Using Rasmol To Examine Protein Structures Biology Essay

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Protein folding is based on the primary, secondary, tertiary and quaternary structure of a protein (5).

Roger Sayle created RasMol, which means "Raster display of Molecules", in 1989 as part of a research project in his undergraduate degree (5). RasMol is a graphical program that can display representations of proteins, ligands, and other macromolecules in 3D (7). Its features include displaying different parts of the macromolecule in various visual forms. Specifically, proteins can be selected in part to display their helices, loops, turns or beta sheets. The computer program's practicality stems from its usefulness to explore the shape of a fully formed protein and determine important to aspects of its active sites and or structural interactions (Tina).

The purpose of this experiment was to implement RasMol to explore the three dimensional shapes of certain proteins obtained from a database which can then provide insight into its capabilities. This program can be applied to determinations of the structure of folded proteins, the components that make the folding structure and the chemical interactions responsible for those folding patterns (7).

Comparison of similar structures between species can potentially connect the species by way of discovering an evolutionary ancestor (Sali). Homology of proteins can provide insight into certain families of proteins based on the homology of their 3D structure (Sali).Methods to improve the search ability and specificity of databases such as those related to RasMol, require complex computation methods that are more easily explained by their application to macromolecules, like proteins, and their residues and active sites of interest (Sali). RasMol allows the user to highlight key residues, interactions and structures within a simulated protein to better interpret and explore its structure (8).

The way a protein is shaped within its respective medium in 3D is based on the relationship of the interactions of its residues with each other and the stability of those bonds (8). These interactions range from relatively strong interactions of the hydrogen bonds to the relatively weaker London dispersion forces (1).

Using RasMol or similar programs can possibly be used to determine the folding patterns of mutated proteins or provide further insight into homology of protein structures or residues conserved in different species in order to better define our understanding of the structure-function relationship (2; 8).

This experiment specifically observes myoglobin, alpha-lactalbumin and steroidgenic factor 1 protein structures. The amino acids in the structure are given the names C, CA CG or NZ. These abbreviations describe the kind of atom: C is for carbon, CA is for alpha Carbon, CG is for gamma carbon and NZ is for zeta Nitrogen. The file is informative but impractical in its word processor format for any 3D modeling.

Opening the pdb file in RasMol gives a 3D visual of the protein of interest. First the visualization of metmyoglobin from horse is featured. The protein is in its ferrous state that can bind oxygen and has the oxidation state of +3 (5).

Experimental Procedure

As per Lab Manual CHEM 335, Concordia University 2011.

Results

Table 1a-Overview of Proteins investigated in this experiment

Protein

Horse Metmyoglobin

Baboon alpha- lactalbumin

Mouse steroidgenic factor 1

Purpose

Oxygen transport

Calcium binding protein

Nuclear receptor

Number of subunits

One

One

One

Table 1b-Proteins structural properties in their 3D conformations

Protein

Horse Metmyoglobin

Baboon alpha- lactalbumin

Mouse steroidgenic factor 1

Alpha helices

8

6

13

Beta sheets

0

2

2

Ligand interaction?

Yes-His 93, His 64

Yes-Asp 88, 87, 84, 82; Lys 79

Yes-Gly 342, Typ 437, Lys 441,Water 571,732 (H bonds))

Rel. distance (angstroms)

4.32-4.36

2.3

2.2-2.3

Hydrogen bond residues

Gly 35 N and Arg 31 O

See above

See above

His 24 and Gln 27

See above

See above

Table 1c--Detailed table for Steroidgenic Factor 1 protein

Name of file

Pdb1ymt.ent

Protein

Steroidgenic Factor 1 protein

Alpha helices

8

Beta sheets

2

First residue

Arg 17B for secondary structure

Last residue

Ala 459 for secondary structure

Cysteine residues

30 (zero with disulfide bonds)

Aromatic residues

Tyr = 84; Phe = 88; Trp = 28

Total amino acids

459 total

Proline residues

56 (located near ligand biding site)

Discussion

The purpose of this experiment was to explore three proteins -myoglobin, alpha-lactalbumin and steroidgenic factor 1-using the computer program RasMol. The protein data used in RasMol is either partially or completely derived from experimental information. The documents that accompany a RasMol pdb (protein databank) file include the notable names of those whom have contributed information about the protein of interest (CHEM 335).

In the case of myoglobin, this protein is well studied because it was one of the first 3D structures resolved using advanced techniques such as x-ray crystallography (myoglo; chem. 335). The structure has 8 alpha helices (Figure 2). The investigation of the heme group provides insight into the orientation of the poryphin ring and which residues are holding it in place (Figure 3). From Fig. 3 and 4 it is seen that the poryphin ring is being stabilized by the 3D structure in some way and the main contributors are His 93 and His 64 that hold the Fe in place with the ring portion of their structure (5). There are many interactions in this protein, but the active site with the poryphin ring and the iron center is flanked by to histidines (numbered 93 and 64) on either side of the reduced iron (Table 1b, Fig. 4).These residues stabilize the iron's state with the histindine ring in non-covalent interaction with the metal. The structures many alpha-helices provide its functionality also further by residues separated by for amino acids hydrogen bonding when possible. This is evident in the case of residues Gly 35 and Arg 31 with their nitrogen-neighboring hydrogen of the former interacting with the oxygen of the latter. This kind of interaction through the helix likely results in the structure (2). In the middle of the helix three interaction of hydrogen bonding is common while 1-2 is common at the ends of the helix based on the observations in RasMol.

In the case of Baboon lactalbumin, a calcium-binding protein, the interactions in the active site are not with histidines but with Lysine and Aspartate (Table 1b). The interactions with the metal ion, Calcium 2+, are with the relatively negative charges of these amino acid residues (2).The hydrogen bonding in the alpha helices conserves the same structure as metmyoglobin which means that this stable structure in proteins serves as an advantageous property. Hydrogen bonding every four residues between residues capable of hydrogen bonding (N-H with O=C for example) providing the helical structure. The structure contains six alpha helices and two beta sheets as stated in the ".ent" file (6). The two beta strands are anti-parallel or slightly misaligned over each other (Figure 6, inset). There are two residues involved here: Glu 49 oxygen with Val 42 Hydrogen on nitrogen.

Upon investigating the disulfide bond s in RasMol there were 8 cysteines and 4 disulfide bonds; this means that all the cysteines in the structure are involved in disulfide bonding. Highlighting the two Tryptophan residues oriented toward the interior and surrounded by hydrophobic residues protects it from salvation of its ring structure group (Figure 7).

The final protein explored was Steroidgenic factor 1 from the common mouse(pdb file 1ymt) (Figure 8). With 8 alpha helices and two beta sheets it is a relatively large protein in comparison to the previous two. The N terminus alpha helix begins with Arg 17 and ends with Alan 459 on the C-terminus. There are 30 cysteine residues but no disulfide bonds (Table 1c). This protein is far more complex than the others which are a testament to the capabilities of the RasMol program.

For proteins to function they have to be folded correctly in the appropriate medium and not readily unfold or be degraded (9). The non-covalent interactions, like in the relatively hydrophobic pocket of the metmyoglobin, are responsible for its tertiary structure. With its interactions with the histidines in the hydrophobic pocket which would exclude water molecules. Future studies can possible apply RasMol to the effects of the solvent or the affect of intermolecular forces (8).

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