Proteins: Biogenesis to Degradation

General

• Biochemistry Online: An Approach Based on Chemical Logic - Biochemistry within the framework of chemical principles and logic. (Henry Jakubowski, College of St. Benedict/St. John's University)
  • Composition, Sequence and Conformational Analysis of Proteins
  • Laboratory Determination of ΔG° for Protein Folding/Unfolding
  • A Model Binding System: Myoglobin. Hemoglobin, and Dioxygen
  • Reversible Binding I: Equations and Curves
  • Reversible Binding II: Experimental Binding Curves, K_d, and Error Analysis
  • Protein Folding - in vivo and in vitro
  • Protein Structure: What's New? Protein Aggregates - Not Junk Anymore
  • The Structure and Property of Amino Acids
  • Thermodynamics and IMFs in Protein Stability
  • Understanding Protein Conformation
• The Medical Biochemistry Page - An excellent biochemistry tutorial with information on a broad range of biochemical pathways. (Michael W. King, Indiana University School of Medicine)
  • Basic Chemistry of Biomolecules
  • Hemoglobin and Myoglobin
  • Ionic Equilibria Review
  • Protein Structure
  • Thermodynamics Review
• The Online Macromolecular Museum - A site for the display and study of macromolecular structures, as determined by crystallographic or NMR methods, including proteins and protein complexes. (California Lutheran University)
• Wikipedia - Free online encyclopedia with basic overviews. (Beginner's Level)
• Protein Idenfitication and Sequencing Using Mass Spectrometry Data - Slide-based lesson covering the use of MALDI-TOF, tandem MS, etc. in protein science.
  • Protein
  • Protein Folding
  • Protein Targeting
  • Proteome
  • Proteomics

See also the Chemical Biology, Enzymes, Metabolism, Cellular Respiration and Photosynthesis and Structural Biology pages.

Post-Translational Modification

• The Medical Biochemistry Page - An excellent biochemistry tutorial with information on a broad range of biochemical pathways. (Michael W. King, Indiana University School of Medicine)
  • Glycoprotein Synthesis
  • Lipoproteins
  • Post-Translational Modification
• PhosphoSitePlus - A site "devoted to commonly studied protein post-translational modifications."
• Wikipedia - Free online encyclopedia with basic overviews. (Beginner's Level)
  • Post-Translational Modification
    • Acetylation
    • Glycosylation
    • GPI Anchor
    • Phosphorylation

See also the Carbohydrates and Glycosylation page for more information on protein glycosylation and the Structure and Function Prediction Servers section of the Structural Biology page for post-translational modification and other sequence-based prediction servers.

Protein Folding and Unfolding

• The Chaperonin Home Page - A repository for information about the chaperonin class of heat shock proteins (GroEL and GroEL).
• Unraveling the Mystery of Protein Folding - Basic introduction to the protein folding problem in PDF format. (W.A. Thomasson) (Just above Beginner's Level)

Protein Sorting, Targeting and Secretion

• Genes Involved in Protein Targeting, Asymmetric Cell Division, Apical/Basal Polarity - From The Interactive Fly: Evolutionarily Conserved Pathways. (Society for Developmental Biology)
• Kimball's Biology Pages: Protein Kinesis - Outline of protein targeting, especially secretory pathway. (Beginner's Level)
• SRPDB (Signal Recognition Particle Database) "provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP."

Membrane Proteins

• Human ATP-Binding Cassette Transporters - Links to nucleic acid and protein database references to human ABC transporters. (M. Müller, University of Groningen, The Netherlands)
• Membrane Protein Libraries (John Ward, University of Minnesota)
  • Arabidopsis Membrane Protein Library
  • Rice Membrane Protein Library
  • Drosophila Membrane Protein Library
  • Yeast Membrane Protein Library
  • C. elegans Membrane Protein Library
  • Human Membrane Protein Library
  • S. pombe Membrane Protein Library
• Inventory, Assembly and Analysis of Bacillus subtilis ABC Transport Systems - An inventory of the ABC transporter systems in the complete genome of Bacillus subtilis. (Gwennaele Fichant, Yves Quentin and François Denizot)
• Ion Channel Web Links - List of resources devoted to ion channel research.
• Membrane Proteins of Known 3-D Structure - List of membrane proteins whose three-dimensional structure has been solved by crystallography. (White Lab, University of California, Irvine)
• Orientation of Proteins in Membranes (OPM) Database - A database of membrane-associated proteins with known structure, providing proteins' spatial arrangement relative to the membrane.
• Wikipedia - Free online encyclopedia with basic overviews. (Beginner's Level)
  • Integral Membrane Protein
  • Peripheral Membrane Protein
  • Transmembrane Protein

Protein Degradation

• Lysosomal Proteolysis - An introduction to protein degradation in the lysosome with diagrams and images of lysosomes. (Emory University)
• Prolysis - Information on proteases, including the proteasome, and protease inhibitors.
• Protein Degradation Resource - Information on cytosolic and lysosomal protein degradation pathways.
• The Ubiquitin System for Protein Modification and Degradation - A broad range of information on the ubiquitin/proteasome pathway.

Protein Classes and Families

• The AAA Server - Information and databases on proteins of this proposed protein superfamily (AAA for ATPases Associated with various cellular Activities), which includes a range of proteins involved in processes such as cell cycle regulation, vesicular transport, mitochondrial function, peroxisome assembly and proteolysis (for instance, certain subunits of the 26S proteasome and metalloproteases). (University of Graz, Austria)
• MEROPS Database: Peptidase Clans and Families - Proteases classified into families, clans, and catalytic type based on structural similarities, with links to major database entries. (Wellcome Trust Sanger Institute, Cambridge, UK)
• Protein Domain Database - "The ProDom protein domain database consists of an automatic compilation of homologous domains." (Jerôme Gouzy and Florence Corpet, ProDom Team, Toulouse, France)
• Pfam - "Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families." (Sanger Institute, UK)

Protein and Proteomics Databases

Enzyme Databases (Collections of Enzyme Functional and Nomenclature Data)

Macromolecular Structure Databases

Discussion Groups

• Usenet newsgroup archives from BIOSCI/bionet (can also be accessed through Google Groups: bionet):
  • FLUORESCENT-PROTEINS/bionet.molbio.proteins.fluorescent - Research on fluorescent proteins and bioluminescence.
  • PEPTIDES/bionet.molecules.peptides - Research involving peptides.
  • PROTEINS/bionet.molbio.proteins - Research on proteins and protein databases.
  • PROTEIN-ANALYSIS/bionet.molbio.proteins - Protein analysis.

See also the Discussion Groups section of the General Resources and Tutorials page.

Labs Studying Aspects of Protein Biogenesis or Degradation