4: The Three-Dimensional Structure of Proteins
- Page ID
- 14940
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- 4.2: Secondary Structure and Loops
- The page provides a detailed exploration of secondary structures in proteins, focusing on ??-helices, ??-sheets (parallel and antiparallel), 310 helices, ?? helices, and loops and turns. It explains the roles of hydrogen bonds in stabilizing structures and discusses sequence determinants that influence structural propensities. The text also covers the characteristics and roles of loops, turns, and linkers, and examines amino acid propensities for forming different secondary structures.
- 4.3: Tertiary, Quaternary, and Symmetrical Structures
- The page discusses the fundamentals of biochemistry with a focus on tertiary and quaternary protein structures. Learning goals include distinguishing between tertiary and quaternary protein structures, understanding forces stabilizing tertiary structures, identifying domains and motifs, and exploring protein folding pathways. It also covers analyzing oligomerization, allosteric regulation, structural organization, interpreting structural data, and the impact of mutations on protein structures.
- 4.4: Secondary Structural Motifs and Domains
- The page provides a comprehensive overview of structural motifs and domains in proteins, aimed at biochemistry majors. It covers the differentiation between motifs and domains, recognizing common structural motifs, exploring their evolutionary significance, and the experimental and computational methods to analyze them. The page also discusses protein architecture, with examples like the TIM barrel, Rossmann fold, and beta-propellers.
- 4.5: Protein with Alpha, Alpha-Beta, Beta and Little Secondary Structure
- The page outlines learning goals related to understanding protein structure, emphasizing the classification of proteins based on their secondary structure. It guides students to distinguish between major classes of protein folds, examining the role of ??-helices, ??-sheets, and disordered regions in shaping protein topology and function.
- 4.6: Intrinsically Disordered Proteins
- This page provides a comprehensive overview of Intrinsically Disordered Proteins (IDPs), detailing their characteristics, biological roles, structural dynamics, and relevance in health and disease. IDPs are unique as they lack fixed three-dimensional structures but are involved in crucial cellular functions like molecular recognition and signaling. The page covers the experimental methods for identifying IDPs, evolutionary perspectives, and implications in disease and therapeutics.
- 4.7: Fibrillar Proteins
- The page discusses various fibrillar proteins, focusing on their structure, function, and role in biological systems. It describes different types of fibrillar proteins, such as collagen, ??-keratin, elastin, and fibrinogen, and highlights their structural characteristics, including unique amino acid compositions and hierarchical organizations.
- 4.8: Protein Folding and Unfolding (Denaturation) - Dynamics
- This page provides a comprehensive overview of protein folding, detailing the processes involved, such as thermodynamics driving Gibbs free energy changes, kinetics of folding pathways, and the transition between native, intermediate, and denatured states. It discusses factors influencing protein denaturation, including temperature and chemical denaturants, and the role of molecular chaperones in assisting folding.
- 4.9: Protein Stability - Thermodynamics
- The page delves into protein stability, discussing the balance between folding and unfolding dynamics influenced by thermodynamic factors. Key forces like hydrogen bonds, ion pairs, van der Waals forces, and the hydrophobic effect affect protein stability. It highlights experimental approaches, such as site-directed mutagenesis, to study these forces. Environmental factors, such as pH and temperature, also influence protein behavior.
- 4.10: Protein Aggregates - Amyloids, Prions and Intracellular Granules
- This comprehensive biochemistry resource outlines the intricate processes leading to protein aggregation and their implications in diseases. It covers amyloid, prion, and protein aggregation types, the mechanisms of amyloid formation, and their connection to neurodegenerative illnesses like Alzheimer's and Parkinson's.
- 4.11: Biomolecular Visualization - Conceptions and Misconceptions
- The page discusses the importance of visualization tools in biochemistry for interpreting biomolecular structures. It emphasizes the role of visualization in understanding molecular geometry, interactions, and functions while acknowledging the limitations and potential misconceptions it may introduce. The text explores common representation styles (e.g.
- 4.12: Laboratory Determination of the Thermodynamic Parameters for Protein Denaturation
- The page offers a detailed exploration of protein denaturation, highlighting the key thermodynamic parameters such as ??G, ??H, and ??S that are central to understanding protein stability. It covers experimental techniques like UV and fluorescence for measuring denaturation, and describes how to interpret denaturation curves to calculate the standard free energy of unfolding.
- 4.13: Predicting Structure and Function of Biomolecules Through Natural Language Processing Tools
- The page discusses the integration of natural language processing (NLP) and machine learning techniques for understanding and predicting protein structures and functions, focusing on protein language models (pLMs) like AlphaFold. It explains key concepts like transformers, attention mechanisms, and tokenization, and explores applications in protein structure and function prediction, protein-protein interactions, and protein sequence generation.
- 4.14: Predicting Structure from Sequence and Sequence from Structure/Function (New 10/24)
- The document describes advancements in biochemistry, particularly the use of machine learning and AI in predicting and designing protein structures. It outlines learning goals for understanding and utilizing computational tools such as AlphaFold and RoseTTAFold for protein structure prediction, analyzing sequence alignments, integrating experimental data with computational models, and evaluating model quality.