P h y s i c s o f b i o l o g i c a l s y s t - PowerPoint PPT Presentation

P h y s i c s o f b i o l o g i c a l s y s t e ms – P H 5 4 9 L E C T U R E 1 3 : b i o l o g i c a l p o l y me r s mithun@phy.iitb.ac.in Office: Physics 303

S I N G L E MO L E C U L E F O R C E S P E C T R O S C O P Y

F O R C E E X T E N S I O N : D N A

F O R C E E X T E N S I O N : R N A Stem Loop https://commons.wikimedia.org/w/index.php?curid=815268 Pseudoknot https://commons.wikimedia.org/w/index.php?curid=806690

F O R C E E X T E N S I O N : P r o t e i n Titin: 244 folded domains, 1 µ m length

P r o t e i n s a s r a n d o m wa l k s

C O MP A C T r a n d o m wa l k s 2 / 3 2 ⟩ ∼ N ⟨ R

T H E P R O T E I N F O L D I N G P R O B L E M SEQUENCE Structure Function Structure How does a protein sequence correspond to a particular structure ? A random search in structure space is IMPOSSIBLE!

T H E H P Mo d e l f o r p r o t e i n s

A T o y mo d e l f o r a n H P p r o t e i n Consider a 6-amino acid protein on a 3x2 lattice 6 = 64 How many possible sequences can we have ? 2 3 How many possible structures can we have ?

A T o y mo d e l f o r a n H P p r o t e i n Sequence: HPHPHP No UNIQUE ground state!

A T o y mo d e l f o r a n H P p r o t e i n Sequence: PHPPHP UNIQUE ground state!

A T o y mo d e l f o r a n H P p r o t e i n What is the probability of the native state ? − 2 βε e p native = − 2 βε + 2 e − 4 βε e

D E S I g n s t r a t e g i e s f o r p r o t e i n s HPPHHPPHPPHHPPH... Enzymatic activity