David Baker (U. Washington / HHMI) Part 1: Introduction to Protein Design

Lecture Overview:
In the second of his talks, Baker tells us how his lab has moved beyond designing new protein structures to designing new protein functions. The first example he describes is the development of an inhibitor of the influenza virus. Baker’s lab designed a protein structure that fits into a highly conserved region of the hemagglutinin protein found on the surface of influenza. Preliminary lab data suggests that this designed protein protects mice from infection with the flu virus. Baker also describes experiments in which proteins were designed to fit together and build multicomponent materials such as nanocages, nanolayers and nanowires.

Speaker Bio:
David Baker received a BA in Biology from Harvard University and a PhD in Biochemistry from the University of California, Berkeley. Currently, Baker is the Head of the Institute for Protein Design and a Professor of Biochemistry at the University of Washington, and a Howard Hughes Medical Institute Investigator. His research utilizes both experimental and computational methods to study the design of protein structures, and the mechanisms of protein folding, protein-protein and protein-small molecule interactions.
Baker has won numerous awards for his work including the Raymond and Beverly Sackler International Prize in Biophysics in 2008. Baker is a member of the National Academy of Sciences and the American Academy of Sciences.

[manuelofosu]

David Baker won the Nobel Prize today!

[brendansullivan]

This guy is an amazing individual and I hope he goes far in life.

[johnlee]

Congratulations! Anyone advancing theories and proving it for protein folding deserves plaudits. Just thinking about atomic attraction, seeking lowest level of energy till it's stable in its final form is truly amazing.

[reyesdiegoarmando]

I'm about to get my bachelors degree in Biochem. Eng. down here in Mexico. People like Mr. Baker inspire me. Great content

[think_tank]

And here we're in the Alphafold/Rosettafold era. Kudos to these guys who worked hard to achieve the solutions.

[tessalittle]

I remember your work so well early 2005 when I was finishing off my PhD in protein folding. Here we are in the days of youtube and myself playing with water clathrate structures and nanobubbles

[juanzegarra]

I literally cried during the protein folding sequence, such beautiful and inspiring work

[Chiranjit]

So unique and motivated work. Thanks for sharing.

[Bannanakick]

Hi,
Im currently working on a presentation for my studies about that exact theme. My Information’s are based on an article from the Nature magazine from the 15th September of 2016. In the article the scientists also use the Rosetta program to design proteins. In my understanding they first try to build the carbon backbone structure by finding the lowest energy state, and then they try to add the different sidechains for the tightest packing together with the lowest energy possible. Here is my question: Don’t alpha helices and ß sheets need specific amino acid residues to even exist, at least at some places? If so does the program calculate these specific amino acids into the primary structure to stabilize the secondary structure?

Ps: The name of the article is: The Protein World

[susanmann]

He is one of my docs'. Believe me! He has/is!

[enyonamfame]

Congratulations 🎉for winning the Noble Prize 🏆

[someguy]

And I thought that the conformation that a protein adopts isn’t necessarily the global energy minimum, but rather a local energy minimum, where the protein would have to overcome a barrier to adopt the global energy minimum

[petersq]

how do you solve the problem with conformation distortion between bound and empty active centre. you probably need a certain deviation from minimal energy hole to allow flexibility and reactivity to substrates
do you have a figure how much the predictive success when the in vivo folding matches to the in silico one?

[Elephantine]

Interesting info and challenge. Nice graphics and good explanations. Thanks. Do you ever think (or worry) about making prions?

[sercanyildirimtugcann]

As a machine learning engineer without knowing anything about biology and protein, Can I be expert on it if I work hard? Im super ubber excited over this topic but a bit scared.

[hannanjaved]

Congratulations 🎉Mr David Baker for Winning the Noble prize 🥇 2024

[davidkincade]

Great, will living things use these??? One wonders if there is an information differential between made in lab and made in cell??? Thanks

[nitinchalla]

loved it, thank you so much for uploading this.

[danieltaylor]

How to send the design to the new protein?

[gizachewdiga]

Best illustrations on drug efficacy, agonist, antagonist, protein design, and computational description of protein design ( Lineard potential, Hydrogen bonding model, and Monte Carlo Methods) and experimental methods particularly Nuclear magnetic resonance (NMR) and magnetic imaging. Thanks.