Computational biochemistry ferenc Bogár György Ferency

Membranes are important int he structure of cells. Membrane proteins are necessarry in the ion channels in the cells. They are built up by phospho lipids. Some of the main phospholipid molecules are DPC (dodecylphosphocholine), DPPC (dipalmitoylphosphatidyl-choline), DPMC (1,2-dimyristoyl-sn-glycero-3-phosphocholine), POPC ([(2R)-3-hexadecanoyloxy-2-[(Z)-octadec-9-enoyl]oxypropyl] 2-(trimethylazaniumyl)ethyl phosphate), POPE ( 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). The animations of the  structures (available in http://people.ucalgary.ca/~tieleman/download.html) are in Figure 1.20. to 1.24.)

Figure 1.20. The animation of a micella (65 DPC lipids without water molecules)

Figure 1.21. The animation of DPPC (128 DPPC without water)

Figure 1.22. The animation of DMPC (128 DMPC without water)

Figure 1.23. The animation of POPC (128 POPC without water)

Figure 1.24. The animation of POPE (128 POPE without water) 

6.  Databases

The experimental structures of biomolecules are deposited in http://www.pdb.org. These structures are the results of XRD and NMR experiments and freely available. Presently, ca. 90424 3D structures (with redundantly) (05.10.2013) are available in the databank. Data includes the 3D structures, experimental details, citation, etc.

ExPASy is the SIB Bioinformatics Resource Portal (http://www.expasy.org/) which provides access to scientific databases and software tools etc. in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. The database inludes the sequence of the proteins, and some larger systems.. No 3D structures are available.

There are special databasis which are commercial and the includes ca. 3.5-4 million compounds (e.g. Available Chemical Database – ACD, Accelrys). Some companies dealing with special fine chemicals suggest compounds on internet or CD with 3D structures and chemical properties (Mayflower, Asinex, etc.). These databases are available for finding the best scaffold in docking (for validation see e.g. Lit. [15]). The ligand molecules checked biologically for cancer and HIV can be found in NCI (National Cancer Institute of NIH) [16].

7. Summary

The main classes of biomolecules were described without completeness. The main databasis which include the biomolecules and ligand structures were also described.

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1. 
   Please, describe the intra- and intermolecular interactions between non-charged groups!
   
2. 
   Please, describe the intra- and intermolecular interactions between point-point, point-dipole and dipole-dipole charged groups (physical chemistry)!
   
3. 
   Please, describe the geometrical description of H-bond by Bondi!
   
4. 
   Please, describe the resonance stabilized peptide bonds!
   
5. 
   Please, describe the π- π interactions!
   
6. 
   Please, describe the π-H-O and π-H-N interactions!