Search bioRxiv⌕ Search

Biology subjects

Khan, G. N.

Publications and source records attributed to Khan, G. N..

2 recordsLinked to original sources

Residues 2-7 of alpha-synuclein regulate amyloid formation via lipid-dependent and -independent pathways

Amyloid formation by -synuclein (Syn) occurs in Parkinsons disease, multiple system atrophy, and dementia with Lewy bodies. Deciphering the residues that regulate Syn amyloid fibril formation will not only provide mechanistic insight, but may also reveal new targets to prevent and treat disease. Previous investigations have identified several regions of Syn to be important in the regulation of amyloid formation, including the non-amyloid-{beta} component (NAC), P1 region (residues 36-42), and residues in the C-terminal domain. Recent studies have also indicated the importance of the N-terminal region of Syn for both its physiological and pathological roles. Here, the role of residues 2-7 in the N-terminal region of Syn are investigated in terms of their ability to regulate amyloid fibril formation in vitro and in vivo. Deletion of these residues (Syn{Delta}N7) slows the rate of fibril formation in vitro and reduces the capacity of the protein to be recruited by wild-type (SynWT) fibril seeds, despite cryo-EM showing a fibril structure consistent with those of full-length Syn. Strikingly, fibril formation of Syn{Delta}N7 is not induced by liposomes, despite the protein binding to liposomes with similar affinity to SynWT. A Caenorhabditis elegans model also showed that Syn{Delta}N7::YFP forms few puncta and lacks motility and lifespan defects typified by expression of SynWT::YFP. Together, the results demonstrate the involvement of residues 2-7 of Syn in amyloid formation, revealing a new target for the design of amyloid inhibitors that may leave the functional role of the protein in membrane binding unperturbed. Significance StatementAmyloid formation of -synuclein (Syn) is associated with Parkinsons disease. Attempts to target Syn aggregation to treat synucleinopathies, thus far, have been unsuccessful. A better understanding of residues that regulate amyloid formation may reveal new targets for therapeutics. Here, six residues at the N-terminus of Syn are identified as regulators of amyloid formation. Deletion of these residues slows lipid-independent assembly, ablates lipid-dependent amyloid formation in vitro, and prevents aggregation and its associated cellular toxicity in vivo. Importantly, these residues are not necessary for binding to synthetic membranes. The work reveals a new target for the prevention of synucleinopathies by disfavouring aggregation without perturbing membrane binding, a property considered to be essential for the physiological function of Syn at the synapse.

biophysics↗

Sculpting conducting nanopore size and shape through de novo protein design

Transmembrane {beta}-barrels (TMBs) are widely used for single molecule DNA and RNA sequencing and have considerable potential for a broad range of sensing and sequencing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels such as CsgG, which have evolved to carry out functions very different from sensing, and hence provide sub-optimal starting points. In contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to the design of transmembrane {beta}-barrel pores with different diameter and pore geometry. NMR and crystallographic characterization shows that the designs are stably folded with structures close to the design models. We report the first examples of de novo designed TMBs with 10, 12 and 14 stranded {beta}-barrels. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 pS ([~]0.5 nm pore diameter) to 430 pS ([~]1.1 nm pore diameter), and can be converted into sensitive small-molecule sensors with high signal to noise ratio. The capability to generate on demand {beta}-barrel pores of defined geometry opens up fundamentally new opportunities for custom engineering of sequencing and sensing technologies. One sentence summaryDe novo design enables the generation of stable and quite transmembrane beta-barrel nanopores with tailored sizes, shapes and properties.

synthetic biology↗