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<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'>RECENT ADVANCES IN COMPUTATIONAL STRUCTURAL BIOLOGY<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'>Michael Levitt<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'>Department of Structural Biology and Computer Science<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'>Stanford University<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'>WEDNESDAY, NOVEMBER 18, 2009<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'>5:00 PM<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'>Building 66, Room 110<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'>(Reception at 4:30 PM in lobby area of Room 66-110.)<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";font-weight:
normal'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>This talk covers two topics selected from many that occupy
us in the Computational Structural Biology group at Stanford: <i>Mesoscale
Modeling of Macromolecular Machines </i>and </span><i><span style='font-family:
"Calibri","sans-serif";color:black;font-weight:normal'>The Nature of the
Protein Universe</span></i><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>. Both topics are my own work.<o:p></o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-align:justify'><i><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>Mesoscale Modeling of Macromolecular Machines. </span></i><span
style='font-family:"Calibri","sans-serif";font-weight:normal'>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 <o:p></o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>(1) systems are large mandating use of simplified
representations; <o:p></o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>(2) modes must be calculated at an energy minimum mandating
the use of accurate energy functions and convergent minimizers; <o:p></o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>(3) numerical accuracy mandates the use of complex step
derivatives; <o:p></o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>(4) there are many independent molecules mandating
combination of rigid body and internal degrees of freedom; and <o:p></o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>(5) resulting matrices are badly ill-conditioned mandating
special eigenvalue<o:p></o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>methods.<o:p></o:p></span></p>
<p class=MsoNormal style='text-align:justify'><span style='font-family:"Calibri","sans-serif";
font-weight:normal'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-align:justify'><i><span style='font-family:"Calibri","sans-serif";
font-weight:normal'>The Nature of the Protein Universe. </span></i><span
style='font-family:"Calibri","sans-serif";font-weight:normal'>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.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:windowtext;font-weight:normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:windowtext;font-weight:normal'><o:p> </o:p></span></p>
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