Dek Woolfson

University of Bristol

Date: Thursday, June 16, 2022
Talk Time: 08:00 am - 08:25 am
Talk Title: Designing New Peptide Assemblies for Fun and for In-Cell Applications

The primary basic research interests of the group are: A the informational aspect of the protein-folding problem; that is, how does the sequence of a protein determine its active, three-dimensional structure or fold? And B, how can we use this information to design completely new proteins from scratch? In addition, we design proteins for applications in synthetic biology and medicine.

We tackle these problems using the following multi-disciplinary approach:

We use bioinformatics to garner sequence-to-structure relationships from protein sequence and structural databases.

We test the relationships, or "rules for protein folding," that we find in two ways: a through ab initio protein-structure prediction; and b via rational protein design, where we engineer natural protein structures, or design new ones completely from scratch, so-called de novo design.

We then test our engineered and design proteins experimentally using biophysical methods. The peptides and proteins are made either by peptide synthesis, or via recombinant DNA methods and the expression of synthetic genes. The products and then characterised using methods including: solution-phase biophysics, CD, FT-IR and fluorescence spectroscopy, AUC, and ITC, high-resolution structural biology, NMR spectroscopy, and X-ray crystallography, and microscopy, EM, AFM and light microscopy.

Finally, we explore potential applications of some the engineered and designed proteins in the burgeoning fields of bionanotechnology and synthetic biology.

Peptide design has come of age. It is now possible to generate a wide variety stable peptide assemblies from scratch using rational and/or computational approaches. A new challenge for the field is to move past structures offered up by nature and to target the so-called "dark matter of protein space," that is, structures that should be possible in terms of chemistry and physics, but which biology seems to have overlooked or not used prolifically.

This talk will illustrate what is currently possible in this nascent field using de novo designed helical peptides.

Coiled coils are bundles of two or more α-helices that wrap around each other in rope-like structures. They are one of the dominant structures that direct natural protein-protein interactions. Our understanding of coiled coils provides a strong basis for building new peptide assemblies. The first part of my talk will present this understanding and our current "toolkit" of de novo coiled coils.

Next, I will describe how the toolkit can be expanded to generate dark-matter structures. For instance, this has led to the rational and computational design of a completely new 310-helical bundle.

Then I will turn to in-cell applications. I will describe two new designs for i de novo cell-penetrating peptides and ii high-affinity kinesin-binding peptides.

Finally, I will show how these two designs can be combined to render peptides that can be delivered exogenously to eukaryotic cells and target subcellular processes. In in this case, hijacking active protein motors.

Dek Woolfson, talk image 2

Dek Woolfson
Dek Woolfson, talk image 1
Dek Woolfson, talk image 3
Dek Woolfson, talk image 4