De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation

Bellows-Peterson, Meghan L.; Fung, Ho Ki; Floudas, Christodoulos A.; Kieslich, Chris A.; Zhang, Li; Morikis, Dimitrios; Wareham, Kathryn; Monk, Peter N.; Hawksworth, Owen A.; Woodruff, Trent M.

doi:10.1021/jm201609k

Cited by 32 publications

(30 citation statements)

References 51 publications

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“…The agonist that we used, a highly potent peptide analog of C3a (22,32), reduced neutrophil mobilization in response to intestinal injury and subsequently their presence in inflamed tissue. Thus, exogenous administration of a C3a agonist analog can augment any constituent activity of C3a generated during the disease process, perhaps because of the extremely short half-life of endogenously generated C3a (33).…”

Section: Discussionmentioning

confidence: 99%

“…A third cohort of WT mice was treated with the CXCR4 antagonist AMD3100 (5 mg/kg s.c.; Merck) or vehicle (water), 1 h before ischemia. A final group of animals were given the selective C3a agonist WWGKKYRASKLGLAR (10 μg/kg i.v) (22,32) or vehicle (saline) 10 min before ischemia. Detailed descriptions of various methods used to measure IR pathology are provided in SI Materials and Methods.…”

Section: Methodsmentioning

confidence: 99%

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The receptor for complement component C3a mediates protection from intestinal ischemia-reperfusion injuries by inhibiting neutrophil mobilization

Brennan

Lynch

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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C3a is a key complement activation fragment, yet its neutrophil-expressed receptor (C3aR) still has no clearly defined role. In this study, we used a neutrophil-dependent mouse model of intestinal ischemia-reperfusion (IR) injury to explore the role of C3aR in acute tissue injuries. C3aR deficiency worsened intestinal injury, which corresponded with increased numbers of tissue-infiltrating neutrophils. Circulating neutrophils were significantly increased in C3aR −/− mice after intestinal ischemia, and C3aR −/− mice also mobilized more circulating neutrophils after granulocyte colony-stimulating factor infusion compared with WT mice, indicating a specific role for C3aR in constraining neutrophil mobilization in response to intestinal injury. In support of this role, C3aR −/− mice reconstituted with WT bone marrow reversed IR pathology back to WT levels. Complement C5a receptor (C5aR) antagonism in C3aR −/− mice also rectified the worsened pathology after intestinal IR injury but had no effect on circulating neutrophils, highlighting the opposing roles of C3a and C5a in disease pathogenesis. Finally, we found that using a potent C3a agonist to activate C3aR in vivo reduced neutrophil mobilization and ameliorated intestinal IR pathology in WT, but not C3aR −/− , mice. This study identifies a role for C3aR in regulating neutrophil mobilization after acute intestinal injury and highlights C3aR agonism as a potential treatment option for acute, neutrophil-driven pathologies.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The receptor for complement component C3a mediates protection from intestinal ischemia-reperfusion injuries by inhibiting neutrophil mobilization

Brennan

Lynch

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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138

157

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“…Two of the sequences were potent agonists while two others were partial agonists. 21 The two potent agonists showed a 58-fold improvement over a previously discovered "superagonist". The design of C5a receptor agonists and antagonists provided a set of 61 sequences.…”

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confidence: 93%

Protein WISDOM: A Workbench for <em>In silico</em> <em>De novo</em> Design of BioMolecules

Smadbeck

Peterson

Khoury

et al. 2013

JoVE

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The aim of de novo protein design is to find the amino acid sequences that will fold into a desired 3-dimensional structure with improvements in specific properties, such as binding affinity, agonist or antagonist behavior, or stability, relative to the native sequence. Protein design lies at the center of current advances drug design and discovery. Not only does protein design provide predictions for potentially useful drug targets, but it also enhances our understanding of the protein folding process and protein-protein interactions. Experimental methods such as directed evolution have shown success in protein design. However, such methods are restricted by the limited sequence space that can be searched tractably. In contrast, computational design strategies allow for the screening of a much larger set of sequences covering a wide variety of properties and functionality. We have developed a range of computational de novo protein design methods capable of tackling several important areas of protein design. These include the design of monomeric proteins for increased stability and complexes for increased binding affinity.To disseminate these methods for broader use we present Protein WISDOM (http://www.proteinwisdom.org), a tool that provides automated methods for a variety of protein design problems. Structural templates are submitted to initialize the design process. The first stage of design is an optimization sequence selection stage that aims at improving stability through minimization of potential energy in the sequence space. Selected sequences are then run through a fold specificity stage and a binding affinity stage. A rank-ordered list of the sequences for each step of the process, along with relevant designed structures, provides the user with a comprehensive quantitative assessment of the design. Here we provide the details of each design method, as well as several notable experimental successes attained through the use of the methods. Video LinkThe video component of this article can be found at

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“…These programs incorporate information from query-template alignments, secondary structure prediction, solvent accessibility prediction, and Phi/Psi (Φ/Ψ) torsional angle prediction to guide the assembly simulations of global folds. Some of these knowledge-based template features have been successfully employed by several protein design algorithms (Bellows-Peterson et al, 2012; Bender et al, 2007; Kuhlman et al, 2003; Poole and Ranganathan, 2006). However, EvoDesign was probably the first method to systematically explore the possibility of integrating threading-based structure profiling to constrain the sequence design search (Mitra et al, 2013a; Mitra et al, 2013b).…”

Section: Introductionmentioning

confidence: 99%

Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering

Shultis

Dodge

Zhang

2015

Journal of Structural Biology

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The Phox homology domain (PX domain) is a phosphoinositide-binding structural domain that is critical in mediating protein and cell membrane association and has been found in more than 100 eukaryotic proteins. The abundance of PX domains in nature offers an opportunity to redesign the protein using EvoDesign, a computational approach to design new sequences based on structure profiles of multiple evolutionarily related proteins. In this study, we report the X-ray crystallographic structure of a designed PX domain from the cytokine-independent survival kinase (CISK), which has been implicated as functioning in parallel with PKB/Akt in cell survival and insulin responses. Detailed data analysis of the designed CISK-PX protein demonstrates positive impacts of knowledge-based secondary structure and solvation predictions and structure-based sequence profiles on the efficiency of the evolutionary-based protein design method. The structure of the designed CISK-PX domain is close to the wild-type (1.54 Å in Cα RMSD), which was accurately predicted by I-TASSER based fragment assembly simulations (1.32 Å in Cα RMSD). This study represents the first successfully designed conditional peripheral membrane protein fold and has important implications in the examination and experimental validation of the evolution-based protein design approaches.

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De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation

Cited by 32 publications

References 51 publications

The receptor for complement component C3a mediates protection from intestinal ischemia-reperfusion injuries by inhibiting neutrophil mobilization

The receptor for complement component C3a mediates protection from intestinal ischemia-reperfusion injuries by inhibiting neutrophil mobilization

Protein WISDOM: A Workbench for <em>In silico</em> <em>De novo</em> Design of BioMolecules

Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering

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