10/14/10
Find 5 independent sources of 5 properties associated with a molecule of your choice. Provide all references. Due November 4, 2010 20:50:

I am thinking of finding the 5 properties on an amino acid, most likely alanine.
1- melting point
2- solubility (water)
3-boiling point
4-density
..
Class Notes:
For Properties Assignment:
-Molec Weight no good for property. Because you need 5 sources for each property. Its not a measured property, its calculated from weights of atoms etc..
-Chemspider not primary source
-Can use predicted/theoretical values
"Reaction Searching using Beilstein and SciFinder"



Assignment 1:

Having trouble finding 5 properties for L-alanine from 5 different sources: Have obtained density, melting point, solubility (water), and have conflicting results for boiling point. Trying to think of another property that I may obtain 5 sources for so that I do not have to change my target compound...I have seen some pka values reported, also hydrophobicity. Are either of these suitable properties?

Melting Point:

292.00 (ChemSpider, (exp database)
314.5 (Sigma Alderich) *
295.00 (AlfaAesar)
295.00 (Knovel)
297.00(FishcherSci, MSDS)

Density:

1.424g/cm3 (Wikipedia)
1.432 g/cm3 (CRC Handbook)
1.432 g/cm3 (AlfaAesar)
1.437 g/cm3 (DrugBank)
1.401 g/cm3 (FischerSci)

´╗┐Solubility (water):

166.5 g/L (25C) (LookChem)
166.9 g/kg (CRC Handbook)
164.0 g/L (ToxNet)
164.0 g/L (DrugBank)
166.5 g/L (FishcherSci, MSDS)

Pka

2.34 (Knovel)
2.33 (CRC Handbook)
2.34 (DrugBank)
2.34 (ToxNet)
2.33 (Wikipedia)
2.35ChemPep)

Pkb

9.69 (Knovel)
9.71 (CRC Handbook)
9.69 (ToxNet)
9.71 (Wikipedia)
9.87 (ChemPep)





Assignment 2:

I would like to do my final project on: Protein Aggregation and Fibrilization: Beta-Amyloid
Therefore, I will do my assignment 2 summary on: "Intersheet Rearrangement of polypeptides during nucleation of Beta sheet Aggregates"
Decatur, S., 2005, PNAS, 102, 14272-14277
DOI (10.1073/pnas.0502804102)
[Full Marks JCB]

Summary


  • 1)
  • Folding and more importantly, misfolding, of peptides/proteins is an important issue in the biomedical field due to the general (and widely accepted) connection of misfolded beta sheets and their subsequent aggregation and fibrilization with many neurological diseases (Alzheimers, parkinsons, amyloidoses, etc..)
  • It has been proposed that the toxic species responsible for these diseases are the soluble oligomers of these misfolded proteins

  • 2)
  • In order to study the mechanistic process of protein aggregation, small model peptides (typically derived from aggregate prone sections of the protein) are generally used. For example the ABeta16-22 segment, which is seen in Alzheimers plaques, is widely studied
  • Many aggregation simulations show that the first step towards aggregation is the formation of misfolded Beta-sheet oligomers
  • Mausseau et all used activation-relaxation simulation to show that the Beta sheets rearrange via reptation of the chains to form well ordered oligomers which may serve as nucleation sites for subsequent fibrilization.

  • 3)
  • Formation of Beta sheet aggregates can be monitored using IR spectroscopy due to the high sensitivity of the Amide I normal mode band to backbone conformation
  • IR using c13 labeled residues is a sensitive technique and can yield structural details on peptide conformation. This is due to the strong vibrational coupling between aligned C13 labeled residues and hence strong coupling of amide I' (i.e., inter-strand coupling enhanced by hydrogen bonding).
  • Spectroscopically, amide I band intensity decreases and a redshift in ftrequency is observed upon formation of ordered Beta-sheet oligomers

  • 4)
  • Previous studies of prion protein H1 show that after incubation, Beta strands align such that the hydrophillic residues associate with solvent while hydrophobic residues pack tightly together, forming sites available for H-bonding and formation of Beta sheets.
  • In addition, residue 117 in this sequence is in register across all the strands causing enhanced vibrational coupling which results in a 10cm-1 redshifting of the amide I' band.

  • 5)
  • This paper details kinetic experiments on the alignment of the H1 peptide with different concentrations/temperature conditions
  • It is found that the rate of alignment increases with increasing temperature
  • It is found that the rate of alignment depends significantly on the concentration of peptide and more specifically, the actual mechism of alignment varies with varying initial concentration.

  • 6)
  • Methods: Two variations of the H1 peptide sequence were prepared. H1 is the unlabeled peptide. H1* has residue 117 c13 labeled.
  • Both H1 and H1* were exchanged with DCL to remove TFA and deuterated amide groups.

  • 7)
  • IR: Respective peptides dissolved in 1:1 acetonitrile:D20 buffer (20mM Hepes/100mM NaCl) in concentration range 6mg/mL-50mg/mL
  • Vector 22 FT IR with 4cm-1 resolution, CaF2 cell, 100um spacer, used. Measurement taken at 35 degrees C every 30-60min untill complete alignment.

  • 8)
  • Isotopes Dilutions: Equal concentration solutions of H1 and H1* were prepared and immediately mixed. H1* forced into allignment with heat was also prepared and mixed with equal concentration H1 (un-aligned). Ir spectra taken for all samples over 24hr period.

  • 9)
  • Data Analysis: Differene IR calculated by subtractin first spectra from the subsequent spectra in each case When alignment occurs, a decrease in absorbance intensity at 1601cm-1 and an increase in intensity of the band at 1591cm-1 is observed. Delta(A) vs T data were fit with a stretched exponential with time constant as a free paramter.

  • 10)
  • AFM: A Digital Instruments Dimensions 3100 AFM was used with silicone probe, tapping mode, 1Hz scan rate, for all measurements. Aliquots from IR samples, diluted 50-fold and deposited onto mica, were used for AFM imaging. DI water rinse was used to remove any residual salt etc...

  • 11) RESULTS
  • 13C isotope labeling of the 117 residue in H1 results in a red shifted shoulder (at 1601cm-1) in the amide I band. When the 117 residues are all in reigster in the sheet the band is downshifted to 1591cm-1.
  • This band then serves as an ideal marker for following the kinetics by plotting the delta(A) vs time at 1591cm-1

  • 12)
  • The kinetic traces for the alignment process at low and high concentrations of peptide canbe fit with a monoexponential function. At intermediate concentrations, a stretched exponential is necessary idicating heterogeneity in the process and a distribution of rate constants.

  • 13)
  • It is found that the time constant varies with concentration, with a maximum time constant (aproximately 448min) found for intermediate concentrations of peptide.

  • 14)
  • The rate of alignment increases eith increasing temperature from 35-55 degrees C. Using an Arrhenius equation, plotting ln(k) vs Temp for 35, 45, and 55 degrres C yields an Activation Energy of 23.5 kJ/mol.

  • 15)
  • Upon mixing of low concentrations of H1 and H1*, the difference IR spectra show that there is no increase of of the marker 1591cm-1 (indicitive of alignment) band nor the concurrent decrease in the 1620cm-1 band. However both Beta sheet bands at 1620 and 1603cm-1 increase with increasing time reflecting an increase in the Bsheet content.
  • Upon mixing of high concentrations of H1 and H1*, the C13 band at 1603 downshifts with time. In addition, Delta(A) increases at 1594cm-1 indicating increased registry alignment of the labeled 117 residues.

  • 16)
  • Incubation and re-cooling of H1* forces the alignment of the residues. The IR of H1* alligned this way and then mixed with un-aligned H1 shows the marker band at 1592cm-1 with an overall increase in beta sheet content over time.

  • 17) Discussion
  • The segment H1 of the prion protein does in fact form Beta Sheet oligomers as seen by the peak at indicative (and well established peak) at 1690cm-1 and 1620cm-1.
  • The propensity of this peptide to form Beta-Sheets is a result of the increased inter-sheet interactions (H-bonding) due to the easy collapse of the hydrophobic core residues (112-122)
  • A distribution of aggregate size is illustrated in by the lack of downshifting in the C13 amide 1' band. If all the chains were in register, this band would shift from 1601 to 1591 due to the strong vibrational coupling.

  • 18)
  • Alignment of the oligomers into ordered aggregates was found to occur by two different mechanisms depending on the initial concentration of monomer peptide.
  • Mechanism 1: Intersheet Rearrangement: involves detachment of an strand which is energetically unfavorable due to improper registry, followed by reattachment of a different strand into the more favorable in-register alignment.
  • Mechanism 2: Intrasheet Rearrangement: involves reptation (or sliding) of the out of register strand within the Beta-sheet into the favorable in register position.

  • 19)
  • If the alignment occurs via Intersheet Rearrangement, then the final ordered Beta sheet would be composed of a mixture of the c12 and c13 labeled peptide strands. This would result in less intense coupling of C13 labeled residues and hence the amide I' would remain at 1601cm-1 (i.e. no downshift) This is exactly what is seen when monomer concentration is low.

  • 20)
  • If the alignment occurs via Intrasheet Rearrangement, then the c12 and c13 labeled strands would stay largely isolted from one another, and hence there would be a larger vibrational coupling observed for 13C and large downshift in the amide I'.
  • This is what is observed at high concentrations.

  • 21)
  • At low peptide concentrations, the aggregate size is smaller, and hence it is much easier for strands to attach and detach to align via Intersheet Rearrangement
  • At high peptide concentrations, the aggregate size is larger, and hence Intrasheet is kinetically favored.
  • Intermediate concentrations offer a mixture of both mechanisms, and hence a distribution is rate constants. This explains why the kinetic traces at intermediate concentrations must be fit with a stretched exponential indicative of inhomogeneity.

  • 22)Conclusion
  • In order for the H1 sequence of the prion protein to form fibrils, it must first aggregate into soluble (in-register) Beta sheet oligomers for proper nucleation. This involves rearrangement of the initial disordered protein aggregates in register aggregates.
  • This process was studied spectroscopically using FT-IR and isotopically labeled H1 to differentiate between inter and inter strand processes. At low peptide concentrations, Intersheet rearrangement dominates, while at high peptide concentrations, intrasheet rearrangement dominates.