Viscosimetric study of poly(2',5'-dialkyl-p-terphenylene terephthalate): statistical segment length and conformational transition

1993 ◽  
Vol 26 (20) ◽  
pp. 5457-5460 ◽  
Author(s):  
J. K. Kallitsis ◽  
K. Gravalos ◽  
A. Dondos
Keyword(s):  
Conformational Transition ◽  
Segment Length ◽  
Statistical Segment

scholarly journals The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics

2018 ◽  
Vol 140 (2) ◽  
Author(s):  
Kevin D. Dorfman
Keyword(s):  
Genome Mapping ◽  
Persistence Length ◽  
Magnetic Tweezers ◽  
Polymer Physics ◽  
Polymer Dynamics ◽  
Segment Length ◽  
Next Generation ◽  
Bending Energy ◽  
Force Microscopy ◽  
Statistical Segment

The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.

Correlation of binary polyolefin phase behavior with statistical segment length asymmetry

1992 ◽  
Vol 25 (20) ◽  
pp. 5547-5550 ◽  
Author(s):  
Frank S. Bates ◽  
Mark F. Schulz ◽  
Jeffrey H. Rosedale ◽  
Kristoffer Almdal
Keyword(s):  
Phase Behavior ◽  
Segment Length ◽  
Statistical Segment

A new approach to the determination of the statistical segment length of wormlike polymers

1995 ◽  
Vol 273 (7) ◽  
pp. 626-632 ◽  
Author(s):  
A. Dondos ◽  
G. Staikos
Keyword(s):  
Segment Length ◽  
New Approach ◽  
Statistical Segment

Treating the polyelectrolytes as polymers with a draining effect. I. The statistical segment length

2004 ◽  
Vol 42 (23) ◽  
pp. 4225-4229 ◽  
Author(s):  
Anastasios Dondos
Keyword(s):  
Segment Length ◽  
Statistical Segment

Viscometric determination of the statistical segment length of wormlike polymers

Polymer ◽  
1998 ◽  
Vol 39 (17) ◽  
pp. 4155-4158 ◽  
Author(s):  
C. Gans ◽  
J. Schnee ◽  
U. Scherf ◽  
G. Staikos ◽  
E. Pierri ◽  
...  
Keyword(s):  
Segment Length ◽  
Statistical Segment

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Proton Release ◽  
Intrinsic Resistance ◽  
Constant Ph ◽  
Wide Range ◽  
Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

Sign in / Sign up

Export Citation Format

Share Document