Protein Chemistry and Engineering
Code: 100935 ECTS Credits: 6| Degree | Type | Year | Semester |
|---|---|---|---|
| 2500253 Biotechnology | OB | 3 | 1 |
Contact
- Name:
- David Reverter Cendros
- Email:
- david.reverter@uab.cat
Teaching groups languages
You can check it through this link. To consult the language you will need to enter the CODE of the subject. Please note that this information is provisional until 30 November 2023.
Teachers
- Irantzu Pallares Goitiz
Prerequisites
There are no official prerequisites, but it is assumed that students have previously acquired enough solid knowledge on subjects like Fundamentals of Chemistry, Organic Chemistry, Biochemistry and Recombinant DNA Technology.
As in most subjects, much of the literature is in the English language, which is also used in the figures projected in theory classes and also for oral communication, when needed.
Objectives and Contextualisation
The course on Protein Chemistry and Engineering belongs to the main subject "Proteins and nucleic acids: structure, function and engineering" of which a part has been taught in the second year of the Biotechnology degree. This course examines the structural and functional characteristics of amino acids, peptides and proteins both from a basic and applied point of view, the methodologies used in their analysis and modification, and their biomedical and biotechnological applications.
Proteins are effector molecules of many biochemical and biological processes, most of which have been studied in the first two years. However, knowledge of their structure and function is crucial to a deep understanding of a number of subjects in the Biotechnology degree. The knowledge acquired in the course of Protein Chemistry and Engineering is complemented by a practical training in the Integrated Laboratory Course 5. The specific objectives are:
- To reach a deeper understanding of the physicochemical characteristics of amino acids and peptides
- To describe and apply methods for the analysis of protein sequences and peptide synthesis.
- To recognize the structural elements, the different complexity levels, the types of protein folding and their capacity to build higher order structures.
- To reach a knowledge on the use of information resources to establish structural classifications of proteins.
- To understand and explain the most common methods for the analysis of the conformation and stability of proteins, including three-dimensional analysis.
- To describe the molecular basis of protein folding, molecular dynamics, post-translational processing and intra- and extracellular protein traffic.
- To establish evolutionary relationships and learn the methods of structural analysis and structure prediction.
- To understand and apply the most common methods for the production and purification of recombinant proteins.
- To design strategies for modifying and optimizing the properties of proteins and to understand the basis for protein design and the methodologies used in these processes.
- To achieve an global vision about the structure-function relationships in proteins and about the application of these biomolecules in medicine, industry and research.
- To integrate the theoretical knowledge in the interpretation of the results of scientific experiments using the appropriate scientific terminology.
Competences
- Act with ethical responsibility and respect for fundamental rights and duties, diversity and democratic values.
- Describe the molecular, cellular and physiological bases of the organisation, functioning and integration of living organisms in the framework of their application to biotechnological processes.
- Interpret experimental results and identify consistent and inconsistent elements.
- Introduce changes in the methods and processes of the field of knowledge to provide innovative responses to the needs and demands of society.
- Make an oral, written and visual presentation of one's work to a professional or non-professional audience in English or in one's own language.
- Obtain information from databases and use the software necessary to establish correlations between the structure, function and evolution of macromolecules.
- Read specialised texts both in English and one's own language.
- Take account of social, economic and environmental impacts when operating within one's own area of knowledge.
- Take sex- or gender-based inequalities into consideration when operating within one's own area of knowledge.
- Use ICT for communication, information searching, data processing and calculations.
Learning Outcomes
- Act with ethical responsibility and respect for fundamental rights and duties, diversity and democratic values.
- Classify proteins in structural families based on data on sequence and secondary and tertiary structures.
- Correctly analyse data on ligand-macromolecule affinity constants and binding points.
- Deduce evolutionary relationships between macromolecules from the analysis of sequential data.
- Describe correctly the molecular bases of protein folding, transport, modification and replacement
- Evaluate the different techniques of structural analysis and decide on their application to specific experimental situations.
- Extract information from genomic and proteomic databases.
- Extract three-dimensional structures of macromolecules from databases and use the software needed to visualise and understand structure-function relationships.
- Identify conserved protein motifs and domains.
- Interpret experimental data on protein stability and folding.
- Interpret experimental results and identify consistent and inconsistent elements.
- Interpret findings from structural studies of proteins and nucleic acids
- Introduce changes in the methods and processes of the field of knowledge to provide innovative responses to the needs and demands of society.
- Make an oral, written and visual presentation of one's work to a professional or non-professional audience in English or in one's own language.
- Read specialised texts both in English and one's own language.
- Take account of social, economic and environmental impacts when operating within one's own area of knowledge.
- Take sex- or gender-based inequalities into consideration when operating within one's own area of knowledge.
- Use ICT for communication, information searching, data processing and calculations.
Content
THEORY
I. Fundamental properties of amino acids and proteins
Proteins, peptides and their functions in living beings. Structure and physicochemical properties of amino acids. Chemical reactivity. Differential contribution of amino acids to protein properties. Evolutionary relationships.
II. The peptide bond and the sequence polypeptide
Stereochemistry of the peptide bond. Types of natural peptides. Chemical reactivity of peptides. The polypeptide sequence. Strategies for determining the sequence of proteins. Chemical synthesis of peptides; combinatorial libraries.
III. Conformational determinants. Secondary structures
Structural hierarchy. Types of conformation-stabilizing forces. Cooperativity of weak interactions. Determinants of protein folding. Main types of secondary structures.
IV. Structural Classification of Proteins
Supersecondary structures and motifs. Structural domains. Tertiary structure. Domain classification. Conformation and function of fibrous proteins. IDPs- intrinsically disordered proteins.
Structure-function correlation . Examples
General functions of proteins. Enzymatic proteins: examples. Proteins that bind to nucleic acids: examples. Molecular motors: examples. Membrane proteins.
VI. Quaternary structure of proteins
Advantages of quaternary structures. Protomers and subunits. General principles: interfaces, geometries, symmetries. Examples of oligomeric proteins: structure-function and regulation of the activity
VII. Determining the three-dimensional structure of proteins
General methodologies for the structural characterization of proteins. Dissolution analysis: IR, DC, UV-Vis, fluorescence. Analysis in solid phase: X-ray crystallography and cryo-electron microscopy. NMR spectroscopy: 3D structure in solution.
VIII. Folding and conformational dynamics
Protein folding and unfolding: native state and unfolded state. Methods for the analysis of folding. Thermodynamics and mechanistics of the folding process; models that describe it. Folding and aggregation; conformational diseases. Protein folding in vivo: the molecular chaperones. Molecular dynamics of proteins.
IX. Post-translational modifications
Types of post-translational modifications and their functional implications. Transport and associated changes. Limited proteolysis: pre-proteins, zymogens. Examples of regulation by limited proteolysis: coagulation, digestive enzymes. Degradation and protein turnover in vivo.
X. Protein-ligand interaction
Forces involved in protein-ligand association. Methods of study of the interaction. Determination of kinetic and thermodynamic parameters. Designing drugs based on the structure.
XI. Biochemical evolution of proteins
Protein evolutionary relationships. Detection and analysis of homologies; sequential databases; phylogenetic trees. Convergent and divergent evolution; examples. Sequence structure and function. 3D structure prediction; conformational modelling. Evolution of genomes and protein evolution.
XII. Protein engineering: rational design
Rational design: directed mutagenesis as a tool for the analysis and modification of proteins. Examples and applications of protein engineering in the analysis, modification and improvement of the structure, stability,and functionality.
XIII. Protein engineering: directed evolution and de novo synthesis
Directed evolution: random mutagenesis and combinatorial protein engineering methods. Methods for the generation and selection of variants. Examples of redesigned proteins. De novoprotein design - computer algorithms.
PROBLEMS
The content of this section will be given in the form of a dossier at the beginning of the semester via the Virtual Campus. It involves a certain amount of problems related to the topics developed in the theory class. The dossier will be updated periodically. The characteristics of the various parts of the theory syllabus make the subjects of the problems class to be concentrated in a limited number of aspects. Thus, the evaluation of problems may vary between partial examinations.
Methodology
The training activities are divided into two sections: theory classes and problem classes, each with its own specific methodology. These activities can be complemented by tutorial 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 expository sessions will constitute the most important part of the theory section.
Problem Classes
At the beginning of the course the class will be divided into 2 subclasses of problems. A set of statements of problems of the subject (related to the topics developed in Theory) will be made available to students and will be accumulated in the form of a dossier in the Moddle classroom, which will be solved throughout the sessions. Students will work on the problems outside class hours individually and there will be some deliveries in a group way. The non-expository face-to-face sessions will be dedicated to problem solving. The solved problems will be delivered that will be discussed and corrected with the participation of all students.
Seminars
In addition or alternatively, seminars may be organized to provide students with this type of teacher training more alive and additional to theory.
Tutorials
They will be made at the request of the students. The objective of these sessions is to resolve doubts, review concepts with a high conceptual difficulty and carry out debates on the topics of the program. These sessions will not be expository nor will they advance 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.
Activities
| Title | Hours | ECTS | Learning Outcomes |
|---|---|---|---|
| Type: Directed | |||
| Problem/practical cases solving | 7 | 0.28 | 3, 4, 7, 10, 12, 11, 6 |
| Theory sessions | 38 | 1.52 | 3, 2, 5, 9, 10, 11, 15, 6 |
| Type: Supervised | |||
| Homework delivery | 4 | 0.16 | 18, 4, 8, 7, 9, 10, 12 |
| Seminar preparation | 4 | 0.16 | 16, 18, 8, 14, 12, 11, 13, 15 |
| Seminar presentations | 3 | 0.12 | 1, 17, 18, 14, 12, 11 |
| Type: Autonomous | |||
| Group or individual work to prepare problems/cases or seminars | 20 | 0.8 | 18, 4, 8, 7, 12, 11 |
| Study - autonomous work | 65 | 2.6 | 3, 2, 4, 5, 8, 7, 9, 10, 12, 11, 15, 6 |
Assessment
Theory. The total weight of the evaluation of the theoretical part will be 75% of the total grade of the subject. The main evaluation of this part of the subject will have the format of continuous evaluation with three partial tests, with another final test that allows to examine the content of each of the three partial tests not previously passed. The objective of the continuous evaluation is to encourage the continuous effort of the student throughout the entire syllabus, also allowing him to become aware of his degree of follow-up and understanding of the subject.
Students who have passed the partial theory and problems with a grade higher than 4.0 out of 10 points, can choose to obtain the average grade of the two partials. Those who have not exceeded the value of 4.0 of any of the two partial theory and problems must be examined on the date set by the final exam of the subject, in this case the qualification of the last partial exam made is the one that will be taken to calculate the final grade of theory.
In order to take the final exam (recovery), students must have previously submitted to a continuous number of activities that at least equal to 2/3 of the final grade.
Problems. The weight of the evaluation of this section will be 25% of the total: 20% of it will be for the 2 particular exams of these activities, which will take place in parallel to the second and third partial of Theory (10% each). The other 5% will be allocated to group deliveries of the problems-exercises.
Seminars (optional). People who choose to prepare a seminar may be added up to 0.5 points to the final grade achieved in the previous calculation.
Overall assessment. To pass the subject it is necessary to obtain an average of ≥ 3.5 in the partial tests and obtain ≥ 5 as an overall grade.
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 75%); as well as 2 problems to be solved (25%).
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.
Assessment Activities
| Title | Weighting | Hours | ECTS | Learning Outcomes |
|---|---|---|---|---|
| In-class delivery of problems/cases | 5% | 1 | 0.04 | 1, 17, 16, 3, 18, 8, 7, 14, 12, 11, 13, 6 |
| Parcial Problems Evaluation | 20% | 3 | 0.12 | 3, 2, 5, 9, 10, 12, 11, 6 |
| Partial exams | 75% | 5 | 0.2 | 3, 2, 4, 5, 9, 10, 12, 11, 15, 6 |
Bibliography
Basic
(from oldest to newest)
- Brandën C. & Tooze J., Introduction to Protein Structure (1999) Garland Science
- Gómez-Moreno C i Sancho J. (eds.) Estructura de Proteínas (2003) Ariel Ciencia
- Petsko, R. & Ringe, D., Protein Structure and Function (2003) Blackwell Publishing
- Whitford, D., Proteins: Structure and Function (2005) Wiley
- Buxbaum, E., Fundamentals of Protein Structure and Function (2015), Springer (2015, Electronic document, UAB accessible)
- Kessel, A. & Ben-Tal, N., Introduction to Proteins: Structure, Function and Motion (2010) CRC Press (2015, Electronic document, UAB accessible)
- Williamson, M., How Proteins Work (2012) Garland Science
- Kuriyan, J., Konforti, B. & Wemmer, D. The Molecules of Life (2013) Garland Science
- Walsh, G. Proteins: Biochemistry and Biotechnology (2014) Wiley (2019, Electronic document, UAB accessible)
- Lesk, A.M., Introduction to Protein Science 3rd ed. (2016) Oxford University Press
- Almeida, P., Proteins. Concepts in Biochemistry (2016) Garland Science
- Bahar I.,Jernigan R.L. & Dill, K.A., Protein Actions (2017) Garland Science
- Backman, L. Protein Chemistry (2020) De Gruyter
Any of these books contains many interesting notions for the course. However, no one of them may be used as a lone-standing textbook. Some are more didactically-oriented (Petsko & Ringe, Williamson, Brandën & Tooze) but every reading will be enjoyable
Complementary
- Buckel, P. (ed), Recombinant Protein Drugs (2001), Birkhäuser Verlag
- Bujnicki, J.M. (ed.) Prediction of protein structure, functions and interactions (2008) Wiley
- 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
- Kyte, J. Structurein Protein Chemistry 2nd ed. (2007) Garland Science
- Lutz, S., Bornscheuer,U.T. (eds.) Protein Engineering Handbook (2008) Wiley
- Nussinov, R. & Schreiber, G. Computational Protein-Protein Interactions (2017) CRC Press
- Oxender D.L. & 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. Principles of Protein Structure (1979) Springer Verlag
- Park, S.J., Cochran, J.R. Protein Engineering and design (2009)CRC Press
- Sternberg M.J.E. Protein Structure Prediction. (1996) IRL- Oxford University Press
- Tompa, P. & Fersht, A. Structure and function of intrinsically disordered proteins (2009) CRC Press
- Twyman, R., Principles of Proteomics (2004) Taylor & Francis
- Veenstra, T.D. & Yates, J.R. Proteomics for Biological Discovery (2006) Wiley
Internet sites
Links to selected sites may be found at: https://catalegclassic.uab.cat/search*cat/r?SEARCH=100935
Software
PyMol: https://pymol.org/2/
JMol: http://jmol.sourceforge.net/