select topics in biophysics
 

Biophysical Mechanisms

Biomedicine

  • HHMI’s BioInteractive.  Educational site for middle school to college/university level with information on cancer, neuroscience, biological clocks, infectious diseases, DNA & RNA, etc., generated and maintained by the Howard Hughes Medical Institute.

 

 

Electrical Behavior of Cells

 

 

Energy Transduction in Membranes (Edited by W.A. Cramer)

 

 

Protein Function

 

 

Membrane Behavior

  • Surface Charge. Gerald Ehrenstein. Previously published in Biophysics Textbook Online.

 

 

Muscle Contraction and Cell Motility

  • Biochemistry of Muscle Contraction.  Description of the mechanisms and physiology of muscle contraction.  Site generated and maintained by Michael Barany and Kate Barany, University of Illinois at Chicago.

  • The Myosin Home Page.  Hosted by the Myosin Group at the MRC Laboratory of Molecular Biology and the Cambridge Institute for Medical Research

 

 

Protein Folding

  • Folding@Home Distributed Computing Project.  “Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.  We use novel computational methods and large scale distributed computing, to simulat timescales thousands to millions of times longer than previously achieved.”  This site provides information about protein folding and its importance and provides software for personal computers that allows individuals to participate in the protein folding computing process.

 

 

Sensation

  • Promenade Round the Cochlea.  A delightful educational site with excellent graphics on the physiology and biophysics of the ear; generated and maintained by the University of Montpellier.

 

 

Molecular Structure & Behavior

 

Proteins

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

 

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.

 

Structure of Membrane 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. 

     

     

     

Nucleic Acids

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.

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    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).

       

       

    Carbohydrates

    • 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.) 

     

     

    Lipids & Membranes

    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. 

      • 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

     
    Membrane Proteins

     

     

    Macromolecular Complexes

      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).

     

     

    Metabolic Pathways

  • 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.

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    Molecular Behavior

    • Molecules in Action.  Christopher Miller. Previously published in the Biophysics Textbook Online (BTOL).

     

     

    Biophysical Techniques

    Much biophysical research involves either the development of novel techniques to investigate the structure, properties, and biological functions of biomolecules or the application of these techniques to monitor how the structure and dynamics of biomolecules enables specific biological functions.  Information about specific biophysical techniques is provided here.

    Electrophysiology

    • The Axon Guide for Electrophysiology & Biophysics is a practical laboratory guide covering a broad range of topics, from the biological basis of bioelectricity and a description of the basic experimental setup, to the principles of operation of the most advanced hardware and software currently available.”  Generated and maintained by Axon Instruments, Inc.


    Hydrodynamics 

      The behavior of large biomolecules—proteins, carbohydrates, and nucleic acids—in solution is complex and directly related to molecular size, shape, and flexibility; the analysis of hydrodynamic behavior thus provides important information about the structure, dynamics, and interactions of biomacromolecules.
       
    • Survey of Biomolecular Hydrodymamics.  Victor Bloomfield. Previously published in Biophysics Textbook Online (BTOL)


    Microscopy & Imaging

    Perhaps the most accessible developments in biophysics have involved improvements in our ability to generate images of cellular and molecular structures with dimensions from microns to nanometers.  It is now possible to “see” individual molecules or cellular structures using atomic force, electron, or confocal fluorescence microscopy.
     
  • Molecular Expressions: Exploring the World of Optics and Microscopy. A delightful and extensive site appropriate for middle school to college/university levels containing a photogallery of microscopic images, a detailed primer on the basics of optical microscopy, as well as historical and educational information on optical microscopy.  Generated and maintained by the National High Field Magnet Laboratory at Florida State University.
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    Confocal Fluorescence Microscopy
      • Nikon Microscopy U.  An extensive and well-organized site with information on the fundamentals of confocal fluorescence microscopy and its applications to biological systems. Content provided by various experts and site maintained by Nikon USA. 
     
    Atomic Force Microscopy
      • Atomic Force Microscopy. Measuring Intermolecular Interaction Forces.  A primer on the fundamentals and applications of AFM by David Baselt.
      • NanoTheatre. Gallery of images generated by Digital Instruments atomic force microscopes; site maintained by Vecco, Inc. (manufacturer of DI atomic force microscopes).
     
    Magnetic Resonance Imaging
      • Magnetic Resonance Imaging.  Information on the biophysical foundations and medical applications of one of the most versatile of medical imaging tools; provided as part of the Breakthroughs in Science series of FASEB, the Federation of American Societies for Experimental Biology.


    Modeling & Simulation

      Visual and numerical modeling and simulation play important roles in the analysis and prediction of protein and nucleic acid sequence and 3D structure, in the calculation of molecular dynamics, and in the simulation of specific biochemical mechanisms, among other important tasks. 
       
    • Protein Structure Prediction From Primary Sequence.  Linda Ellis and Kim-Hung Chow. Previously published in Biophysics Textbook Online (BTOL).
    • Berkeley Madonna is a fast, easy to use mathematical model building program that runs on both Windows and Mac OS.  Using ordinary math notation, it provides numerical solutions to differential/difference equations together with a number of devices for analyzing results without any programming input from the user.  Developed on the Berkeley campus under the sponsorship of NSF and NIH, it is currently used by academic and commercial institutions for both research and teaching.  A visual tour of the program as well as a demo version can be downloaded from the web site 


    Single Molecule Techniques

      Perhaps the most exciting development in biophysical technique in recent times involves the ability to manipulate single molecules and measure their properties and biological functions both in solution and within cells. 
       
    • Molecules in Action.  Christopher Miller. Previously published in Biophysics Textbook Online (BTOL).
     
    Spectroscopy
    The interaction of electromagnetic radiation, x-rays, ultraviolet, visible, and infra red light, and radio waves, with molecules provides a wealth of information about the structure, dynamics, and function of biomolecules and biological processes. 

    Fluorescence

      • Molecular Probes, Inc. is the major commercial source for fluorescent probes and diagnostic reagents.  Their website provides spectroscopic data on a wide variety of molecular probes (with access to an extensive bibliography of biophysical applications), information about fluorescence techniques, as well as other resources for optical biophysics research. 
     
    Magnetic Resonance
      • Fluorine NMR. J.T. Gerig. Previously published in Biophysics Textbook Online (BTOL).
     
    Thermodynamics & Related Topics


     


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