scholarly journals Shark Antibody Variable Domains Rigidify Upon Affinity Maturation—Understanding the Potential of Shark Immunoglobulins as Therapeutics

2021 ◽  
Vol 8 ◽  
Author(s):  
Monica L. Fernández-Quintero ◽  
Clarissa A. Seidler ◽  
Patrick K. Quoika ◽  
Klaus R. Liedl

Sharks and other cartilaginous fish are the phylogenetically oldest living organisms that have antibodies as part of their adaptive immune system. As part of their humoral adaptive immune response, they produce an immunoglobulin, the so-called immunoglobulin new antigen receptor (IgNAR), a heavy-chain only antibody. The variable domain of an IgNAR, also known as VNAR, binds the antigen as an independent soluble domain. In this study, we structurally and dynamically characterized the affinity maturation mechanism of the germline and somatically matured (PBLA8) VNAR to better understand their function and their applicability as therapeutics. We observed a substantial rigidification upon affinity maturation, which is accompanied by a higher number of contacts, thereby contributing to the decrease in flexibility. Considering the static x-ray structures, the observed rigidification is not obvious, as especially the mutated residues undergo conformational changes during the simulation, resulting in an even stronger network of stabilizing interactions. Additionally, the simulations of the VNAR in complex with the hen egg-white lysozyme show that the VNAR antibodies evidently follow the concept of conformational selection, as the binding-competent state already preexisted even without the presence of the antigen. To have a more detailed description of antibody–antigen recognition, we also present here the binding/unbinding mechanism between the hen egg-white lysozyme and both the germline and matured VNARs. Upon maturation, we observed a substantial increase in the resulting dissociation-free energy barrier. Furthermore, we were able to kinetically and thermodynamically describe the binding process and did not only identify a two-step binding mechanism, but we also found a strong population shift upon affinity maturation toward the native binding pose.

2020 ◽  
Vol 17 ◽  
Author(s):  
Nandini Sarkar ◽  
Vidyalatha Kolli ◽  
Taraka Prabhu MP ◽  
Arbin Basak ◽  
Hitesh Mandal

Background: Amyloids are a class of ordered protein aggregates which have been implicated in the onset of several degenerative diseases such as Alzheimer's disease, Parkinson's disease, Type II diabetes and so on. Despite extensive research, the exact mechanism and the driving factors for the amyloidogenesis process remain elusive. Identifying molecules which can effectively inhibit and/or disaggregate the fibrils may be one effective therapeutic strategy against amyloidosis Objectives: In the current study, few hydroxy-benzoic phytochemicals were selected to study their effects on formation as well as disaggregation of hen egg white lysozyme (HEWL) amyloids, namely gallic acid, syringic acid, vanillic acid and iso-vanillic acid. Method: Amyloidogenesis was monitored using methods like the thioflavin T assay, field emission scanning electron mi-croscopy (FESEM) and dynamic light scattering (DLS) studies. Further protein conformational changes were monitored us-ing methods like 8-Anilino-naphthalene-1-sulfonate (ANS) fluorescence, circular dichroism (CD) spectroscopy and guani-dine hydrochloride mediated stability studies. Computational approach was also employed to get an insight on the interac-tion(s) between the selected compounds and HEWL using docking studies Result: The selected compounds exhibited significant inhibitory as well as disaggregation effects on HEWL amyloids. In-teraction with the phytochemicals was also associated with considerable conformational changes in HEWL. Docking studies show role of hydrogen bonding between HEWL and the phytochemicals. Conclusion: Thus the current study throws light on the key factors that drive amyloid formation and hence will be helpful for development of effective therapeutics against amyloidosis.


Author(s):  
Joao Ramos ◽  
Valerie Laux ◽  
Michael Haertlein ◽  
V. Trevor Forsyth ◽  
Estelle Mossou ◽  
...  

The biological function of a protein is intimately related to its structure and dynamics, which in turn are determined by the way in which it has been folded. In vitro refolding is commonly used for the recovery of recombinant proteins that are expressed in the form of inclusion bodies and is of central interest in terms of the folding pathways that occur in vivo. Here, biophysical data are reported for in vitro-refolded hydrogenated hen egg-white lysozyme, in combination with atomic resolution X-ray diffraction analyses, which allowed detailed comparisons with native hydrogenated and refolded perdeuterated lysozyme. Distinct folding modes are observed for the hydrogenated and perdeuterated refolded variants, which are determined by conformational changes to the backbone structure of the Lys97–Gly104 flexible loop. Surprisingly, the structure of the refolded perdeuterated protein is closer to that of native lysozyme than that of the refolded hydrogenated protein. These structural differences suggest that the observed decreases in thermal stability and enzymatic activity in the refolded perdeuterated and hydrogenated proteins are consequences of the macromolecular deuteration effect and of distinct folding dynamics, respectively. These results are discussed in the context of both in vitro and in vivo folding, as well as of lysozyme amyloidogenesis.


1997 ◽  
Vol 94 ◽  
pp. 356-364 ◽  
Author(s):  
M Faraggi ◽  
E Bettelheim ◽  
M Weinstein

2021 ◽  
pp. 138830
Author(s):  
Baoliang Ma ◽  
Haohao Wang ◽  
Yujie Liu ◽  
Fang Wu ◽  
Xudong Zhu

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