[CSBi-events] Tomorrow: Seminar Michael Levitt 5 PM, Rm. 66-110

[CSBi events]

RECENT ADVANCES IN COMPUTATIONAL STRUCTURAL BIOLOGY

 

Michael Levitt

 

Department of Structural Biology and Computer Science

Stanford University

 

WEDNESDAY, NOVEMBER 18, 2009

5:00 PM

Building 66, Room 110

(Reception at 4:30 PM in lobby area of Room 66-110.)

 

This talk covers two topics selected from many that occupy us in the
Computational Structural Biology group at Stanford: Mesoscale Modeling of
Macromolecular Machines and The Nature of the Protein Universe. Both topics
are my own work.

 

Mesoscale Modeling of Macromolecular Machines. Most of the central
biological functions of iving cells are performed by large complexes of
individual protein domains, whose movement plays a crucial role in their
biological function. I present a unique approach to this motion based on
normal modes calculated in torsional angle space. Special problems arise
because 

(1) systems are large mandating use of simplified representations; 

(2) modes must be calculated at an energy minimum mandating the use of
accurate energy functions and convergent minimizers; 

(3) numerical accuracy mandates the use of complex step derivatives; 

(4) there are many independent molecules mandating combination of rigid body
and internal degrees of freedom; and 

(5) resulting matrices are badly ill-conditioned mandating special
eigenvalue

methods.

 

The Nature of the Protein Universe. After a decade of serious
structure-determination and sequencing efforts there are over 50,000
structures and over 6 million protein sequences; an overview of the set of
all proteins of all organisms is becoming an essential roadmap. Here I
analyze the protein universe in terms of sequence families that have single
or multi-domain architectures, with or without known structures. Growth of
single domain families has saturated: almost all growth comes from
multi-domain architectures that are combinations of about 25,000 domains.
Multi-domain architectures, which are specific to the major groups of
organisms, account for species diversity. There are known structures for a
quarter of the single domain families and half of all sequences can be
partially modeled due to their membership in these families.

 

 

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