biological modeling experience

2010-04-12T01:45:00.000-07:00

CASTP: protein surface computing server.
(NB: pockets prediction)
http://sts.bioengr.uic.edu/castp/calculation.php

Anion transporters research using MD simulations.

2010-03-31T07:10:00.000-07:00

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate

Docking and homology modeling explain inhibition of the human vesicular glutamate transporters

molecular dynamics results analysis

2010-03-11T07:52:00.000-08:00

Good explanation of Essential Dynamics: PDF.

IAPP, pt 2.

2010-02-22T07:11:00.000-08:00

Secondary structure, intrinsic disorders, proIAPP:

Amyloidogenic Propensity of ProIAPP and IAPP in the Presence of Negatively Charged Lipid Bilayers
Suman Jha
Biophysical Journal, Volume 96, Issue 3, Supplement 1, February 2009, Page 93a
(only abstract is free available)

Our CD studies show that the secondary structure content of ProIAPP and IAPP is predominantly unordered with small amounts of ordered secondary structure elements as confirmed by ATR-FTIR spectroscopy. However, in the presence of anionic membranes, ProIAPP forms predominantly α-helices and loops that subsequently transform to intermolecular β-sheet structures. For comparison, IAPP forms intermolecular β-sheets largely via unordered and loop structures.

The ATR-FTIR and fluorescence spectroscopy studies performed also reveal that ProIAPP has a higher amyloidogenic propensity in the presence of negatively charged membranes, but is still less amyloidogenic than IAPP.

Amylin aka IAPP

2010-02-22T06:52:00.000-08:00

On mechanism:
Intracellular amyloid-like deposits contain unprocessed pro-islet amyloid polypeptide (proIAPP) in beta cells of transgenic mice overexpressing the gene for human IAPP and transplanted human islets.

J. F. Paulsson . A. Andersson . P. Westermark .G. T. Westermark
Diabetologia (2006) 49: 1237–1246
http://www.springerlink.com/content/w824704516157312/fulltext.pdf

Fig. 8 Proposed sequence of events leading to islet amyloidosis.

a First, the processing of proIAPP is affected by factors such as high levels of NEFAs or glucose. Granules with amyloid-like fibres fuse and form an intracellular proIAPP amyloid-like deposit.

b Over time this aggregate enlarges and replaces most of the cell.

c This cell dies and the amyloid becomes extracellular and can act as a template for further amyloid formation.

d Amyloid is now made up by IAPP secreted from neighbouring beta cells. Formation of extracellular amyloid fibrils is preceded by the formation of toxic intermediates, which can interact with the cell membrane of surrounding cells and cause ionic influx, triggering the apoptosis cascade.

Formation of any amyloid fibril is a nucleationdependent process, and preformed fibrils may catalyse the conversion of a soluble protein to its fibrillar form. Human IAPP is a highly amyloidogenic peptide, and the release of insoluble intracellular aggregates into the extracellular space (e.g. by cell death) may stimulate the conversion of secreted IAPP. Consequently, elucidation of the initial step in amyloidogenesis, which may be an intracellular event, is particularly important.

Steered MD again

2009-12-18T05:35:00.000-08:00

guys compared different pulling rates

Steered MD in GROMACS (pull code)

2009-12-17T04:32:00.001-08:00

The pull code allows to apply a force between two centers of mass (for >1 groups). It appears to be useful to simulate protein penetration into lipid membrane (channel formation). Config must have a following lines:
pull_start = yes
pull_init1 = 0
pull = umbrella
pull_geometry = direction
pull_group0 = Protein
pull_group1 = POPC
pull_vec1 = 0 0 0.5
pull_k1 = 3000
pull_rate1 = 0.01 ; nm/ps Extreme parameters for extreme pulling

discussions: [1], [2]

b-Amyloid Ion Channels

2009-10-02T01:05:00.000-07:00

Models of b-Amyloid Ion Channels in the Membrane Suggest That Channel Formation in the Bilayer Is a Dynamic Process: amyloid ion channel formation mechanism suggested (src)

Amyloid ion channels: oligomerization

2009-10-02T00:22:00.000-07:00

results indicate that in lipid bilayers, a significantly higher percentage of these amyloids are oligomers (trimers and larger), while a small percentage of monomers and dimers are also present. On the contrary, soluble amyloid peptides are primarily monomers or dimers with a small percentage of higher-order oligomeric complexes. In the lipidic environment, thus, amyloid peptides undergo conformational changes favoring larger oligomeric complexes, although some large oligomeric complexes of soluble peptides can still retain their structure when inserted in a lipidic membrane (5, 23). A presence of large oligomeric complexes in membrane suggests that they could form supramolecular structures.

trimers are observed for amylin and Ab(1– 40), and tetramers are observed for ABri, amylin, Ab(1– 40), and a-synuclein

Also observed are pentamers for amylin and Ab(1– 40); hexamers for a-synuclein, SAA, ADan, amylin, and Ab(1– 40); and heptamers and octamers for a-synuclein and SAA.

Significantly, unlike earlier reports indicating amyloids’ tendency to form large fibrillar aggregates in solution, we confirmed that these peptides retained their globular structure over a period of several hours with no significant change in the size distributions and without significant aggregation, even at physiologically high concentrations.

multimeric peptide complexes have disk-like shapes with an outer diameter of 8–12 nm and often contain a central pore-like concavity with a diameter of 1–2 nm

Pentamers were mainly observed for amylin.

(src)

2009-09-07T08:34:00.000-07:00

NOMAD: a Normal Mode Analysis Server.

Coarse-Grained lipid MD simulation

2009-08-26T05:01:00.000-07:00

GROMACS appears to be able to perform coarse-grained (CG) lipid MD simulation (CG is simplified lipid representation model). Some dudes use this representation to reveal membrane-bound protein orientation relative to lipid bilayer. Results were refined with atomistic MD to obtain more detailed info.
src

Analysis of disease-related polypeptide sequences: Intrinsically unstructured proteins

2009-08-25T04:33:00.000-07:00

Analysis of disease-related polypeptide sequences: Intrinsically unstructured proteins

Amyloid-β-protein
The most abundant forms found in amyloid plaques are a 40-mer (Aβ40) and a 42-mer (Aβ42). Although less abundant, Aβ42 is more amyloidogenic than Aβ40 and is the major component of neuritic plaques. Two main regions with high aggregation propensity can be distinguished in the aggregation profile for this polypeptide. The second region arises from the contribution of two sequence stretches comprising residues 30–36 and 38–42, respectively.

key residues: 16-21 (located in the core of Aβ fibrils)

A short 7 residues fragment comprising residues 16–22 is able to form ordered amyloid fibrils and, more interestingly, 16-LVAFF-20 and derived peptides have been shown to bind to Aβ42 and act as potent inhibitors of amyloid formation.

Islet amyloid polypeptide
Beta-cell failure in type II diabetes correlates with the formation of pancreatic islet amyloid. Islet amyloid polypeptide (IAPP, amylin), the major component of islet amyloid, is co-secreted with insulin from beta-cells.
In type II diabetes, this peptide aggregates to form amyloid fibrils that are toxic to beta-cells [26]. IAPP is an unstructured peptide hormone of 37 amino acid residues. Two "hot spots" of aggregation comprising residues 12–18 and 22–28 are detected for this peptide.
Interestingly enough, a 8–37 IAPP-fragment including both "hot spots", has been shown to form amyloid fibrils under physiological conditions.
Residues 12–17 and 22–27 are proposed to form the inner β-sheets in the fibril protofilament structure. According to this hypothesis, peptides corresponding to residues 8–20, 10–19, 20–29 of human IAPP, which include one of the "hot spots" described here, all form amyloid.
Smaller peptides derived from these regions have also been shown to form amyloid, and a recent investigation suggests that the minimal amyloid forming fragment of IAPP consists of residues 22–27. This hexapeptide fragment, NFGAIL, forms β-sheet-containing fibrils that coil around each other in typical amyloid fibril morphology.

proposed mechanisms:
- increased production and secretion of IAPP associated with increased demand for insulin might result in accumulation and aggregation of IAPP.

- impaired processing of the IAPP precursor molecule, proIAPP, by islet betacells may lead to hypersecretion of unprocessed or partially processed forms of proIAPP that may have a higher tendency for aggregation compared to mature IAPP

α-Synuclein
Several large aggregation-prone stretches were predicted for the α-Synuclein sequence: region 1–18, region 27–56 and specially region 61–94. A peptide comprising residues 68–78 of α-synuclein has been shown to be the minimum fragment that, like α-synuclein itself, forms amyloid fibrils and exhibits toxicity towards cells in culture. This fragment is included in the region 62–80 which we predict as the sequence stretch with the highest aggregation propensity. All the α-synucleinopathies are characterized by the accumulation of the 35 residues NAC fragment in the insoluble deposits. [NAC= non-Aβ component, amino acids 61–95]

(src)

transmembrane protein modeling pt. 3

2009-08-20T07:44:00.000-07:00

After several days of brainfucking the following system was obtained:

The membrane protein metodology, described on Bevan Lab site, recommends to perform an NVT (constant: particles number, volume and temperature) equilibration. But due to unknown reason the membrane separates into two layers looking like a sandwich (process takes 0.38 ps).

Solution: using lipid pos. restraints in z-dimension + simulated annealing 0..315 (310 is phase transition temperature for POPC) + NPT (constant number, pressure, temp.) ensemble conditions.

transmembrane protein modeling pt. 2

2009-08-19T06:45:00.001-07:00

Protein-lipid_bilayer system generated with Schroedinger`s Desmond gives too large bilayer hole, which can contain water molecules after solvation. Some manuals recommended to make a local vdwradii.dat copy with modified C radius (0.5 [0.15 is default]). But 0.5 appears to be not enough (0.6 was used).

The Desmond Membrane Builder fuckup lies in fact that I can manually implement protein into membrane more accurately, but having more brainfucking post-processing. So it goes.

transmembrane protein modeling

2009-08-19T05:02:00.000-07:00

Lipid topology (.itp required for GROMACS MD simulations) contains 52 atoms. But lipid bilayer PDB structure consists of (>52)-atom molecules (such a difference is a result of using united-atom force field) with all hydrogens, which were considered in GROMOS96 53a6 FF. It was obtained 52-atom molecules system with:

cat lipid.pdb | grep -v "0.00 H" > lipid-noH.pdb

Output PDB format details depends on software:

mdrun -deffnm box-min -c box-min.pdb -v -nice 0 # output is box-min.pdb [box-min.tpr assumed to be exist]

mdrun -deffnm box-min -c box-min.gro -v -nice 0 # output is box-min.gro

vmd box-min.gro # box-min.gro was converted to box-min(from_gro).pdb with vmd

spdbv box-min.pdb # warning 1: at least one HETATM group lacked proper CONNECT informations. Connection will be generated between atoms that are closer than 2.000A, which can generate false bonds. [CONNECT section was removed manually] warning 2: File ignored (either or is not a valid PDB file, or it contains only a Carbon Alpha trace). => spdbv doesn`t understand GROMACS PDB output

spdbv box-min(from_gro).pdb #warning 1: the same; => successfully opened

MAPAS

2009-08-12T07:17:00.000-07:00

It’s All About Geometry: Protein Contact Surfaces Hold Key to Cures
Server for protein-membrane contact points is described.

MAPAS Membrane-Associated Protein Assessments
http://cancer-tools.sdsc.edu/MAPAS/pro2.html

protein aggregation

2009-08-11T04:55:00.000-07:00

0) http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1828741&blobtype=pdf&tool=pmcentrez
AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides
Aggrescan.

transmembrane proteins

2009-08-11T04:43:00.000-07:00

0) http://www.iop.org/EJ/abstract/0953-8984/18/28/S07
Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins
Arguments on using combination of OPLS and united-atom force field in GROMACS.

1) http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm
Explicit Membrane Protein Simulations in NAMD/VMD
Transmembrane protein modeling manual. Human glycophorin (1AFO) made with NAMD software.