What Can Studies Of Serine Proteases Tell Us About The Relationship Between Protein Structure, Function And Evolution?

1. Describe the anatomic location of the pancreas relative to the other organs in the upper portion of the abdominal cavity. - The pancreas is about 6 inches long and sits across the back of the abdomen, behind the stomach and liver, leveled with the top of the small intestine

A protein’s tertiary structure, the compact, biologically active and most stable form of the protein, results from further folding of the amino acid chain. The environment in which a protein is synthesized and allowed to folded is a significant determinant of its final shape. If the tertiary structure of a protein is disrupted, the protein is said to be denatured, and it loses its activity. Based on their tertiary structure, proteins can be classified as globular, fibrous and membrane proteins. Globular proteins participate in sophisticated processes such as enzyme-mediated catalysis, transport of molecules, signal transduction, defense and regulation.

The analysis of a complete set of proteins (proteome) of a given cell or organism can be defined as proteomics (Phillips & Bogyo, 2005). The primary aim of proteomic analysis is to separate, identify and characterize proteins and understand their interactions with other proteins. There are four branches of proteomics which are sequence and structural proteomics, expression proteomics, interaction proteomics and functional proteomics.

Proteins with his-tags are purified using IMAC, immobilized metal affinity chromatography. The protein product interacts with a metal that is reversibly bound to an immobilized chelating group. The immobolized chelating group acts as a Lewis base (electron-pair donor) to which the Lewis acid (electron-pair acceptor) metal ion is coordinated. The support to which the metal ion binds is called a ligand. When an electron donor group is replaced by another, the action is referred to as ligand exchange. The donor atoms involved in this exchange are the electronegative nitrogen, sulfur, or oxygen. These atoms scavenge for sources of electrons. The structure formed when the metal ions are added to form the chelate result in free coordination

Nariel Monteiro CHEM 456 Exploring Protein Structure with the Molecular Visualization FirstGlance in Jmol Introduction: The goal of this experiment was to practice using the FirstGlance in Jmol molecular visualization to examine key structural features of proteins. This work is important because protein structure can be related to function, multiple-sequence alignments and evolutionary

Biochemistry Task 2 Donna Whittington 000337251 July 22 , 2016 A. (Wolfe 2000) B. (Borges 2014) (Wolfe 2000a) (Wolfe 2000c) (Wolfe 2000b) C. (Hudon­Miller 2012) D. (Hudon­Miller 2012) E. Hydrophobic Interactions: Proteins are composed of amino acids that contain either hydrophilic or hydrophobic R­groups.  It is the nature of the interaction of the R­groups in the The normal prion protein structure is believed to consist of a number of flexible coils called alpha helices.  In the abnormal form of the protein, some of these helices are stretched out into flat structures called beta sheets.  The normal protein is broken down by cellular enzymes called proteases but the abnormal protein shape is resistant to protease and as a result, these prions replicate and are not broken

Reports indicate that the extracellular serine protease inhibitor, C1INH, can effectively bind HABP2 in the blood (27). We therefore examined whether C1INH can colocalize with HABP2 in

Basic secretions from the pancreas then enter the small intestine to neutralize the pH-decreasing effect of the acidic chyme. Thus these basic and acidic fluid secretions in the duodenum, cause the pH in the duodenum to fluctuate from an acidic pH of 2 to a basic pH of 7.5 (Woodtli & Werner, 1995). We wanted to investigate the question of how these fluctuations of pH in the duodenum affect the activity of the enzyme Trypsin. Enzymes play a very important physiological role in the human body because they speed up the rates of reactions vital to our survival. Enzymes bind to specific substrates and configure their positions, geometry or interactions relative to one another in such a way, that the activation energy required for a reaction to occur is lowered, and thus the reaction rate is increased. The activity of an enzyme depends on many environmental factors such as pH and temperature, because changes in temperature and pH affect the intermolecular interactions between amino acids in the backbone, holding the tertiary structure of the enzyme together. Thus each enzyme has an optimal pH range, below which, and above which its activity declines. Trypsin is an important enzyme that catalyzes the breakdown of specific peptide bonds in the duodenum of the small intestine so that we can extract nutrients and energy from the proteins we eat (Nelson & Cox, 2013). Trypsin is a

Proteins are complex macromolecules which are essential for life of all organisms. They are manufactured through the processes of transcription and translation, which take place inside the cells. More specifically, they are synthesised by ribosomes (Shakhnovich, 2007). Figure 1.1 shows the overall processes that can occur in making a fully functionally active protein. (Ghelis, 2012). Functional properties of certain proteins include, but is not limited to: structural composition of the cytoskeleton in cells, catalysing biochemical reactions and hormones such as insulin to regulate blood sugar concentration (O’Connor & Adams, 2014). Proteins must therefore have a specific 3-dimentional shape to allow them to carry out these functions. If their

Chymotrypsin is a digestive enzyme component of pancreatic juice acting in the duodenum where it performs proteolysis, the breakdown of proteins and polypeptides. Chymotrypsin preferentially cleaves peptide amide bonds where the carboxyl side of the amide bond (the P1 position) is a largehydrophobic amino acid (tyrosine, tryptophan, and phenylalanine). These amino acids contain an aromatic ring in their sidechain that fits into a 'hydrophobic pocket' (the S1 position) of the enzyme. It is activated in the presence of trypsin. The hydrophobic and shape complementarity between the peptide substrate P1 sidechain and the enzyme S1 binding cavity accounts for the substrate specificity of this enzyme. Chymotrypsin also hydrolyzes other amide bonds in peptides at slower rates, particularly those containing leucine and methionine at the P1 position.

In the present study, 2 types of mutations were observed with different frequencies. Amino acid frequencies at each position in the NS3 protease sequence were determined with the VESPA software program. 24 Genotype 4 -specific amino acid signatures were present in almost all of our

The proteins produced are mainly to be used within the cell and the enzyme which are products by proteins help in speeding up certain biological processes.

The multi-step inhibition mechanism of PIs can result in complex mutation pathways that lead to PI resistance in HIV-1. The cause of virological failure in patients taking PIs are drug resistance mutations outside the active site of HIV-1 protease, but rather throughout the matrix and capsid proteins of the Gag

Caspase-1, found in Homo sapiens (Human) has been extensively studied. The PBD code for this enzyme is 3E4C. Using this PBD code, and the Uniprot Knowledge Base, the entry of the studied enzyme was found: P29466. From this accession code, a homologous protein with 48.6% similarities was found. This homologous protein was called Caspase-4 isoform alpha (Uniprot accession number: H9Z2M5) found in Macaca mulatta (Rhesus macaque). Using the BLAST results, an alignment (Figure 1) between chosen sequences were analyzed.

The fluorescence of RepA70-YFP increased as more RepA70-CFP was produced (Fig. 3C), and this indicated that ClpAP protease could be overloaded and a proteolytic-queue forms similar to what was observed with the LAA tagged proteins targeted to ClpXP8. We also tested two other tags, MarA and MarAn20 (20 amino acids from the N-terminal of MarA), which target proteins to be degraded by the Lon protease. The Lon protease was weakly overloaded by MarA tagged proteins but was overloaded more by MarAn20 tagged proteins (Fig. 3C-D). This made us wonder if Lon could be overloaded when both MarA and MarAn20 were co-produced. Indeed, this was the case (Fig. 3E).