Enrico Gratton,Instructor for Physics 450PhysicsLoomis Labs, Room 184Tel. 244 5620enrico@scs.uiuc.edu

Biomolecular physics

Biomolecular Physics (Spring 2004)http://wug.physics.uiuc.edu/courses/phys450/index.htmlhttp://wug.physics.uiuc.edu/courses/phys450/index.html

Ziggy Majumdar TA for Physics 450Physicsmajumdar@uiuc.edu

We might have a lot to learn from biology

Which book?

Molecular BiophysicsStructures in Motion

Michael Daune

Oxford University Press

The Physics 450 web site has a lot of information, and many links

http://wug.physics.uiuc.edu/courses/phys450/index.htmlhttp://wug.physics.uiuc.edu/courses/phys450/index.html

Cells look very different depending on how you look at them; either as models or the real thing.s.prayha

Most biological systems become complex when we analyze in more detail. Then the problems begin, and the textbooks become dangerous.

30 nm11 nm

HIGH in histone H1 Often low in histone H1

acetylatedhistone tail

+chargedhistone

tail

In the beginning of the course we will use the computer to look at structures and for homework

There is lots of neat interesting informative sites. For instance:Looking:

http://www.imb-jena.de/misc.htmlhttp://www.proweb.org/kinesin

http://www.proweb.org/kinesin//FxnVessTrans.htmlhttp://www.proweb.org/kinesin//KinesinMovies.html

Modeling and understanding the physicshttp://perso.curie.fr/Frank.Julicher/mmm_rmp/

http://www.imb-jena.de/IMAGE.html

Data baseshttp://mcb.harvard.edu/BioLinks/Sequences.html

There are lots of web sites with information for:

Some sites lead you to a LOT of other valuable sites:http://sciweb.nyu.edu/~pja6129/mathbio/generalbookmarks.html

cell biologyhttp://www.cellbio.com/courses.html

Structures of biological moleculeshttp://www.imb-jena.de/IMAGE.html

Structures of nucleic acidshttp://www.imb-jena.de/RNA.html

(this site is somewhat sophisticated)http://www.dnaftb.org/dnaftb/

Data baseshttp://mcb.harvard.edu/BioLinks/Sequences.html

A great site with lots of information, links, papers and ideas on molecular information theory, molecular machines and nanotechnology. But there are many others.

http://www.lecb.ncifcrf.gov/~toms/

General outline of Physics 450 Biological Physics

Spring 2004Molecular and Cellular Biophysics

•Introduction to biophysics•Biomolecules

General properties of polymers important for biologyAmino acids & ProteinsBases & Nucleic Acids (DNA & RNA)Lipids & membranesSmall molecules

•Characteristics of biological macromoleculesStructuresFunctionsDynamics

•Overview of the biological cellGeneral structure and interrelationshipsSome general functions

•EvolutionImportance of evolution for understanding biomolecules and biological systemsTheories of molecular evolution

N

O

NO N

OO

Cα carbon atoms

peptide bonds

•Water•Inter(intra)molecular forces important for biomolecular systems

Electrostaticvan der WaalsIonic Interactions (ion-ion & polyelectrolytes)Ion-dipole interactionsHydrogen bondsHydrophobic effectsCharge-transfer processesHydration forces

•FluctuationsGeneral descriptionImportance for biomolecular systems

•Transport & diffusionTranslational (3-, 2- &1-D)Rotational – different models

•Movement and diffusion in cellsTheoretical description – of random diffusionExamples for macromolecular and cellular functioningMolecular motors – shifting components around in cellsExperimental techniques

FRAPFCSTrackingTriplet-phosphorescence

0

04

ri

elz e e

r

κ

ψπε ε

−

=2

2 02resG

RTn n e∆−=

•Spatial organization of membrane components•Thermodynamic description of molecular interactions - Review

Kdiss & free energy viewsMultisubunit systemsBinding & specificity

•Introduction to polymer statistics & biological examples•Supercoiled DNA - theoretical description, measurement & applications•Introduction to statistical mechanical descriptions for helix-coil•Cooperative conformational changes•Conformational transitions of proteins, folding and activity

Important concepts in biochemical systems, e.g. allosteric systemsAllosteric effects and relationship to binding and activityBiological importance

•Molecular interactions and catalytic activity•Kinetics in biochemistry and molecular biology

Importance of dynamic studiesActivation state & Kramer’s

theory of chemical ratesRapid kineticsFlow systemsrelaxation systemsEnzyme kinetics – formal & models of enzyme catalytic activity

•Examples from the literature of kinetic studies•Some basic important current biological problems (during the whole semester)

2 22 1 exppp p

L LR l l l⎡ ⎤⎛ ⎞ ⎛ ⎞= − + −⎜ ⎟ ⎜ ⎟⎢ ⎥⎝ ⎠ ⎝ ⎠⎣ ⎦

ur

-0.2

0

0.2

0.4

0.6

0.8

1

1.2

260 280 300 320 340 360 380 400 420

fraction helix 7kcalfraction helix 70 kcal

fract

ion

helix

7kc

al

temperature

Techniques and instrumentation that will be discussed (not necessarily all at one time)

•Spectroscopy – we will not cover X-ray or NMR (see me for references and other courses)Basic theoretical description of spectroscopic transitionsAbsorption (single and double photon excitation)Fluorescence

Steady-state (spectra, polarization, solvent effects)Anisotropy (theory of molecular rotation and

applications of polarization measurements)Lifetime-resolved measurements

Phosphorescence (long lifetime probes and their uses)Raman and resonance Raman, light scattering, NMR, ESR, EM– probably will not cover these topics

•Light traps - laser tweezersContainment or movement of particles & organelles in cellsManipulate the interactions of macromolecular systemsForce measurements – directed and diffusion

•Scanning probe microscopyAtomic force microscopy (scanning force microscopy)Instrument – measurement & detectionApplications

•Light microscopyOverview of far field microscopySensitivity, resolution & general applicationsNSOM (near-field scanning optical microscopy)Modern & New techniques

Scanning confocal microscopySingle-molecule experimentsFluorescence correlation microscopy – FCSFluorescence recovery after photobleaching - FRAPFluorescence lifetime-resolved imaging microscopy - FLIMDouble-photon excitationImprovements in spatial resolutionPolarization microscopy

•Patch-clamp (?)•Medical biophysics – probably will not cover

While the number of physicists doing biology is still relatively small, it is one of the fastest growing fields in the discipline. Just next

month in Boston, the American Physical Society, the professionalorganization for physicists, is putting on a conference for young

scientists titled ''Opportunities in Biology for Physicists.''

Biology is increasingly drawing in scientists from many disciplines beyond physics, including mathematics, computer science, and

engineering.

Indeed, some of science's most vibrant areas reside at the boundaries of the old disciplines - proof, some say, that the old ways of

conceptualizing problems are holding back progress.

This class was started by Hans Frauenfelder. The present and future of biological physics is very different than it was at that time.

The article at the following web site is interesting:http://www.boston.com/dailyglobe2/225/science/Bio_envy+.shtml

The following quotes from this article are even more applicable than it was in the early days:

''The whole problem is that we are living in the 21st century with these 19th century guilds,''

said John Hopfield, a Princeton scientist, one of the first physicists to move into biology.

''Biology has provided physics with its new frontier,'‘said Robert Laughlin, who won the 1998 Nobel prize in physics (quantum Hall effect)

and now devotes himself to theoretical problems in biology.

''Ask not what physics can do for biology,'‘said Hans Frauenfelder, one of the field's pioneers,

''Ask what biology can do for physics.'' .

Fundamental aspects of Physics

•Systems with a large number of atoms •Molecular crystals: Repetitive structures •Importance of fluctuations •Difference between forces in biomolecules and forces in solids and liquids •Use of quantum physics (photosynthesis) •Complexity and hierarchy of structures •Order-disorder phenomena. Ising model •Dissipative processes. Origin of life •Information storage and transfer •Production, storage and transfer of energy

Biomolecular Physics

Determination of the structurex-ray, NMR, EPR, hydrodynamics, ε, χ, computational methods

Equilibrium propertiesThermodynamics Statistical mechanics Cooperative phenomena

Kinetic propertiesRelaxation Chemical kinetics Fluctuations

Biomolecules & Biopolymers

Constituents :H, C, N, O, P, S, Ca, Cu, Mg, Fe, Zn, Mn

Biomolecules -- Atoms -- Quantum Physics

SOLIDS: strong forcesLIQUIDS: weak forcesBIOMOLECULES: strong + weak forces

kT=1.38 x 10-23 x 300 J=4.14x10 -21 J

kT/M=2.4kJ/M=0.6kcal/M

Determination of the structureGeometrical distribution of atoms within molecules, crystals and liquids

Methodsx-ray diffraction NMR Electron microscopy Tunneling microscopy Computational methods

The scattering of electrons and x-rays depends on interatomic distances For H-atoms, neutron diffraction is used

Microwave spectroscopy gives information on vibrational levels, moment of inertia -- atomic distances

Thermodynamics

Statistical mechanics provide the relations between Thermodynamics quantities and structure

Partition function

Ei= Energy of the i-th level of the system gi= Number of states in the system with energy Eik = Boltzmann constant T = Absolute temperature

kTEi

iegQ −∑=

Free Energy (Heltmholtz) A=U-TS=kT ln Q ----> Q=e-A/kT

Internal energy U=kT2 dlnQ/dT

Entropy S=(U-A)/T=kT dlnQ/dT+klnQ

At equilibrium, the fraction of molecules with energy Ei is

xi=gi e-Ei/kT/Q

gi=e Si/k

x2/x1 =g2/g1 e-∆E/kT (at constant volume)

Two-state system

1 Reactants 2 Products

E1

E2

E3

Ea=E3-E1

∆E=E2-E1

Fluctuations and Kinetic Phenomena

The probability for a system to pass from state 1 to state 2 depends on the barrier height

W1->2=A1 e -Ea/kT A1 is a proportionality constant u1->2=n1W1->2=n1A1 e -Ea/kT This is the Arrhenius law

For the transition from 2 to 1 we have

W2->1=A2 e -Ea/kT+∆E/kT

u2->1=n2 W1->2 = n2 A2 e -Ea/kT+∆E/kT

At equilibrium u1->2= u2->1 K=n2/n1=A2/A1 e- ∆E/kT

The barrier height controls the rate The energy difference determines the equilibrium population

Quantum mechanics

Structure and spectra of atoms and molecules Chemical bonds Dispersion forces

Mutations Photochemical processes Photosynthesis Vision

Biomolecules ----> LifeThe interaction between biomolecules determinesthe development and evolution of living systems

Biomolecules contain a large number of atoms (102 to 1010)

The hierarchy of living things

Organism >1020

Cell 1010

Organelle 105 – 106

Biomolecule 103 – 104

Molecule 10 – 100Atom 1

Physics

Atom Quantum mechanicsMolecule Vibration-rotations Chirality

-radiationless transitionsMacromolecule Conformations, phase transitions,

phonons, solitons, catalysisMacromolecular complex Collective modes,

cooperative phenomena, multiple excitationCell Metabolism, signaling, trafficking,

individuality, differentiation

Energy levels Energy landscape

Information + ConstructionInstruction how to assemble Parts Assembler Self reproducing

Information contentInformation capacity = Nbd = bd

b= basis d=digits

System basis digits N bits4 letter words 26 4 264 18.8Protein 20 100 20100 432Nucleic acid 4 107 410000000 2x107

SOLIDS PROTEINS

Periodic non-periodicdisorder<-> random

Strong forces in all directions Strong+weak

Local vibrations Large motions

Energy levels Energy landscape Enormous number of states Profound difference in dynamic behavior

Elastic motions Plastic motionsTime scale Enormous number

Proteins

20 building blocks, aminoacids

100-200 per protein (range from 15 to 3000)

l-amino acids only!!!

Large number of possible sequences

20 100 ¸ 200 (about infinity)

For each sequence large number of conformations

2 200 about 10 60

Instantaneous vs average quantities

Proteins and functions

Enzymes Lysozyme, Ribonuclease, LADH, Carbonic anhydrase

Storage Ferritin, Ovalbumen, CaseineTransport Hemoglobin, Myoglobin

HemocyanineProtection Antibodies, Fibrinogen, Trombin

HSPOrmones Insulin, Growth factorStructure Collagen, a-KeratinLight harvesting Rhodopsin, reaction centersLight production Luciferase

Myoglobin

Lysozyme

BPTI, different representations

Annexin V

BFB

GFP

Hemoglobin

Porin

Potassium channel

Packing density

Spheres 0.74 ProteinsCylinders 0.91Solid 1.0

To function, proteins must be flexible