Erciyes University - Info Package

Dersin Adı	Dersin Seviyesi	Dersin Kodu	Dersin Tipi	Dersin Dönemi	Yerel Kredi	AKTS Kredisi	Ders Bilgileri
PROTEIN RESEARCH METHODS	Birinci Düzey	BIOL 576		1	7.50	7.50	Yazdır

Dersin Tanımı

Ön Koşul Dersleri	NON
Eğitimin Dili	English
Koordinatör	PROF. DR. ABDURRAHMAN AYVAZ
Dersi Veren Öğretim Eleman(lar)ı	PROF. DR. ABDURRAHMAN AYVAZ
Yardımcı Öğretim Eleman(lar)ı	NON
Dersin Veriliş Şekli	The theoretical framework for this postgraduate "Protein Research Methods" course must be highly interactive, literature-driven, and centered on critical analysis. The course will be structured as a series of weekly seminars and guided discussions, moving systematically from the foundational principles of protein biochemistry, purification, and classical Mass Spectrometry (MS) to the most cutting-edge, high-throughput methodologies. Each week, students will be required to critically read, present, and analyze recent high-impact research papers to understand the practical application and current limitations of techniques such as Quantitative Proteomics (e.g., TMT, DIA), Advanced Interactomics (e.g., TurboID), and Structural Biology innovations (Cryo-EM). The latter part of the course will focus heavily on emerging fields like Single-Cell Proteomics and AI-driven protein prediction/design (AlphaFold), integrating bioinformatics and computational tools for data interpretation. The ultimate goal is to foster independent research competence by enabling students to critically evaluate experimental designs, troubleshoot methodological challenges, and propose sophisticated, multi-faceted proteomic strategies for addressing complex biological questions.
Dersin Amacı	The primary objective of this course is to equip postgraduate students with a comprehensive and critical understanding of the state-of-the-art methodologies used in modern protein science and proteomics. Students will master the theoretical and practical principles behind essential techniques, ranging from classical protein purification and characterization to advanced Mass Spectrometry (MS)-based quantitative proteomics (TMT, DIA), structural analysis (Cryo-EM), and interactomics (Proximity Labeling). Furthermore, the course aims to develop the student’s ability to critically evaluate research literature, design robust experimental workflows, integrate bioinformatics and AI tools (e.g., AlphaFold) for data interpretation, and ultimately, apply these advanced skills to propose and execute high-impact research strategies addressing complex biological questions in fields like disease mechanism and drug discovery.
Dersin Tanımı	This advanced graduate-level course provides an in-depth exploration of the essential and cutting-edge methodologies currently employed in protein science and high-throughput proteomics. The curriculum comprehensively covers the entire spectrum of protein analysis, beginning with foundational principles of protein purification, characterization, and separation techniques (Chromatography, Electrophoresis). The core of the course focuses on modern Mass Spectrometry (MS) applications, including the theory and practice of label-free and label-based quantitative proteomics (DIA, TMT), as well as the identification of Post-Translational Modifications (PTMs). Significant emphasis is placed on advanced techniques for mapping cellular Protein-Protein Interactions (Interactomics) using Proximity Labeling (BioID/TurboID), and on the structural determination methods of Cryo-EM and X-ray Crystallography. Finally, the course integrates emerging technologies, such as Single-Cell Proteomics and AI-driven protein structure prediction (AlphaFold), enabling students to utilize these tools for systems-level biological inquiry, biomarker discovery, and contemporary protein engineering efforts.

Dersin İçeriği

1	Introduction to Proteomics and Protein Fundamentals Significance of Proteomics (Structural, Expression, Functional). Levels of Protein Structure (Primary, Secondary, Tertiary, Quaternary). Physicochemical Properties of Proteins. Bioinformatics Databases (UniProt, PDB).
2	Protein Purification and Characterization (Classical Methods) Cell Lysis and Differential Centrifugation Techniques. Chromatographic Methods: Size-Exclusion, Ion-Exchange, and High-Resolution Affinity Chromatography (His-tag, GST-tag). Purity Check and Concentration Determination.
3	Electrophoresis and Immunological Techniques Principles of SDS-PAGE and Native PAGE. Isoelectric Focusing and 2D-Electrophoresis (Advanced Separation). Western Blotting and sensitive immuno-detection methods.
4	Mass Spectrometry (MS) Fundamentals Components of Mass Spectrometry: Ionization (ESI, MALDI) and Mass Analyzers (TOF, Orbitrap). Tandem MS (MS/MS) principle and Peptide Sequencing. Data-Dependent Acquisition (DDA) strategies.
5	Quantitative Proteomics I: Label-Based Approaches SILAC (Stable Isotope Labeling with Amino acids in Cell culture). Chemical labeling techniques like iTRAQ and TMT (Tandem Mass Tag). Data analysis and Multiplex Comparative Proteomics.
6	Quantitative Proteomics II: Label-Free Approaches Spectral Counting and Intensity-Based Methods. Data-Independent Acquisition (DIA) strategies (SWATH-MS). Proteomic data processing and statistical evaluation with MaxQuant and other software.
7	Protein-Protein Interaction (PPI) Analysis I Yeast Two-Hybrid System (Y2H) and Co-Immunoprecipitation (Co-IP). Protein Pull-down assays. In situ interaction visualization using Proximity Ligation Assay (PLA).
8	Protein-Protein Interaction (PPI) Analysis II & Interactomics Affinity Purification-Mass Spectrometry (AP-MS). Proximity Labeling: BioID and TurboID for mapping in vivo interaction networks (Latest Studies).
9	Protein Structural Analysis I: X-ray Crystallography and NMR X-ray Crystallography: Crystallization, Diffraction, and the Phase Problem. Nuclear Magnetic Resonance (NMR) Spectroscopy: Solution structure determination. Advantages and Limitations.
10	Protein Structural Analysis II: Cryo-Electron Microscopy (Cryo-EM) Cryo-EM principles and workflow. Single-Particle Analysis and Cryo-Electron Tomography (Cryo-ET). The Resolution Revolution in Structural Biology and current applications (Latest Studies).
11	Post-Translational Modifications (PTM) Analysis Key PTMs such as Phosphorylation, Ubiquitination, and Glycosylation. PTM Enrichment Strategies (e.g., Phosphopeptide enrichment). PTM identification and mapping via MS.
12	Protein Engineering and Artificial Intelligence (AI) Directed Evolution and Rational Design. Phage Display and its applications. AI-Based Protein Structure Prediction (AlphaFold and ESM-Fold) and De Novo Protein Design (Latest Studies).
13	Single-Cell and Spatial Proteomics Challenges and new strategies in Single-Cell Proteomics (SCoPE2, TMT-16plex/24plex). Spatial Proteomics: Imaging protein distribution within tissue (e.g., IMC/MIBI). (Latest Studies).
14	Clinical Proteomics and Multi-Omics Integration Biomarker Discovery and Applications in Precision Medicine. Multi-Omics Integration of Proteomic, Transcriptomic, and Metabolomic data in Systems Biology. In-Depth Case Studies and Future Trends.
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Dersin Öğrenme Çıktıları

1	Skills Acquired Upon Completion of the Protein Research Methods Course A student who successfully completes this course (Protein Research Methods, Postgraduate Level) will acquire comprehensive and up-to-date skills in both theoretical knowledge and practical application. These competencies are critical for academic careers, R&D laboratories, and the biotechnology/pharmaceutical industry. I. Core Laboratory and Protein Chemistry Skills 1. Protein Purification and Characterization: o Ability to isolate proteins from various sources (cells, tissues) and perform cell lysis. o Proficiency in using chromatographic techniques (Affinity, Ion-Exchange, Size-Exclusion) to purify target proteins with high purity and yield. o Competence in applying SDS-PAGE, Native PAGE, and Western Blotting techniques for purity assessment and molecular weight determination. 2. Quantitative and Qualitative Protein Analysis: o Ability to accurately determine protein concentration and establish standards for experiments. o Proficiency in using immunological techniques to determine protein expression levels and cellular localization.
2	II. Advanced Proteomics and Mass Spectrometry Skills 3. Mass Spectrometry (MS) Competency: o Understanding the basic working principles of MS and comparing different ionization/analyzer types (MALDI, ESI, Orbitrap). o Ability to interpret peptide sequencing (MS/MS) data to identify proteins. o Developing sample preparation and analysis strategies for MS mapping of Post-Translational Modifications (PTMs). 4. Quantitative Proteomics Applications: o Ability to design experiments and measure relative or absolute protein quantities using label-based methods like SILAC, TMT/iTRAQ, and label-free methods like DIA/SWATH-MS. o Making critical decisions during the data acquisition phase of proteomics experiments (DDA vs. DIA).
3	III. Protein Function and Interaction Network Skills 5. Protein Interaction Analysis (Interactomics): o Applying classical methods like Co-IP and Y2H to detect Protein-Protein Interactions (PPIs). o Mapping complex cellular protein interaction networks in a high-throughput manner using AP-MS and especially advanced techniques like Proximity Labeling (TurboID/BioID) (Current and Advanced Skill).
4	IV. Structural Biology and Bioinformatics Skills 6. Proficiency in Structural Biology Methods: o Understanding the principles, advantages, and limitations of X-ray Crystallography and NMR. o Grasping the potential of modern methods like Cryo-Electron Microscopy (Cryo-EM) and Cryo-Electron Tomography (Cryo-ET), and analyzing data from current research articles utilizing these techniques. 7. Bioinformatics and Data Analysis: o Ability to use proteomic software (MaxQuant, Proteome Discoverer, etc.) to process mass spectrometry data and statistically evaluate results. o Competence in predicting protein structures using AI-based tools (like AlphaFold) and evaluating these predictions critically. o Effective use of protein and interaction databases (PDB, UniProt, STRING).
5	Advanced Research and Systems Biology Skills 8. Protein Engineering and Design: o Understanding the principles of Directed Evolution or rational design to engineer proteins with new or improved functions. 9. Grasp of Single-Cell and Spatial Proteomics: o Understanding the challenges and novel methods of Single-Cell Proteomics (SCoPE2) to study cellular heterogeneity at the proteome level. o Understanding the methods to analyze protein distribution within tissue architecture via Spatial Proteomics. 10. Systems Biology and Translational Skills: o Interpreting biological systems holistically by integrating Multi-omics data (genomics, transcriptomics, proteomics). o Knowing how to translate proteomic knowledge into applications for biomarker discovery and Precision Medicine.
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*Dersin Program Yeterliliklerine Katkı Seviyesi

1	Fiziksel kavramları öğrenme ve bu kavramlarla düşünebilme becerisi kazanır.
2	Doğadaki olay ve olguları gözleme, arkasındaki temel ilkeleri anlama ve ilişkilendirme yeteneğini geliştirir.
3	Doğru soruları sormayı ve bu sorulara yanıt verecek deneyleri tasarlama becerisini geliştirir.
4	Deney yapma ve deney sonuçlarını analiz etme ve yorumlama becerisi kazanır.
5	Problemi tanımlama, çözme sonuç çıkarma ve yorumlama becerisi kazanır.
6	Problemin çözümünü zorlaştıran bazı ayrıntıları ihmal ederek, karmaşık ve zor problemleri üstesinden gelinebilir hale getirmek için, idealleştirilmiş model oluşturma becerisi kazanır.
7	Evrende bilinen bütün etkileşmeler (nükleer, gravitasyonel, elektromanyetik) hakkında, mikro ölçekten makro ölçeğe kadar madde ve enerji hakkında bilgi sahibi olur.
8	Tüm mühendislik ve teknolojinin temeli olan fiziğin evrensel ve toplumsal boyutlarda etkilerini anlar.
9	Bilgiye ulaşabilme, analiz edip çözüm geliştirebilme becerisi kazanır.
10	Verinin toplanması, yorumlanması, duyurulması ve uygulanması aşamalarında toplumsal, bilimsel ve etik değerlere sahip olur.
11	Disiplinler arası gruplarda çalışabilme becerisi kazanır.
12	Analitik düşünme, sorgulayıcı ve eleştirel düşünme yeteneğini kazanır.
13	Yaşam boyu öğrenmenin gerekliliği bilinci ve bunu gerçekleştirebilme becerisi kazanır.
14	Etkin iletişim kurma becerisi kazanır.
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Yıldızların sayısı 1’den (en az) 5’e (en fazla) kadar katkı seviyesini ifade eder

Planlanan Öğretim Faaliyetleri, Öğretme Metodları ve AKTS İş Yükü

	Sayısı	Süresi (saat)	Sayı*Süre (saat)
Yüz yüze eğitim	14	3	42
Sınıf dışı ders çalışma süresi (ön çalışma, pekiştirme)	14	2	28
Ödevler	2	6	12
Sunum / Seminer hazırlama	1	2	2
Kısa sınavlar	1	2	2
Ara sınavlara hazırlık	1	10	10
Ara sınavlar	1	2	2
Proje (Yarıyıl ödevi)	1	5	5
Laboratuvar	2	10	20
Arazi çalışması	1	2	2
Yarıyıl sonu sınavına hazırlık	1	20	20
Yarıyıl sonu sınavı	1	2	2
Araştırma	4	10	40
Toplam iş yükü			187
AKTS			7.50

Değerlendirme yöntemleri ve kriterler

Yarıyıl içi değerlendirme	Sayısı	Katkı Yüzdesi
Ara sınav	1	60
Kısa sınav	2	20
Ödev	2	20
Yarıyıl içi toplam		100
Yarıyıl içi değerlendirmelerin başarıya katkı oranı		40
Yarıyıl sonu sınavının başarıya katkı oranı		60
Genel toplam		100

Önerilen Veya Zorunlu Okuma Materyalleri

Ders kitabı	Principles and Techniques of Biochemistry and Molecular Biology Seventh edition Edited by Keith WILSON AND John WALKER
Yardımcı Kaynaklar	INTRODUCTION TO PROTEOMICS, By DANIEL C. LIEBLER, PhD, Humana Press Totowa, NJ

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