Structural Principles

• The Protein Data Bank provides a wealth of information on the structure, synthesis, and function of biological macromolecules at their education page.Content is suitable for students from middle school (advanced elementary) to college/university.

• Primary Structure, Secondary Motifs, Tertiary Architecture And Quaternary Organization. Jannette Carey and Vanessa Hanley. 

Proteins are organized in a hierarchy of structures including primary structure (the amino acid sequence), secondary structure (a-helix and b-sheet), tertiary architecture (the specific atomic structure), and quaternary organization (arrangement of distinct polypeptide chains).  Previously published in the Biophysics Textbook Online (BTOL).

 
Protein Sequences

UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.


 

• The UniProt/Swiss-Prot Protein Knowledgebase is an annotated protein sequence database established in 1986.

Protein Structures

Protein Data Bank.  The PDB is “the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data”, providing access to images of 3-D structures and atomic coordinates for all published protein and nucleic acid X-ray crystal and NMR solution structures.  It is operated and maintained by Rutgers, The State University of New Jersey, the San Diego Supercomputer Center of the University of California—San Diego, and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology.

• PDBsum is “a database of the 3D structures of known proteins and nucleic acids” maintained by the Department of Biochemistry and Molecular Biology, University College, London.

• The Protein Information Resource is “an integrated public resource of protein informatics to support genomic and proteomic research and scientific discovery” maintained by the Georgetown University Medical Center.

• The GenBank Entrez Protein website is a protein information search and retrieval system maintained by the National Center for Biotechnology Information (NCBI). 

• Jena Image Library of Biological Macromolecules

 

Structure of Membrane Proteins

Membrane Protein Structure. Suzanne Scarlata. Proteins embedded in the lipid bilayers of biological membranes are subject to special physical constraints that influence their 3D structure.  An explanation of these principles is provided here. Previously published in the Biophysics Textbook Online (BTOL).

• A listing membrane proteins of known 3D structure is maintained by the laboratory of Stephen White, University of California—Irvine. The principles governing the assembly and energetics of proteins in biological membranes and the hydrophobicity of membrane proteins are outlined in websites maintained by the laboratory of Dr. Stephen White, University of California—Irvine. 

Assembly of membrane proteins

Energetics of interaction of proteins with membranes

Hydrophobicity of proteins

 

Behavior of Proteins

Protein-Protein Interactions.  Catherine Royer. Outline of the thermodynamic and structural principles governing the ways that proteins interact with other proteins. Previously published in the Biophysics Textbook Online (BTOL).

• Structural Symmetry and Protein Function. David S. Goodsell and Arthur J. Olson. Many cellular proteins are composite structures consisting of two or more associated polypeptides. A description of the principles governing the symmetry of these complexes is described at the following site. 
 

Structural Principles

The Protein Data Bank provides a wealth of information on the structure, synthesis, and function of biological macromolecules.  Content is designed for students from middle school (advanced elementary) up to college/university level.

 
Nucleic Acid Sequences

Genbank is the NCBI database for gene sequences.  “Established in 1988 as a national resource for molecular biology information, NCBI (the National Center for Biotechnology Information) creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.” 

• EMBL-Bank.  “The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource.” 

 

Nucleic Acid Structures

The Protein Data Bank (PDB) is “the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data”, providing access to images of 3-D structures and atomic coordinates for all published nucleic acid and protein X-ray crystal and NMR solution structures.  It is operated and maintained by Rutgers, The State University of New Jersey, the San Diego Supercomputer Center of the University of California—San Diego, and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology. 

 
Behavior of Nucleic Acids

DNA Condensation.  Victor Bloomfield. DNA molecules are often considerably longer than the largest dimension of the cell and must thus condense into compact structures within the chromosomes of cells.  Previously published in the Biophysics Textbook Online (BTOL).

• Circular DNA.  Alexander Vologodskii. Some DNA molecules form closed circular structures that exhibit complex behavior related to variations in extent of internal twisting present in the molecules.  Previously published in the Biophysics Textbook Online (BTOL).
 

• The sugars and polysaccharides found in cells and organisms are complex and diverse.  The structures of many carbohydrates are available at the following website.  (This site is no longer updated regularly.) 

Lipid Structures

• The Lipid Data Bank provides information about the molecular structures, phases and phase transition temperatures, miscibility and phase diagrams, and critical micelle concentrations of biological lipids. 

• Data on the crystal structures of membrane lipids are available at a site hosted by the Department of Biochemistry, U of Missouri. 

• The Lipid Bank for the Web, operated by the Japanese Conference on the Biochemistry of Lipids, provides information on the properties of biological lipids. 

Membrane Structures

The principles governing the structures of biological membrane are outlined in a website maintained by the laboratory of Dr. Stephen White, University of California—Irvine.

 
Membrane Proteins

• The principles governing the assembly and energetics of proteins in biological membranes and the hydrophobicity of membrane proteins are outlined in a website maintained by the laboratory of Dr. Stephen White, University of California—Irvine.

 

Assembly of Membrane Proteins

Energetics of interaction of proteins with membranes

Hydrophobicity of proteins

Proteins, nucleic acids, and other biological molecules can self-assemble into complex, often large macromolecular structures such as filaments, chromosomes, and ribosomes.  Information on select macromolecular complexes is provided below.
 
• Actin filaments.  Paul Janmey

Actin filaments are major structural elements of cells and play essential roles in muscle contraction and cell motility. Previously published in the Biophysics Textbook Online (BTOL).
 

The International Union of Biochemistry and Molecular Biology supports a website that makes Nicholson Minimaps of the metabolic pathways available in a variety of file formats.  These metabolic pathways charts were developed by Dr. Donald Nicholson, Department of Biochemistry and Molecular Biology, The University, Leeds, England. 

KEGG Pathways Database.  “Current knowledge on molecular interaction networks, including metabolic pathways, regulatory pathways, and molecular complexes.”  Generated and maintained by the Kyoto Encyclopedia of Genes and Genomics.