Prediction and design of protein structures and interactions / David Baker.

Format:

Video

Author/Creator:

Baker, David, author.

Language:

English

Subjects (All):

Protein folding.

Physical Description:

1 online resource (1 streaming video file (46 min., 43 sec.)) : sound, color

Place of Publication:

London, England : Henry Stewart Talks, 2007.

System Details:

video file

Summary:

Audio-visual presentation : Modeling of macromolecular interactions ; Conformational sampling ; Docking low-resolution search ; High resolution refinement ; Docking protocol ; Side chain flexibility and modeling ; Ab initio structure prediction ; Computational protein design ; Simultaneous sequence-structure optimization ; Protein interface design ; Properties of free energy landscapes of macromolecules.

Contents:

Introduction

Structural biology should be computable

The computer program - Rosetta

Model of macromolecular interactions

Example: hydrogen bonding

Formamide dimer

Conformational sampling

Docking low-resolution search

Rosetta high resolution refinement (1)

Docking protocol

Side chain flexibility

Details of T12 interface

Example of target 15

Accurate side chain modeling

Details of T15 interface

Example of target 14

Details of T14 interface

Backbone changes

Modeling backbone movement

CASP6 T0198: PhoU domain repeat

CASP6 T0272_1

CASP6 T0212

Automated domain parsing: CASP6 T0248

Rosetta high resolution refinement (2)

Movie of refinement process

Sharp decrease in free energy close to native state

T0281 ab initio prediction

High resolution search figure of 1R69

Prediction of 1R69

High resolution search figure of 1ubq

Prediction of 1ubq

High resolution search figure of 1b72

Prediction of 1b72

High resolution search figure of 2REB

Prediction of 2REB

High resolution search figure of 1DTJ

Prediction of 1DTJ

Inadequate sampling causes mistake in prediction

High resolution refinement of CASP target 199

High resolution refinement of CASP target 263

Computing structural biology

Computational protein design

A novel backbone and topology

Possible low energy arrangement of side chains

Flexible backbone protein design

TOP7 is highly stable and well-folded

TOP7 x-ray structure has correct topology

TOP7 folding landscape

Protein interface design

E-DreI structure versus design

Design of novel H bond network

High resolution modeling is starting to work

High resolution prediction: why does it work?

Macromolecules free energy landscares

Properties of free energy landscapes

Acknowledgements.

Notes:

Description based on: online resource; title from PDF information screen (Henry Stewart Talks Biomedical and Life Sciences Collection, viewed April 13 2024).

Retrieved April 13, 2024, from https://hstalks.com/bs/446/.