new snps: sift, polyphen, etc. sift: predicting amino acid changes that affect protein function...
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New SNPs: Sift, Polyphen, etc.
SIFT: predicting amino acid changes that affect protein functionPauline C. Ng and Steven Henikoff, Nucleic Acids Research, 2003, Vol. 3 1, No. 13 3812-3814
“Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?”
Lovelock, et al. 2007
4
Gene-Gene Interactions
"Model...erythrocytes of [glutathione peroxidase] GPX1*2 heterozygotes should be more efficient in sheltering the cell
membrane from irreversible oxidation and binding of hemoglobin caused by the oxidant stress exerted by Plasmodium
falciparum... we observed a clear trend toward a dissociation between the HBB*A/*S and GPX1*2/*1 genotypes in the
overall data." Destro-Bisol et al. Hum Biol 1999; 71:315-32. (Pub)
7
Human Red Blood CellODE model
GLCe GLCi
G6P
F6P
FDP
GA3P
DHAP
1,3 DPG
2,3 DPG
3PG
2PG
PEP
PYR
LACi LACe
GL6P GO6P RU5PR5P
X5P
GA3P
S7P
F6P
E4P
GA3P F6P
NADPNADPH
NADPNADPH
ADPATP
ADPATP
ADP ATPNADHNAD
ADPATP
NADHNAD
K+
Na+
ADP
ATPADP
ATP
2 GSH GSSGNADPH NADP
ADO
INO
AMP
IMPADOe
INOe
ADE
ADEeHYPX
PRPP
PRPP
R1P R5PATP
AMPATP
ADP
Cl-
pH
HCO3-
ODE model
Jamshidi et al.
2000 (Pub)
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Sickle cell
Average HbSE6V HbE6WModeling SNP to 3D to
cell morphology & pathology
Harrington et al. Crystal structure of deoxy-human hemoglobin 6 Glu -->
Trp. Implications for the structure and formation
of the sickle cell fiber. J Biol Chem. 1998,
273:32690-6. (Pub)
Pro3
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Red Blood Cell Function• Transport O2 from lungs to tissues – using
hemoglobin to carry the O2
• Hemoglobin is maintained in its functional state (reduced) by the metabolic machinery
• Cell membrane separates the internal environment from the external environment– subject to physicochemical constraints
• Electroneutrality, Osmotic balance
– Cause of the imbalance:• impermeable polyions inside the cell
– hemoglobin, organic phosphates
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www.wadsworth.org/chemheme/heme/cytocritique
Echinocytes (crenated);
hyperosmotic medium
Dacrocytes;
pernicious anemiaAcanthocytes;
abetalipoproteinemia
Macrocytes 9-12µm;
megaloblastic anemia
Spherocytes;
enzyme deficiencies
Sickle cell;
HbS
Normal RBC 6-8 µm;4e12 per L3D-structure to function
to morphology to function
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Ab Initio Structure Prediction: CASP4
http://depts.washington.edu/bakerpg/
(2 pt for largelycorrect prediction, 1
point for a somewhat)
12
Where do 3D structures come from?
Research Collaboratory for Structural BioinformaticsProtein Data Bank (RCSB PDB)
HEADER COMPLEX (TRANSCRIPTION REGULATION/DNA) 23-NOV-93 1HCQ 1HCQ 2COMPND 2 MOLECULE: HUMAN/CHICKEN ESTROGEN RECEPTOR; 1HCQ 4REMARK 2 RESOLUTION. 2.4 ANGSTROMS 1HCQ 39REMARK 3 PROGRAM 1 X-PLOR 1HCQ 42REMARK 3 R VALUE 0.204 1HCQ 46SEQRES 1 A 84 MET LYS GLU THR ARG TYR CYS ALA VAL CYS ASN ASP TYR 1HCQ 60SEQRES 1 C 18 C C A G G T C A C A G T G 1HCQ 74FORMUL 9 ZN 8(ZN1 2+) 1HCQ 107FORMUL 10 HOH *158(H2 O1) 1HCQ 108HELIX 1 1 GLU A 25 ILE A 35 1 1HCQ 109ATOM 1 N MET A 1 50.465 24.781 79.460 1.00 60.88 1HCQ 133ATOM 2 CA MET A 1 50.332 26.116 80.055 1.00 61.13 1HCQ 134CONECT 2983 2747 2789 1HCQ4038MASTER 22 3 8 9 8 0 0 6 3864 8 34 36 1HCQ4039END 1HCQ4040
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Crystallographic refinement
(ref)
Minimize Fo-Fc.Linearize with a
first order Taylor expansion; parameters p (e.g. = x,y,z)
Fourier transform relates scattered X-rays, F, to electron density, k is the scattering vector.
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Crystallography & NMR System(CNS)X-plor
Heavy atom searching, experimental phasing (MAD & MIR), density modification, crystallographic refinement with
maximum likelihood targets.
NMR structure calculation using NOEs, J-coupling, chemical shift, & dipolar coupling data.
http://cns.csb.yale.edu/v1.0/
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Measure Structure Quality
R factor = ||Fo|-|Fc|| / |Fo| < 0.25 good > 0.4 crude
Correlation Coefficient > 0.7
RMSD (root mean square deviation) = sqrt[ (Xi1 - Xi2)2 ] compare models 1 & 2 i = 1 to n (#atoms)
canonical peptide geometry
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20 Amino acids of 280
www.people.virginia.edu/~rjh9u/aminacid.htmlwww-nbrf.georgetown.edu/pirwww/search/textresid.html
T
N CO
R
19 L-amino acids:H toward you; CO R N
clockwise.
19
E = Eb + E + E+ Evdw + Eelectrostatic
Eb = 0.5 kb(r-r0)2
Ek02
E = k [ 1 + cos( n - l)]
Evdw = A(r/rv0)-12 -B(r/rv0)-6 Eelectrostatic = qi qj / e r
Molecular mechanics
(Ref)
F = m a-dE/dri = Fi = mi d
2ri/dt2 r = position (radius)
dt ~= 1 fs (1e-15 sec)vi(t+dt/2) = vi(t-dt/2) + ai(t) dt update velocity & r
ri(t+dt) = ri(t)= v(t+dt/2)dt
b
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