergent, high-affinity hcAb families were confidently identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of > 100,000 antigen-antibody complexes. Our results revealed a surprising diversity of high-affinity hcAbs for specific antigen binding on a variety of dominant epitopes. hcAbs perfect both shape and charge complementarity to target challenging antigens specifically; they can rapidly evolve to recognize a conserved, promiscuous cellular protein interaction interface, unraveling the convergent force that drives protein-protein interactions.

scholarly journals Mapping Protein–Protein Interactions of the Resistance-Related Bacterial Zeta Toxin–Epsilon Antitoxin Complex (ε2ζ2) with High Affinity Peptide Ligands Using Fluorescence Polarization

Toxins ◽  
2016 ◽  
Vol 8 (7) ◽  
pp. 222 ◽  
Author(s):  
María Fernández-Bachiller ◽  
Iwona Brzozowska ◽  
Norbert Odolczyk ◽  
Urszula Zielenkiewicz ◽  
Piotr Zielenkiewicz ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Fluorescence Polarization ◽  
Peptide Ligands ◽  
Protein Protein Interactions ◽  
High Affinity ◽  
Affinity Peptide
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