Structure and Dynamics of Confined Polymers

Polymers are essential to biology because they can have enough stable degrees of freedom to store the molecular code of heredity and to express the sequences needed to manufacture new molecules. Through these they perform or control virtually every function in life. Although some biopolymers are created and spend their entire career in the relatively large free space inside cells or organelles, many biopolymers must migrate through a narrow passageway to get to their targeted destination. This suggests the questions: How does confining a polymer affect its behavior and function? What does that tell us about the interactions between the monomers that comprise the polymer and the molecules that confine it? Can we design and build devices that mimic the functions of these nanoscale systems? The NATO Advanced Research Workshop brought together for four days in Bikal, Hungary over forty experts in experimental and theoretical biophysics, molecular biology, biophysical chemistry, and biochemistry interested in these questions. Their papers collected in this book provide insight on biological processes involving confinement and form a basis for new biotechnological applications using polymers. In his paper Edmund DiMarzio asks: What is so special about polymers? Why are polymers so prevalent in living things? The chemist says the reason is that a protein made of N amino acids can have any of 20 different kinds at each position along the chain, resulting in 20 N different polymers, and that the complexity of life lies in this variety.

Inhalt

Preface. Contributing Authors. Workshop Participants. Profound implications for biophysics of the polymer threading a membrane transition; E.A. DiMarzio. Phage DNA transport across membranes; L. Letellier. Translocation of macromolecules across membranes and through aqueous channels: Translocation across membranes; S.M. Simon. Protein translocation across the outer membrane of mitochondria: Structure and function of the TOM complex of Neurospora crassa; S. Nussberger, W. Neupert. Protein translocation channels in mitochondria: TIM & TOM channels; K.W. Kinnally. Sizing channels with neutral polymers; O.V. Krasilnikov. Dynamic partitioning of neutral polymers into a single ion channel; S.M. Bezrukov, J.J. Kazianowicz. Branched polymers inside nanoscale pores; C. Gay, et al. Physics of DNA threading through a nanometer pore and applications to simultaneous multianalyte sensing; J.J. Kasianowicz, et al. Mechanism of ionic current blockades during polymer transport through pores of nanometer dimensions; D.W. Deamer, et al. Using nanopores to discriminate between single molecules of DNA; D. Branton, A. Meller. Use of a nanoscale pore to read short segments within single polynucleotide molecules; M.A. Akeson, et al. Polymer dynamics in microporous media; B. Åkerman. Entropic barrier theory of polymer translocation; M. Muthukumar. Polymer translocation through a 'complicated' pore; D.K. Lubensky. The polymer barrier crossing problem; W. Sung, P. Jun Park. Brownian tatchets and their application to biological transport processes and macromolecular separation; I. Derényi, R.D. Astumian. Composition and structural dynamics of vertebrate striated muscle thick filaments Role of myosin-associated proteins; Z.A. Podlubnaya. Force-driven folding and unfoldingtransitions in single polymer strand manipulation; M.S.Z. Kellermayer, et al. Dynamics of actin filaments in motility assays. A microscopic model and its numerical simulation; Z. Farkas, et al. Conformation-dependent sequence design of copolymers. Example of bio-evolution mimetics approach; A.R. Khokhlov, et al. Single molecule nucleic acid analysis by fluorescence flow cytometry; P.M. Goodwin, et al. Fluorescence energy transfer reagents for DNA sequencing and analysis. High throughout fluorescent DNA; J. Ju. Index.