Contact Us
Sign In / Sign Up for FREE
Go to advanced search...

Computational Biology The Serine Protease Active Site - Essay Example

Comments (0) Cite this document
The structure of the enzymes determines the activity and the specificity of the protein. This field has been widely studied in the form of structure…
Download full paperFile format: .doc, available for editing
GRAB THE BEST PAPER94.3% of users find it useful
Computational Biology The Serine Protease Active Site
Read TextPreview

Extract of sample "Computational Biology The Serine Protease Active Site"

Download file to see previous pages Chymotrypsin belongs to the trypsin family of serine proteases and is usually secreted in inactive form (zymogen) in the small intestine. The structure of chymotrypsin was elucidated via the X-ray crystallography.Below is the structure of chymotrypsinogen (see Error: Reference source not found)
The active site is the catalytic unit of an enzyme. The determination of the three-dimensional structure of chymotrypsin by X-ray crystallography was the basis of greater insight into the mechanism of action of serine proteases.
The Swiss-PDB Viewer software available at was used to manipulate the coordinates of chymotrypsin and subtilisin serine proteases retrieved from the protein data bank (PDB available at
The catalytic site of most srine peptidaeses including chymotrypsin is composed of a catalytic traid of serine, histidine and aspartic acid residues. The ezyme the experimnt dealt with are are serine proteases and they have been known to exhibit similar spatial arrangements. However, the residues of the enzymes may adopt different order in the amino acid sequence.
Catalytic triad is composed of Ser195 on one side and Asp102 and His57 on the other side inside the active site cleft. An extensive hydrogen bonding network exists in the triad for instance Nδ1-H of His57 and Oδ1 of Asp102 and also between OH of Ser195 and the Nε2-H of His57. However in the event that His57 is protonated the latter bond is lost (Hedstrom, 2002).
Figure 8: The positions of the backbone nitrogens are shown; the residues are Ser195 and Gly193 and the distances from these nitrogens to the peptide carbonyl oxygen. This brings the two residues closer for interactions to occur
The catalytic triad in subtilisin contains residues 32, 64 and 221; the oxyanion hole comprises the side chain of Asn155 and the backbone NH of Ser 221; the mouth of the specificity ...Download file to see next pagesRead More
Cite this document
  • APA
  • MLA
(“Computational Biology The Serine Protease Active Site Essay - 1”, n.d.)
Computational Biology The Serine Protease Active Site Essay - 1. Retrieved from
(Computational Biology The Serine Protease Active Site Essay - 1)
Computational Biology The Serine Protease Active Site Essay - 1.
“Computational Biology The Serine Protease Active Site Essay - 1”, n.d.
  • Cited: 0 times
Comments (0)
Click to create a comment or rate a document

CHECK THESE SAMPLES OF Computational Biology The Serine Protease Active Site

Computational MCMC Bayesian Inference

...? Computational MCMC Bayesian Inference Computational MCMC Bayesian Inference The Markov Chain Monte Carlo (MCMC) method employs Markov Chain to simulate Monte Carlo experiments. These experiments provide estimates to quantities by executing statistical experiments. MCMC takes a Bayesian approach to conduct the essential mathematical integration using simulation. In the Bayesian inference framework, probability estimation is used to quantify the uncertainty in the parameters (Chen, 2010). The data is certain and is considered fixed. On the other hand, parameters are uncertain and thus are represented as random variables. Since it is not usual to consider a single value of a parameter, we get a posterior distribution. A posterior... as This...
10 Pages(2500 words)Assignment

Active learning

...?Reflective Essay on Active Learning Recently, the learning experience I have gained has made a remarkable change in the way I approach learning and deal with people. I can claim that the change has made me transition into a more mature learner and would definitely help me in dealing with future challenges in my career. The experience relates to the idea of Reg Revan’s Action Learning, which we applied in fulfilling an important academic requirement for the (Course/Subject) class. In this paper, I will expound on the learning I had and the insights I gained, and relate the relevance of Action Learning to my experience. As part of the requirements of the course (Name), we were assigned as a group to report on injection...
7 Pages(1750 words)Essay

Emerging Technology: Computational sustainability

...modeled on the efforts aimed at conservation of the environment (Sharma & Mudhoo, 2011). The models can also be used to measure the extent and level of human activities affecting the environment such as deforestation as well as prioritizing the various areas that need policy intervention in an effort of minimizing damage on the ecosystem such as large scale fishing (Starrett, 2009). Discussion on Computation Sustainability, Biodiversity, Solutions and Threats Computational sustainability models focus on the development of frameworks for decision making on managerial level, focusing more on resource allocation and generation of solutions on problems affecting the society (Thrift &...
4 Pages(1000 words)Essay

Computational Fluid Dynamics

.... There are problems associated with the meshing mechanism as it easy to say the word splitting but in reality it is extremely difficult. Therefore the skill is to produce a mesh with exactly the right sub-volumes. If the sub volumes are too big then the solution will have errors; if the volumes are too small then the calculation will take too long to be useful in a design process. The past tells that in 1990 CFD was an activity for owners of CRAY super-computers, but by 2000 the airflow is analyzed by starting from an initial flow, which can be either a guess at the solution or a specific initial condition. This has lead to a change such that using this initial flow the conservation equations are...
8 Pages(2000 words)Essay

Computational Fluid Dynamics

...of values of and at time zero at and . If we wanted to work out the values of and at time then we would need to do this on the basis of values of and at time zero at and , see figure 2. Figure 2: It shows the characteristic method in action. So the smaller the time step is made, the finer the spatial grid must be and vice versa: must hold. This constraint means that the computation time will vary with the square of either the number of time-steps or spatial segments chosen. We have adopted the following physical properties for both pipe and fluid: Pipe properties: Diameter Length Wall thickness Elasticity Lame coefficient Roughness Fluid properties: assumed constant,...
5 Pages(1250 words)Outline

Computational Phylogenetic

...):0.02387,Frog/1-294:0.13403); Question 3. Using the resulting “neighbor.outtree” generated as your answer in Question 2, generate the corresponding dendrogram using the “drawgram” program found at the MOBYLE Portal under phylogeny/display. Keep all program parameters set to default except for the “Drawgram options” parameter; you will need to change this parameter to a file type you can visualize on your computer (e.g., Windows – BitMap). Copy/Paste the resulting image as your answer. Answer: Question 4. Using the following MSA (copy all lines including the line with the 5 and 13): 5 13 Alpha AACGUGGCCAAAU Beta AAGGUCGCCAAAC Gamma CAUUUCGUCACAA Delta GGUAUUUCGGCCU Epsilon GGGAUCUCGGCCC Run the...
2 Pages(500 words)Essay

Computational recruits lab

...Computational RC circuit Lab Introduction In this lab, the major objective was to simulate a RC circuit that could allow us to measure the current and voltage across the resistor and capacitor. Meeting the above objective provided a platform for exploring how charge on capacitor changes with time when different parameters were varied. Apart from a graph of charge on capacitor against time, another one for current against time was also plotted to current is affected by change on charge on capacitor. This could the give an immediate overview about the activities of a capacitor in a circuit. Parameters that were changed to meet the objective of this study includes charge across, capacitance and resistance. Conclusion Both simulation...
1 Pages(250 words)Lab Report

Computational Exercise 3 : Cyclotron motion

...Computational Exercise 3 Worksheet: Cyclotron motion What is cyclotron motion? (1pt) A charged particle is moving in the magnetic field with velocity. It moves in a circle at the end 2 Why does a charged particle moving in a direction perpendicular to a magnetic field move in a circle? (1pt) Taking the equation of, the cross product between will produce a perpendicular force for the magnetic field. 3 What is the force from the magnetic field on a charged particle moving parallel to a magnetic field? What is the force on a charged stationary particle in a magnetic field? (1pt) forces on charged stationary particles will be 4 Write down the magnitude of the Lorentz force for a particle in a magnetic field. Write down...
1 Pages(250 words)Lab Report

Computational Fluid Dynamic

...Introduction Computational fluid Dynamics (CFD) can be described as the art of replacing existing PDE systems with a set of algebraic equations which can be solved using digital computers. Computational fluid Dynamics (CFD) usually provides a qualitative prediction of the fluid flow by the means of mathematical modeling, numerical methods and software tools (Ferziger and Peric, 2006). CFD enables engineers and scientists to perform numerical environments in virtual flow laboratories. Computational fluid Dynamics (CFD) has a wide range of uses in the engineering and scientific research. It can be used by architects to produce 3D models of their buildings, by engineers...
11 Pages(2750 words)Assignment

Active Listening

...Active listening Active listening Social challenges require an active listener. Similarly, addressing a personal problem entails empathy, active listening, persuasion, self-awareness, and coordination. Therefore, the report comprises a practical issue I encountered and how I helped the client to find peace through active listening. Mrs. Hirst sought my assistance to deal with her drinking problems. She first requested my time to discuss confidential information about her life. I organized a meeting between us out of my office where we discussed the concerns. Even though she felt uneasy, I cooled her nerves to share the problems through...
1 Pages(250 words)Essay
sponsored ads
We use cookies to create the best experience for you. Keep on browsing if you are OK with that, or find out how to manage cookies.

Let us find you another Essay on topic Computational Biology The Serine Protease Active Site for FREE!

Contact Us