Protein structure and engineering

• List the most common strategies and methods in protein engineering.
• Identify practical applications of protein engineering in biotechnology.
• Distinguish the methods of representing the structures of biomolecules and know how to use software for their analysis.
• Identify the factors that influence protein folding.

Lectures
• Introduction to protein engineering.
• Fundamentals of protein structure. Structure and properties of amino acids, conformational analysis. Protein folding: thermodynamics and kinetics of folding.
• Protein determination methods. Structural databases and software for biomolecule structure representation.
• Major interactions stabilizing elements of secondary structure and tertiary structure. Design of α-helices. Rational design of proteins.
• Directed protein evolution: mutagenesis and recombination. Screening methods of evolved proteins.
• Representative cases of modified proteins.

Seminars
• Presentation by students of real cases of protein engineering and evolution.

Computer classroom
• Representation and study of biomolecule structures. Use of the UCSF Chimera program (https://www.cgl.ucsf.edu/chimera/).
• Use of structural databases (PDB, https://www.rcsb.org/).
• Use of modeling servers (ROSIE, https://rosie.graylab.jhu.edu/ , ROSIE is a web interface to the Rosetta 3.x molecular modeling software package that provides experimentally proven and rapidly evolving tools for three-dimensional structure prediction and high-resolution protein design), and AlphaFold 3 (https://golgi.sandbox.google.com/about, AlphaFold is a web service that can generate highly accurate predictions of biomolecular protein structures).
• Use of the Swissmodel server to analyze protein variants.
• Reinforcement of structural concepts by solving problems in the FoldIt program (https://fold.it/). FoldIt is a popular online science game in which players use the principles of protein folding to enable them to solve 3D protein structures. The educational version consists of 29 puzzles divided into 9 levels that guide the student through a standard set of topics in teaching biochemistry, including atomic interactions, the hydrophobic effect, amino acids, primary structure, secondary structure, tertiary structure, protein binding, and folding pathways.

Periodic tests
• As part of the continuous evaluation process and in order to monitor the attendance and knowledge acquisition by the students, small quizzes (about 10 minutes long) will be given periodically at the beginning of some lectures.

Group tutorials
• Reinforcement of the contents of the subject through presentations or discussion of topics related to the subject in the context of biotechnology.
Exam
• As part of the evaluation (70% of the final grade) an exam will be held on the dates indicated in the annual program. The exam will consist of two parts, corresponding to structural fundamentals and biochemical techniques of protein engineering.

• V. Köhler (Ed.) Protein Design, Methods and Applications in Methods in Molecular Biology, 2014 Humana Press.
• K. J. Jensen (Ed.). Peptide and Protein Design for Biopharmaceutical Applications, 2009 John Wiley & Sons.
• E Buxbaum, Fundamentals of Protein Structure and Function, 2007 Springer.
• C. Köhrer, U. L. RajBhandary (Eds.). Protein Engineering in Nucleic Acids and Molecular Biology series no. 22, 2009, Springer.
• P. Kaumaya, Protein Engineering, 2012, InTech.

Competencies
• Comp01: That students have the ability to gather and interpret relevant data (usually within their area of study) to make judgments that include reflection on relevant social, scientific or ethical issues.
• Comp02: That students are able, both in writing and orally, to discuss and convey information, ideas, problems and solutions related to Biotechnology to both specialized and non-specialized/general audiences.
• Comp03: That students have developed those learning skills necessary to undertake further studies with a high degree of autonomy.
• Comp04: That students know how to apply the theoretical-practical knowledge acquired in the degree in a professional manner and are competent in the approach/solution of problems, as well as in the elaboration/defense of arguments in both academic and professional contexts related to innovation and the biotechnology industry.
• Comp05: Study and learn autonomously, with organization of time and resources, new knowledge and techniques in Biotechnology and acquire the ability to work in a team.

Skills and Abilities
• H/D01: Think in an integrated way and approach problems from different perspectives with critical reasoning.
• H/D02: Search, process, analyze/interpret and synthesize relevant information and results from various sources and draw conclusions on topics related to Biotechnology.
• H/D03: Organize and plan their work.
• H/D04: Interpret experimental results and identify consistent and inconsistent elements.
• H/D06: Maintain an ethical commitment, as well as a commitment to equality and inclusiveness.
• H/D11: Understand and know how to apply the physicochemical principles of biological processes with application in Biotechnology, as well as the main tools used to investigate them.
• H/D12: To know how to apply the instrumental techniques and work protocols in a laboratory, applying the regulations and techniques related to safety and hygiene, waste management and quality.

Knowledge/Contents
• Con01: To know the most important concepts, methods and results of the different branches of Biotechnology.
• Con04: To know the techniques to determine the properties of proteins and to be able to analyze and manipulate their structure according to their application in Biotechnology.

• The expository and interactive teaching (including practical exercise) will be face-to-face. Exceptionally, face-to-face teaching may be combined with virtual teaching up to a maximum of 10% of the total hours of the subject.
• Lectures. The professor will develop the content of the program using exercises and practical examples that illustrate the concepts explained. The explanations will be combined with materials from the bibliography, as well as references from scientific journals.
• Seminars and group tutorials. Students will individually present work on real cases of peptide and protein design and evolution in the seminars. Students will be encouraged to participate actively in the seminars throughout the course, being this participation one of the evaluation criteria. Problems may be posed for the student to try to solve them autonomously, giving their solution to the teacher in advance of the seminar classes in which they will be solved. In these classes, the students will present their solutions, and the professor will oversee resolving any doubts and difficulties that may arise. Occasionally, in the seminars will also be proposed short exercises to solve on the fly, which will be considered in the evaluation.
• Individual tutorials. The tutorials will be fundamentally of face-to-face character, although they will be able to be carried out partially in a virtual way. A closer follow-up of the student's work will be made, reinforcing the official teaching with personal tutorials according to the needs of each student.
• Practical classes in the computer classroom. Two sessions in which students will be able to familiarize themselves with different tools used for the structural representation of biomolecules, the most relevant databases, as well as some software for protein design. The computer practices may be in virtual modality, in any case with a maximum of 25% of the practical hours of the subject.
• Virtual classroom (Moodle). The course will have a virtual classroom in which all the teaching support material of the course, calendars, links to pages of interest, etc. will be included. This platform also contains discussion forums and internal mail which provides excellent communication between teachers and students.

1. General criteria
• The evaluation criteria will be the same for all the students in both calls.

2. Attendance and participation
• Attendance to theory classes, seminars and practical classes (laboratory and computer room) is compulsory, except for justifiable reasons.
• Attendance to the final exam is mandatory to pass the course. Likewise, the presentation of all individual and group activities (individual practice questionnaire and group work) is mandatory for all students (except for those students with official dispensation) and a requirement to pass the subject.

3. Continuous evaluation (30% of the final grade)
• The continuous evaluation combines face-to-face activities (team work, presentations, problem solving in class) and online activities (use of Virtual Classroom-Moodle and Microsoft Teams).
• There will be quizzes (approx. 10 minutes) at the beginning of some classes to assess attendance and learning.
• The continuous evaluation grade will only be added to the final exam grade if the final exam grade is equal or higher than 4.0 (out of 10).
• Learning outcomes assessed in the continuous assessment: Comp01, Comp02, H/D01, H/D02, H/D03, H/D04, H/D06, H/D11, H/D12.

4. Final Exam (70% of the final grade)
• The final exam will cover all the contents of the subject, including those taught in the practical classes and tutorials. Learning outcomes assessed in the exam: Comp03, Comp04, Comp05, H/D01, H/D02, H/D03, H/D04, H/D06, H/D011, H/D012, Con01, Con04.
• The final exam will consist of two parts corresponding to the teaching of each of the blocks of the course. In order to pass the final exam it will be necessary to pass in each of the two parts of the exam the established minimum cut-off mark.
• For cases of fraudulent performance of exercises or tests, the "Regulations for the evaluation of the academic performance of students and review of qualifications" will be applied, which can be consulted at the following link: https://bit.ly/3btFiUI.

Student work, 72 h

It is important to highlight that the student's personal work has to be continued throughout the subject, since it is a subject in which the contents that are taught as the program progresses are based on the knowledge acquired in the previous topics