Secondary Structure Prediction

Once the gonococci gain entrance into the mucous membranes of these areas, they target columnar non-ciliated epithelial cells. Neisseria gonorrhoeae uses a type IV pilus (twitches, forms bundles and able to take up DNA) to anchor itself at the infection site. The pilE gene has been found to be the main factor for adherence to epithelial cells. In a study, missense mutations of the pilE gene revealed altered fiber morphology. PilE mutants had a defect in filament assembly, hence, less adherence to human epithelial cells. In a wild type sample there are significant interconnections of cells, then compared to a sample with a missense PilE polypeptide, we can see reduced interconnections of the cells and filamentous structure. These defects only are expressed when the pilT gene is activated.

A protein has multiple existing structures, these are the primary, secondary, tertiary and quaternary structures which occur progressively. A protein is essentially a sequence of amino acids which are bonded adjacently, and interact with one another in various ways depending on the R group that the amino acid contains. There are 20 different amino acids which are able to be arranged in any given order, thus giving rise to a potential 2.433x1018 (4.s.f) different combinations, and therefore interactions between the various amino acids.

Proteins are made of amino acids, which are compounds built around a central carbon atom. Amino acids then join together through dehydration reactions. These are called peptide bonds. Many amino acids joined together are called polypeptides. A polypeptide becomes a protein when it folds into a three dimensional structure. This is the primary structure of a protein. The next structure in the hierarchy is the secondary structure. Secondary structures can either form alpha helixes, where an amino acid sequence forces the polypeptide to twist into a helical shape; or beta sheets, where an amino acid sequence forces the polypeptide into a zigzag shape. In the tertiary structure, the polypeptide folds several times on itself to form a more complex three dimensional shape. A quaternary structure is when two tertiary structures interact with each other. This is when a protein becomes a functional

Proteins are polymeric chains that are built from monomers called amino acids. All structural and functional properties of proteins derive from the chemical properties of the polypeptide chain. There are four levels of protein structural organization: primary, secondary, tertiary, and quaternary. Primary structure is defined as the linear sequence of amino acids in a polypeptide chain. The secondary structure refers to certain regular geometric figures of the chain. Tertiary structure results from long-range contacts within the chain. The quaternary structure is the organization of protein subunits, or two or more independent polypeptide chains.

results are found from each respective database. What’s the main reason for this discrepancy? Also, how many species represented in each and do each species appear to be equally represented by similar proportions of records? Provide a 3D image of this protein from H. sapiens, appropriately cited. ( 10 pts

. The 3-D tertiary structure of polypeptide proteins globular and is the result of interactions that occur between R groups. Tertiary structure is a result of the bonds between sidechains of amino acids, the R groups. The structure and bonds involve alpha helices, beta pleated sheets, and also regions unique to each protein. Tertiary proteins are held together by four different types of forces; hydrogen bonds, hydrophobic interactions (including Van der Waals interactions), ionic bonding (electrostatic interactions), and disulfide bridges (strong covalent bonds). Hydrogen bonds occur within and between polypeptide chains and the aqueous environment. Hydrogen bonding forms between a highly electronegative oxygen atom or a nitrogen atom and a hydrogen atom attached to another oxygen atom or a nitrogen atom. This links the amino acid

The active site of the protein is located at the cleft between the subdomains. It is characterized as a mix of type 1 and type 2 RIPs. Around the N-terminus, there are 6 β-sheets, 4 antiparallel strands and 2 parallel strands. The C-terminus has 8 α-helices where the 310-helix crosses over on the parallel β-strand giving a canonical geometry. Unlike RIPs, Saporin-S6 has 2 β-strands (7 & 8) that are shorter that increases the accessibility to a particular substrate. This plays a role with its resistance to denaturing agents, the ability to survive in extreme pH, the modifications that are necessary to create immunotoxin and the stability in extreme temperatures.

zipper, enabling these residues to interact with the water in the surrounding. This arrangement reduces the free-energy of protein folding by burying the hydrophobic residues in the interior of the protein, while exposing the hydrophilic residues to the water containing environment and thereby, stabilizing the coiled-coil structure.

For the second part of the experiment, one had to use the knowledge learn from viewing protein molecules in FirstGlance in Jmol to analyze the protein PDB ID: 4EEY. The analysis of this protein was done using the RSCB protein data bank (PDB) at (http://www.rcsb.org/pdb/home/home.do).2

In the picture used in class, the DNA is oriented 3'-->5' from top to bottom (moving from the beginning of the station where the boyfriend grabs his cup--> the register). The mRNA is oriented 5'-->3' from right to left (vanilla ice cream --> strawberry ice cream). The largest protein product is seen towards the 5' end of the DNA and the 3' end of the mRNA (3 layered ice cream once he reaches the register).

It provides five models based on the amino acid sequence and each model is assigned an individual C-score(confidence scores) calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations[16]. A higher C-score indicates greater confidence and vice-versa. It also provides a TM (template modelling) Score which measures the structural similarity between two structures. A TM-score >0.5 indicates a model of correct topology whereas a TM-score <0.17 indicates a random similarity. It also predicts solvent accessibility and ligand binding sites. Protein sequence was submitted to the webserver and the protein structure was obtained.

Bettelheim, Brown, Campbell and Farrell assert that polypeptide chains do not extend in straight lines but rather they fold in various ways and give rise to a large number of three-dimensional structures (594). This folding or conformation of amino acids in the localized regions of the polypeptide chains defines the secondary structure of proteins. The main force responsible for the secondary structure is the non-covalent

The production of new proteins in the cell is fraught with danger arising from the dynamic and error prone protein folding pathways. In order to maintain proper cellular function, eukaryotes require rigorous quality control process to ensure correct production of proteins which can then be utilized by the organism. An essential form of quality control is the examination of newly-formed proteins to ensure correct folding.

Functionally similar proteins (i.e. Orthologous protein BLOCKs) evolve to create amino acid divergence at locus specific positions (Gaucher, Miyamoto and Benner, 2001; Wang and Gu, 2001). Different BLOCKs evolve at a different rate. However, for a given family (or BLOCK) it is constant (Dickerson 1971; Dayhoff and Schwartz, 1978). The divergence, although alters primary sequences, sequence of secondary structure largely remains unaltered, the one that acts as a determinant for functional state of proteins of homologous family (Shen, Jones and Mohrenweiser, 1998). The fact that not all hetero-pairs (total 190) contribute equally to the evolution of a BLOCK (Figure 2, A1 and A2), characterizing their differential role in relation to its properties is of central importance. Further, it remains a challenge to understand the acquired substitutions at the primary sequence level and the maintenance of secondary structures for functional state. Present study is an attempt to gain insight into the mechanism of substitutions based on observed hetero-pairs and positional diversity in relation to protein’s structure and function.

Familiarising with structure and functions of proteins is vital in being able to manipulate it and employ the DNA, and working with it. Nowadays, science and technology is slowly advancing everyday, which have leads to; scientists discovering the new advances in algorithms, which is a software and a hardware for molecular dynamics (MD). It