The B-Z conformational transition in folded oligodeoxynucleotides: loop size and stability of Z-hairpins

Biochemistry ◽  
1988 ◽  
Vol 27 (17) ◽  
pp. 6327-6331 ◽  
Author(s):  
Luigi Emilio Xodo ◽  
Giorgio Manzini ◽  
Franco Quadrifoglio ◽  
Gijs A. Van der Marel ◽  
Jacques H. Van Boom
Keyword(s):  
Conformational Transition ◽  
Loop Size

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>

scholarly journals Stu2p binds tubulin and undergoes an open-to-closed conformational change

2006 ◽  
Vol 172 (7) ◽  
pp. 1009-1022 ◽  
Author(s):  
Jawdat Al-Bassam ◽  
Mark van Breugel ◽  
Stephen C. Harrison ◽  
Anthony Hyman
Keyword(s):  
Conformational Change ◽  
Conformational Transition ◽  
Budding Yeast ◽  
Microtubule Dynamics ◽  
Open Structure ◽  
Microtubule Associated Proteins ◽  
Associated Proteins ◽  
The Common

Stu2p from budding yeast belongs to the conserved Dis1/XMAP215 family of microtubule-associated proteins (MAPs). The common feature of proteins in this family is the presence of HEAT repeat–containing TOG domains near the NH2 terminus. We have investigated the functions of the two TOG domains of Stu2p in vivo and in vitro. Our data suggest that Stu2p regulates microtubule dynamics through two separate activities. First, Stu2p binds to a single free tubulin heterodimer through its first TOG domain. A large conformational transition in homodimeric Stu2p from an open structure to a closed one accompanies the capture of a single free tubulin heterodimer. Second, Stu2p has the capacity to associate directly with microtubule ends, at least in part, through its second TOG domain. These two properties lead to the stabilization of microtubules in vivo, perhaps by the loading of tubulin dimers at microtubule ends. We suggest that this mechanism of microtubule regulation is a conserved feature of the Dis1/XMAP215 family of MAPs.

scholarly journals DNA Aptamer Functionalized Hydrogels for Interferometric Fiber-Optic Based Continuous Monitoring of Potassium Ions

Biosensors ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 266
Author(s):  
Nataša Žuržul ◽  
Bjørn Torger Stokke
Keyword(s):  
Conformational Transition ◽  
Polymer Network ◽  
Potassium Ion ◽  
Ion Concentration ◽  
Dna Aptamer ◽  
Blood Levels ◽  
Label Free ◽  
Practical Applications ◽  
Hydrogel Matrix ◽  
K Concentration

In the present paper, we describe a potassium sensor based on DNA-aptamer functionalized hydrogel, that is capable of continuous label-free potassium ion (K+) monitoring with potential for in situ application. A hydrogel attached to the end of an optical fiber is designed with di-oligonucleotides grafted to the polymer network that may serve as network junctions in addition to the covalent crosslinks. Specific affinity toward K+ is based on exploiting a particular aptamer that exhibits conformational transition from single-stranded DNA to G-quadruplex formed by the di-oligonucleotide in the presence of K+. Integration of this aptamer into the hydrogel transforms the K+ specific conformational transition to a K+ concentration dependent deswelling of the hydrogel. High-resolution interferometry monitors changes in extent of swelling at 1 Hz and 2 nm resolution for the hydrogel matrix of 50 µm. The developed hydrogel-based biosensor displayed high selectivity for K+ ions in the concentration range up to 10 mM, in the presence of physiological concentrations of Na+. Additionally, the concentration dependent and selective K+ detection demonstrated in the artificial blood buffer environment, both at room and physiological temperatures, suggests substantial potential for practical applications such as monitoring of potassium ion concentration in blood levels in intensive care medicine.

Conformational Transition‐Triggered Disassembly of Therapeutic Peptide Nanomedicine for Tumor Therapy

2021 ◽  
pp. 2100333
Author(s):  
Guo‐Qiao Wang ◽  
Jia Yang ◽  
Da‐Yong Hou ◽  
Rui Zheng ◽  
Muhetaerjiang Mamuti ◽  
...  
Keyword(s):  
Conformational Transition ◽  
Tumor Therapy ◽  
Therapeutic Peptide

scholarly journals Spectroscopic signatures of the T to R conformational transition in the insulin hexamer

1989 ◽  
Vol 264 (32) ◽  
pp. 19081-19085 ◽  
Author(s):  
M Roy ◽  
M L Brader ◽  
R W Lee ◽  
N C Kaarsholm ◽  
J F Hansen ◽  
...  
Keyword(s):  
Conformational Transition ◽  
Spectroscopic Signatures

Hydrophobic interactions in human casein micelle formation: β-casein aggregation

1989 ◽  
Vol 56 (3) ◽  
pp. 427-433 ◽  
Author(s):  
Charles W. Slattery ◽  
Satish M. Sood ◽  
Pat Chang
Keyword(s):  
Light Scattering ◽  
Conformational Transition ◽  
Hydrophobic Interactions ◽  
Micelle Formation ◽  
Tryptophan Fluorescence ◽  
Phosphate Esters ◽  
Casein Micelle ◽  
Protein Association ◽  
P Protein ◽  
Micelle Size

SummaryThe association of non-phosphorylated (0-P) and fully phosphorylated (5-P) human β-caseins was studied by fluorescence spectroscopy and laser light scattering. The tryptophan fluorescence intensity (FI) level increased between 20 and 35 °C, indicating a change in the environment of that residue. A similar transition occurred when ANS was used as a probe. Transition temperatures were slightly lower in 10 mM-CaCl2 but were not affected by an equivalent increase in ionic strength caused by NaCl. The magnitude of the FI change was less for the 5-P than the 0-P protein but was increased for both by CaCl2 addition. These FI data were characteristic of a conformational change and this was supported by fluorescence polarization which indicated that with CaCl2, tryptophan and ANS mobility increased at the transition temperature even though the extent of protein association also increased. Light scattering suggested that protein association proeeeded with the primary formation of submicellar aggregates containing 20–30 monomers which then associated further to form particles of minimum micelle size (12–15 submicelles), and eventually larger. The temperature of precipitation of the 5-P form in the presence of CaCl2 was lower than the conformational transition and suggested that both hydrophobic interactions and Ca bridges between phosphate esters on adjacent molecules are important in micelle formation.

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