Protein Engineering
Code: 102521 ECTS Credits: 6| Degree | Type | Year |
|---|---|---|
| 2502444 Chemistry | OT | 4 |
Contact
- Name:
- David Reverter Cendros
- Email:
- david.reverter@uab.cat
Teachers
- David Reverter Cendros
Teaching groups languages
You can view this information at the end of this document.
Prerequisites
There are no previous formal requirements, but it is assumed that the student acquired beforehand solid knowledge on the subjects of the three first courses, particularly on the subjects Fundamentals of Molecular and Cellular Biology of the 1st course and Biochemistry of the 3rd course,
As in other subjects, most of the bibliography is in english, language that is also used in an important way in the presentations displayed at the classes and other activities. The use of this language by the students in the supervised activities (Problems and Practical classes, Seminars ....etc), will be positively evaluated.
Objectives and Contextualisation
General goals. This subject will deal with the structural and functional characteristics as well as with the reactivity/interaction of amino acids, peptides and proteins. Also, on how they have evolved biologically and how they can be transformed by rational redesign, directed evolution or chemo-biological modifications at the laboratory in order they adopt structures, superstructures and properties of fundamental and applied interest. Proteins are structural molecules, regulatory and effectors in most biochemical and biological processes, natural/ pathological/ of industrial interest, as well as frequent protagonists, and among the most diverse among them. The knowledge on their properties and strategies to transform them is fundamental for the deep understanding of a significant number of subjects within the degree of Chemistry.
Specific goals.
- Get a deep knowledge of the physico-chemical characteristics of amino acids, peptides and proteins, as well as of their reactivity and modifications.
- Describe and apply the methodologies for the analysis of the sequence of proteins and the synthesis of peptides.
- Recognize the structural elements, the different levels of complexity, the types of folding for proteins and their capability in the formation of higher order structures..
- To know how to consult and get access to the information sources to analyze and classify proteins structurally.
- To know and be able to describe and apply the most used methods for the analysis of the conformation and stability of proteins, including the three-dimensional analysis.
- Describe the molecular basis of the folding of proteins, of its molecular dynamics, post-translational modification, intra- and extra- cellular transit.
- To know how to establish the evolutionary relationships among proteins, and know the methods for the structural analysis and prediction.
- Understand and know how to apply the most usual methodologies for the production and purification of recombinant proteins.
- To know how to select the best strategies for the modification and optimization of the properties of peptides and proteins. Understand the basis for its design, for the construction of mini-, super-structures and mimetics, and the methodologies used in such processes. Also, to know about approaches that have been valid to form nanostructures and nanoprobes with them.
- Get an overall view of the structure-function relationships in proteins, and about the applications of such biomolecules in medicine, industry and research.
- Integrate the acquired theoretical knowledge to interpret the results of scientific experiments and to solve experimental problems, using the proper scientific terminology.
Competences
- "Interpret data obtained by means of experimental measures, including the use of IT tools; identify their meaning and relate the data with appropriate chemistry, physics or biology theories."
- Adapt to new situations.
- Communicate orally and in writing in one's own language.
- Learn autonomously.
- Manage the organisation and planning of tasks.
- Manage, analyse and synthesise information.
- Obtain information, including by digital means.
- Propose creative ideas and solutions.
- Reason in a critical manner
- Recognise and analyse chemical problems and propose suitable answers or studies to resolve them.
- Resolve problems and make decisions.
- Show an understanding of the basic concepts, principles, theories and facts of the different areas of chemistry.
- Show initiative and an enterprising spirit.
- Show sensitivity for environmental issues.
- Use IT to treat and present information.
- Work in a team and show concern for interpersonal relations at work.
Learning Outcomes
- Adapt to new situations.
- Analyse data on constants of affinity and places of ligand-macromolecule interaction.
- Classify proteins in structural families based on data on sequence and secondary and tertiary structures.
- Communicate orally and in writing in one's own language.
- Deduce evolutionary relationships between macromolecules from the analysis of sequential data.
- Describe the basic methodologies of recombinant DNA technology for application to the expression of recombinant proteins.
- Describe the fundamental properties of amino acids and proteins.
- Extract information from genomic and proteomic databases.
- Extract three-dimensional macromolecule structures from databases.
- Handle the necessary software to visualise three-dimensional macromolecule structures and understand structure-function relationships.
- Identify conserved protein motifs and domains.
- Interpret experimental data on protein stability and folding.
- Interpret the reactivity of chemical groups of proteins in the context of the structures and environments which they act.
- Learn autonomously.
- Manage the organisation and planning of tasks.
- Manage, analyse and synthesise information.
- Obtain information, including by digital means.
- Propose creative ideas and solutions.
- Propose strategies to obtain mutants of a recombinant protein and for the purification of the same.
- Reason in a critical manner
- Recognise the capacity of different techniques for the structural analysis of macromolecules and decide how to apply them to specific experimental situations.
- Resolve problems and make decisions.
- Show initiative and an enterprising spirit.
- Show sensitivity for environmental issues.
- Use IT to treat and present information.
- Work in a team and show concern for interpersonal relations at work.
Content
List of topics of theory proposed for the subject PROTEIN CHEMISTRY AND ENGINEERING
I. Fundamental properties of amino acids and proteins
II. The peptide bond and the polypeptidic sequence
III. Structural determinants. Secondary structures
IV. Structural classification of proteins
V. Structure-function correlations in proteins. Examples
VI. Protein quaternary structure
VII. Determination of the three-dimensional structure of proteins
VIII. Protein folding and conformational dynamics
IX. Post-translational processes and modifications
X. Interaction protein-llgand
X. Protein engineering: heterologous production
XI. Protein engineering: redesign and de novo synthesis
Activities and Methodology
| Title | Hours | ECTS | Learning Outcomes |
|---|---|---|---|
| Type: Directed | |||
| Problems | 18 | 0.72 | 14, 4, 5, 6, 15, 16, 11, 12, 13, 10, 17, 19, 21, 22, 26, 25 |
| Theory classes | 34 | 1.36 | 2, 3, 5, 6, 7, 9, 11, 12, 13, 10, 19, 21 |
| Type: Supervised | |||
| Tutorials | 8 | 0.32 | 4, 23, 15, 16, 18, 20 |
| Type: Autonomous | |||
| Problems | 22.5 | 0.9 | 2, 3, 4, 5, 6, 15, 16, 11, 13, 10, 22, 26 |
| Study, in general | 61.5 | 2.46 | 2, 3, 5, 23, 6, 7, 9, 8, 15, 16, 11, 12, 13, 17, 19, 18, 21, 22, 26, 25 |
The training activities are divided into two sections: theory classes and problem classes and / or seminars, each one with its specific methodology. These activities will be complemented by a series of tutoring sessions that will be programmed additionally.
Theory classes The teacher will explain the content of the syllabus with the support of audiovisual material that will be made available to students in the Moddle classroom of the subject. These lectures will be the most important part of the theory section.
Problem Classes and / or Seminars A set of statements of subject problems (related to the topics developed in Theory) will be made available to students and will be accumulated in the form of a dossier on the Virtual Campus, which will be resolved throughoutthe sessions. Students will work out problems outside class hours individually. Non-expositive classroom sessions will be devoted to the resolution of previously worked problems during the previous week. Complementary or alternatively, seminars may be organized to provide students with this type of teaching that is more lively and additional to that of theory.
Tutorials Students will be made available. The purpose of these sessions is to resolve doubts, revise concepts with a high conceptual difficulty and carry out debates on the topics of the program. These sessions will not be exhibited nor in them will be advanced matter of the official agenda, but will be sessions of debate and discussion.
Annotation: Within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.
Assessment
Continous Assessment Activities
| Title | Weighting | Hours | ECTS | Learning Outcomes |
|---|---|---|---|---|
| Problem evaluation | 30 | 3 | 0.12 | 1, 14, 4, 23, 8, 15, 16, 24, 17, 18, 20, 22, 26, 25 |
| Theory evaluation | 70 | 3 | 0.12 | 2, 3, 5, 6, 7, 9, 11, 12, 13, 10, 19, 21 |
Theory.
The main evaluation of this part of the subject will have the format of continuous evaluation with two partial tests (35% each), with another final test that allows to examine the content of each one of the two partial not previously surpassed, or both simultaneously, in case you do not pass any of the partial ones. The objective of the continuous assessment is to encourage the continuous effort of the student along the entire subject, allowing also to become aware of its degree of follow-up and understanding of the subject. Students who have passed the theory and problems partitions with a score greater than 4.0 on 10 points, may choose to obtain the average mark of both partial. Those who have not passed the value of 4.0 of either partial shall be examined on the date signed for the final exam of the subject of the partial or partial question, in this case the qualification of the student, The last partial exam is the one that will be taken to calculate the final grade.
Problems and / or Seminars.
The weight of the evaluation of this section will be 30% of the total: 15% of this total will be allocated to individual deliveries, problems-exercises and / or active participation in class, seminars, and the other 15% will be for exams Individuals of these activities, which will take place in parallel to the Theory exams.
Global evaluation
The subject will be passed when the sum of the different parts weighted by their specific weight in the subject exceeds 5,0 on 10 points. Students who do not, with just cause, participate in the continuous evaluation, can be evaluated through the final test. To opt for the recovery (final exam) it is necessary to present 2/3 of the activities of the subject.
If the student has only been evaluated for a maximum of 25% of the tests and withdraws, the final grade will be NOT EVALUATED.
Single Evaluation:
The single assessment consists of a single synthesis test with multiple-choice questions (may include short questions) on the contents of the entire theory program (70%); as well as 2 problems to be solved (30%).
The single assessment test shall be carried out coinciding with the same date fixed in the calendar for the last continuous assessment test and the same recovery system shall be applied as for the continuous assessment.
Bibliography
Basic
- Brandën C. i Tooze J., Introduction to Protein Structure (1999) Garland Pub.
- Buxbaum E. Fundamentals of Protein Structure and Function (2007) Springer.
- Gómez-Moreno C i Sancho J. (eds.) Estructura de Proteínas (2003) Ariel Ciencia.
- Kessel A. & Ben-Tal N., Introduction to Proteins. Structure, Function and Motion (2011) CRC Press
- Petsko, R. & Ringe, D.,Protein Structure and Function (Primers in Biology) (2008) Blackwell Publishing.
- Whitford, D., Proteins: Structure and Function (2005, 1ª edic / 2016, 2ª edic, sortirà ?) Wiley.
Complementary
-Buckel, P. (ed), Recombinant Protein Drugs (2001), Birkhäuser Verlag
-Bujnicki, J.M. (ed.) Prediction of protein structure, functions and interactions (2008) Wiley
-Buxbaum, E., Fundamentals of Protein Structure and Function (2007), Springer
-Creighton T.E., Proteins. Structures and Molecular Properties. (1993) (2nd ed.) Freeman W.H. & Co.
-Fersht A. Structure and Mechanism in Protein Science (1999) W.H. Freeman & Co.
-Glick, B.R. & Pasternak, J.J. Molecular Biotechnology (1998) ASM Press
-Kamp, R.M., Calvete, J. J., Choli-Papadopoulou, T. Methods in Proteome and Protein Analysis (2004) Springer-Verlag
-Kraj, A. & Silberring, J. (eds) Introduction to Proteomics (2008) Wiley
-Lesk, A.M. Introduction to Protein Science (2010) Oxford University Press
-Lutz, S., Bornscheuer, U.T. (eds.) Protein Engineering Handbook (2008) Wiley
-Oxender D.L. i Fox C.F., Protein Engineering (1987) Alan Liss Inc.
-Patthy, L. Protein Evolution (2007) (2nd ed.) Wiley
-Perutz M., Protein Structure. New Approaches to Disease and Therapy. (1992). Freeman W.H. & Co.
-Schultz, G.E. & Schirmer, R.H. Principlesof Protein Structure (1979) Springer Verlag
-Park, S.J., Cochran, J.R. Protein Engineering and design (2009)CRC Press.
-Remigopalakrishnan V., Carey P.R. & Smith I.C.P. Proteins : Structure, Dynamics & Design (2013).
-Sternberg M.J.E. Protein Structure Prediction. (1996) IRL- Oxford University Press.
-Twyman, R., Principles of Proteomics (2004) Taylor & Francis
-Veenstra, T.D. & Yates, J.R. Proteomics for Biological Discovery (2006) Wiley
-Walsh, G. Proteins: Biochemistry and Biotechnology (2001) Wiley
Software
The subject will not use specific computer programs
Language list
| Name | Group | Language | Semester | Turn |
|---|---|---|---|---|
| (PAUL) Classroom practices | 1 | Catalan | second semester | morning-mixed |
| (TE) Theory | 1 | Catalan | second semester | morning-mixed |