Biothermodynamics, Part C

In the past several years, there has been an explosion in the ability of biologists, molecular biologists and biochemists to collect vast amounts of data on their systems. Biothermodynamics, Part C presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions.

The use of thermodynamics in biological research is used as an "energy book-keeping system.” While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the sources of energy that drive the function? Which of the pathways are of biological significance?

As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions will continue to expand as well.

In the past several years, there has been an explosion in the ability of biologists, molecular biologists and biochemists to collect vast amounts of data on their systems. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions.The use of thermodynamics in biological research is used as an energy book-keeping system. While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the sources of energy that drive the function? Which of the pathways are of biological significance? As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions will continue to expand as well.

1. Measurement and Analysis of Equilibrium Binding Titrations: A beginner's guide

Dorothy Beckett

2. Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule - Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs

Wlodzimierz Bujalowski and Maria J. Jezewska

3. Analysis of PKR-RNA interactions by sedimentation velocity

C. Jason Wong, Katherine Launer-Felty and James L. Cole

4. Structural and Thermodynamic Analysis of PDZ/Ligand Interactions

Tyson R. Shepherd and Ernesto J. Fuentes

5. Thermodynamic analysis of metal ion-induced protein assembly

Andrew B. Herr and Deborah G. Conrady

6. Thermodynamic Dissection of Colicin Interactions

Nicholas G Housden and Colin Kleanthous

7. Energetics of Src homology domain interactions in receptor tyrosine kinase-mediated signaling

John E. Ladbury and Stefan T. Arold

8. Structural and Functional Energetic Linkages in Allosteric Regulation of Muscle Pyruvate Kinase

J. Ching Lee and Petr Herman

9. Analysis of Free Energy versus Temperature Curves in Protein Folding and Macromolecular Interactions

Vince J. LiCata and Chin-Chi Liu

10. Application of the Sequential n-Step Kinetic Mechanism to Polypeptide Translocases

Aaron L. Lucius_, Justin M. Miller and Burki Rajendar

11. A Coupled Equilibrium Approach to Study Nucleosome Thermodynamics

Andrew J. Andrews and Karolin Luger

12. Quantitative methods for measuring DNA flexibility in vitro and in vivo

Justin P. Peters, Nicole Becker, Emily M. Rueter, Zeljko Bajzer, Jason D. Kahna and L. James Maher

13. A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands

Hui-Ting Lee, Caroline Carr, Hollie Siebler, Lela Waters, Irine Khutsishvili, Fany Iseka, Brian Domack, Chris M. Olsen, and Luis Marky

14. Thermodynamics of Biological Processes

Hernan G. Garcia, Jane Kondev, Nigel Orme, Julie Theriot and Rob Phillips

15. Protein stability in the presence of co-solutes

Luis Marcelo F. Holthauzen, Matthew Auton, Mikhail Sineva and Jorg Rosgen

16. Small Angle X-ray Scattering Studies of Peptide-Lipid Interactions using the Mouse Paneth Cell a-Defensin Cryptdin-4

Abhijit Mishra, Kenneth P. Tai, Nathan W. Schmidt, André J. Ouellette and Gerard C. L. Wong

17. Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery

Rebecca Strawn, Thomas Stockner, Milan Melichercik, Lihua Jin, Wei-Feng Xue, Jannette Carey and Rüdiger Ettrich

18. Using tryptophan fluorescence to measure the stability of membrane proteins folded in liposomes

C. Preston Moon1 and Karen G. Fleming

19. Non-B Conformations of CAG Repeats Using 2-aminopurine

Natalya N. Degtyareva and Jeffrey T. Petty

20. Disulfide bond-mediated passenger domain stalling as a structural probe of autotransporter outer membrane secretion in vivo

Jonathan P. Renn & Patricia L. Clark

21. Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native State: Application to the LID Domain of Adenylate Kinase from Escherichia coli

Travis P. Schrank, W. Austin Elam, Jing Li and Vincent J. Hilser