Acknowledgments:
Laboratory of Chemical Physics
Laboratory of Biochemistry and Genetics
*Support provided by the Intramural Research Division of the NIDDK, NIH.
Protein Structure
Primary structure (sequence)
GSIGAASMEF CFDVFKELKV HHANENIFYC PIAIMSALAM VYLGAKDSTR TQINKVVRFD KLPGFGDEIE AQCGTSVNVH
SSLRDILNQI TKPNDVYSFS LASRLYAEER YPILPEYLQC VKELYRGGLE PINFQTAADQ ARELINSWVE SQTNGIIRNV
LQPSSVDSQT AMVLVNAIVF KGLWEKAFKD EDTQAMPFRV TEQESKPVQM MYQIGLFRVA SMASEKMKIL ELPFASGTMS
MLVLLPDEVS GLEQLESIIN FEKLTEWTSS NVMEERKIKV YLPRMKMEEK YNLTSVLMAM GITDVFSSSA NLSGISSAES
LKISQAVHAA HAEINEAGRE VVGGAEAGVD AASVSEEFRA DHPFLFCIKH IATNAVLFFG RCVSP
helices [red], sheets [blue
3D structure
complexes, aggregation
Ovalbumin, Egg white protein PDB:1OVA, Crystal Structure, Carrell et al., J. Mol. Biol. (1991)
SEM Aggregate structure, Zabik et al., J. Poul. Sci. (1980)
SEM Aggregate structure, Zabik et al., J. Poul. Sci. (1980)
Primary Structure
Twenty residue "alphabet" forms polypeptide chain
Chemical Structure of the Twenty Common Amino Acids, Compound Interest
Protein folding problem
Predict structure from sequence
Sequence Structure Function
Native structure, folding pathways, ...
Energy Landscape, Wolynes, Phil. Trans. A (2004)
MD simulation of WW-domain, Best and Mittal, J. Phys. Chem. B (2010)
MD simulation of WW-domain, Best and Mittal, J. Phys. Chem. B (2010)
Scientific Philosophy
Theoreticians need to keep in close contact with experimentalists.Imagination must be constrained by reality.
Higher order structure
Phase separations lead to sudden changes in liquid structure.
How do we model many protein-protein interactions?
Can we predict aggregates from experimental structure?
PDB:1AO6
PDB:1OVA
PDB:1W6Z
PDB:3V03
Experimental Measurements
Second virial coefficient, , measurementusing light scattering at different pH.
The Process
Start with the crystallized PDB Structure
e.g. Human Serum Albumin PDB:1A06
Electrostatics: Poisson-Boltzmann
Solve for with the Adaptive Poisson-Boltzmann Solver (APBS),
Typically (in the absence of ions), and .
APBS by Baker et al. Proc. Natl. Acad. Sci. 2001, Bjerrum length
Macrocharge fitting
Best fit macrocharges to approximate the field.
Decompose the field, determine a region of excluded volume +
spherical harmonic decomposition for large distances.
Matching experiments
Theoretical predictions of the second virial coefficientconsidering only excluded volume and reduced electrostatics.
Matching experiments
Theoretical predictions of the second virial coefficientconsidering only excluded volume and reduced electrostatics.
A Simplified Representation of Anisotropic Charge Distributions within Proteins, Hoppe, J. Chem. Phys. (2013)
Paradigm shift
Proteins were thought to adopt stable, folded conformations.Solving the structure was paramount for understanding the function.
Intrinsically disordered proteins
Structure
- Lack tertiary structure (disorder!)
- Still may form secondary structure
- Different primary structure (residue propensity)
- More charged, less hydrophobic and aromatic residues
Binding
Barnase-Barstar complex
Hif-1 α/CBP
SIC1 binding to CDC4
Statistical Potentials
Residue-residue interactions, quasi-chemical lattice-gas
Potentials constructed from Top 8000 Protein Database, Richardson Group
Residue-residue interaction matrix, MJ
Other statistical potentials: Tanaka and Scheraga (1976), Spil (1990), Miyazawa and Jernigan (1996),
Betancourt and Thirumalai (1999), Skolnick, Kolinski and Ortiz (2000)
Betancourt and Thirumalai (1999), Skolnick, Kolinski and Ortiz (2000)
MJ matrix reveals biophysical structure
H (hydrophobic), P (polar), C (charged)
MJ contact energy reproduces MF energy
Energy per residue shows good correlation as well.
MF Energy distributions: Physically reasonable
IDP Propensity, Coeytaux & Poupon, Bioinformatics (2005)
Hydrophilicity index, Kyte & Doolittle, J. Mol. Biol. (1982)
Amyloidogenic regions, Garbuzynskiy et. al. Bioinformatics (2010)
Hydrophilicity index, Kyte & Doolittle, J. Mol. Biol. (1982)
Amyloidogenic regions, Garbuzynskiy et. al. Bioinformatics (2010)
Protein Networks
- Target protein interacts with a range of possible surfaces.
- Measure average binding affinity of protein to surfaces.
- Measure binding specificity of protein to surfaces.
Schwikowski & Fields et al., Nature 2000.
Binding affinity
Binding specificity
MF IDP Summary:
- MF models reproduce MJ contact energies. MF IDP's bound to native structures show increased specificity with lower affinity.
What's next? Add structure to mean field calculations.
Lattices may be optimal for IDP's, they can reproduce native-energies but quickly sample extended conformational space.
Active research projects & collaborations
Crowding, surface adsorption and protein fibrillation, Biophys (in press).Programmable Nanoscaffolds and Multivalent Effects, JACS.
Integer sequence discovery from small graphs, Discrete Math. (submitted).
Dependence of Internal Friction on Folding Mechanism, JACS (submitted).
Quantification of plasma HIV RNA, Nature Comm.
