Abstract:
:Combining an azobenzene chromophore with the bis-cysteinyl active-site sequence of the protein disulfide isomerase (PDI) we constructed a simple but promising model for allosteric conformational rearrangements. Paralleling cellular signaling events, an external trigger, here absorption of a photon, leads to a structural change in one part of the molecule, namely the azobenzene-based chromophore. The change in geometry translates to the effector site, in our case the peptide sequence, where it modifies covalent and nonbonded interactions and thus leads to a conformational rearrangement. NMR spectroscopy showed that the trans-azo and cis-azo isomer of the cyclic PDI peptide exhibit different, but well-defined structures when the two cystine residues form a disulfide bridge. Without this intramolecular cross-link conformationally more variable structural ensembles are obtained that again differ for the two isomeric states. Ultrafast UV/Vis spectroscopy confirmed that the rapid isomerization of azobenzene is not significantly slowed down when incorporated into the cyclic peptides, although the amplitudes of ballistic and diffusive pathways are changed. The observation that most of the energy of an absorbed photon is dissipated to the solvent in the first few picoseconds when the actual azo-isomerization takes place is important. The conformational rearrangement is weakly driven due to the absence of appreciable excess energy and can be described as biased diffusion similar to natural processes.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Löweneck M,Milbradt AG,Root C,Satzger H,Zinth W,Moroder L,Renner Cdoi
10.1529/biophysj.105.067363subject
Has Abstractpub_date
2006-03-15 00:00:00pages
2099-108issue
6eissn
0006-3495issn
1542-0086pii
S0006-3495(06)72394-3journal_volume
90pub_type
杂志文章abstract::The origin of Ibetanull, the Ca2+ current of myotubes from mice lacking the skeletal dihydropyridine receptor (DHPR) beta1a subunit, was investigated. The density of Ibetanull was similar to that of Idys, the Ca2+ current of myotubes from dysgenic mice lacking the skeletal DHPR alpha1S subunit (-0.6 +/- 0.1 and -0.7 +...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77507-1
更新日期:1998-07-01 00:00:00
abstract::A method for combining calculations of residue pKa's with changes in the position of polar hydrogens has been developed. The Boltzmann distributions of proton positions in hydroxyls and neutral titratable residues are found in the same Monte Carlo sampling procedure that determines the amino acid ionization states at ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78851-9
更新日期:1997-05-01 00:00:00
abstract::When a dissolved macromolecule is in chemical equilibrium with a free ionic species, the charge configuration, and hence the dipole vector, of the macromolecule is fluctuating. Expressions for the static dielectric constant and the relaxation spectrum of such a mixture are here derived in terms of the components of th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(65)86740-6
更新日期:1965-09-01 00:00:00
abstract::Atomic force microscopy (AFM) can be used to probe the mechanics of molecular recognition between surfaces. In the application known as "chemical force" microscopy (CFM), a chemically modified AFM tip probes a surface through chemical recognition. When modified with a biological ligand or receptor, the AFM tip can dis...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77447-3
更新日期:1999-06-01 00:00:00
abstract::CLC anion channels are homodimeric proteins. Each subunit is comprised of 18 α-helices designated "A-R" and an intracellular carboxy-terminus containing two cystathionine-β-synthase (CBS1 and CBS2) domains. Conformational coupling between membrane and intracellular domains via poorly understood mechanisms is required ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.09.037
更新日期:2016-11-01 00:00:00
abstract::Many studies of specific protein-nucleic acid binding use short oligonucleotides or restriction fragments, in part to minimize the potential for nonspecific binding of the protein. However, when the specificity ratio is low, multiple nonspecifically bound proteins may occupy the region of DNA corresponding to one spec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75847-X
更新日期:2001-10-01 00:00:00
abstract::FKBP12 was removed from ryanodine receptors (RyRs) by incubation of rabbit skeletal muscle terminal cisternae membranes with rapamycin. The extent of FKBP12 removal was estimated by immunostaining Western blots of terminal cisternae proteins. Single FKBP12-depleted RyR channels, incorporated into planar lipid bilayers...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78654-5
更新日期:1997-01-01 00:00:00
abstract::We study the lateral headgroup interactions among phosphatidylcholine (PC) molecules and among phosphatidylethanolamine (PE) molecules in monolayers and extend our previous models. In this paper, we present an extensive set of pressure-area isotherms and surface potential experiments on monolayers of phospholipids ran...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81964-1
更新日期:1992-06-01 00:00:00
abstract::The mathematics of the binomial model for quantal neurotransmitter release is considered in general terms, to explore what information might be extractable from statistical aspects of data. For an array of N statistically independent release sites, each with a release probability p, the compound binomial always pertai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(97)78709-5
更新日期:1997-02-01 00:00:00
abstract::Motor enzymes use energy from ATP dephosphorylation to generate movement by a mechanical cycle, moving and pushing in one direction while attached to their cytoskeletal substrate, and recovering by moving relative to their substrate to a new attachment site. Mainstream models assert that movement while attached to the...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78126-8
更新日期:1997-08-01 00:00:00
abstract::Small RNA-mRNA binding is an essential step in RNA interference, an important cellular regulatory process. Calculations of binding free energy have been used in binding site prediction, but the cost of stretching the mRNA loop when the small RNA-mRNA duplex forms requires further exploration. Here, using both polymer ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.12.017
更新日期:2013-01-22 00:00:00
abstract::Individual ion activities were calculated for Ca(2+) in pure solutions of CaCl(2) and in mixtures of CaCl(2) with MgCl(2) and with NaCl, using different conventions to obtain gamma(Ca2+). The results were compared with potentiometric measurements, using calcium specific electrodes. It is found that significant differe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(68)86528-2
更新日期:1968-08-01 00:00:00
abstract::Nonphotochemical quenching is the protective mechanism against overexcitation of photosystem II, triggered by excess ΔpH in photosynthetic membranes. The light-harvesting complexes (LHCs), the de-epoxidation of violaxanthin to zeaxanthin, and the photosystem II subunit S (PsbS) work in synergy for an optimized multile...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.09.034
更新日期:2017-12-05 00:00:00
abstract::Efficient and rapid immune response upon challenge by an infectious agent is vital to host defense. The encounter of leukocytes (white blood cells of the immune system) with their targets is the first step in this response. Analysis of the kinetics of this process is essential not only to understanding dynamic behavio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82620-5
更新日期:1990-05-01 00:00:00
abstract::The sorting of lipids and proteins in cellular trafficking pathways is a process of central importance in maintaining compartmentalization in eukaryotic cells. However, the mechanisms behind these sorting phenomena are currently far from being understood. Among several mechanistic suggestions, membrane curvature has b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.11.067
更新日期:2009-04-08 00:00:00
abstract::The molecular code of specific DNA recognition by proteins as a paradigm in molecular biology remains an unsolved puzzle primarily because of the subtle interplay between direct protein-DNA interaction and the indirect contribution from water and ions. Transformation of the nonspecific, low affinity complex to a speci...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.063263
更新日期:2005-08-01 00:00:00
abstract::Topical microbicide products are being developed for the prevention of sexually transmitted infections. These include vaginally-applied gels that deliver anti-HIV molecules. Gels may also provide partial barriers that slow virion diffusion from semen to vulnerable epithelium, increasing the time during which anti-HIV ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.08.010
更新日期:2009-11-04 00:00:00
abstract::Encapsulation of proteins within lipid inverse bicontinuous cubic phases (Q2) has been widely studied for many applications, such as protein crystallization or drug delivery of proteins for food and pharmaceutical purposes. However, the use of the lipid sponge (L3) phase for encapsulation of proteins has not yet been ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.07.031
更新日期:2019-09-03 00:00:00
abstract::The oxygen concentration in tissue can vary on several length scales. The basic scale of variation is determined by capillary spacing. It is this scale that is manifest in the simplest Krogh cylinder model. A second, smaller scale of variation is associated with the consumption of oxygen by mitochondria. This paper gi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83856-X
更新日期:1985-12-01 00:00:00
abstract::The effect of transepithelial potential difference (psi) on Na and Cl flux across toad bladder was assessed by measuring isotopic flux between identical media at various values of psi. The contribution of edge damage to ionic permeability was eliminated, resulting in relatively high spontaneous psi (-97 +/-4 mv) and l...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(72)86089-2
更新日期:1972-04-01 00:00:00
abstract::Aggregated Markov models are a widely used tool to model patch clamp data measured from single ion channels. These channels must obey the principle of detailed balance in thermodynamic equilibrium; otherwise, the channel is driven by an external source of energy. We investigate the power of a likelihood ratio test for...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76529-5
更新日期:2000-12-01 00:00:00
abstract::Many proteins are anchored to lipid bilayer membranes through a combination of hydrophobic and electrostatic interactions. In the case of the membrane-bound nonreceptor tyrosine kinase Src from Rous sarcoma virus, these interactions are mediated by an N-terminal myristoyl chain and an adjacent cluster of six basic ami...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.06.051
更新日期:2015-08-04 00:00:00
abstract::We have studied the combined effects of X-irradiation and nitrogen mustard treatment on the colony-forming ability of Chinese hamster cells. In contrast to X-irradiation, nitrogen mustard acting by itself yields an exponential dose-effect relationship. Moreover, whether delivered in immediate sequence or after varying...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(69)86439-8
更新日期:1969-09-01 00:00:00
abstract::Nanodiscs that hold a lipid bilayer surrounded by a boundary of scaffold proteins have emerged as a powerful tool for membrane protein solubilization and analysis. By combining nanodiscs and cell-free expression technologies, even completely detergent-free membrane protein characterization protocols can be designed. N...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.03.026
更新日期:2017-09-19 00:00:00
abstract::Biological systems often have to measure extremely low concentrations of chemicals with high precision. When dealing with such small numbers of molecules, the inevitable randomness of physical transport processes and binding reactions will limit the precision with which measurements can be made. An important question ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.12.030
更新日期:2014-02-18 00:00:00
abstract::The structure of a membrane-embedded alpha-helical reference protein, the M13 major coat protein, is characterized under different conditions of hydrophobic mismatch using fluorescence resonance energy transfer in combination with high-throughput mutagenesis. We show that the structure is similar in both thin (14:1) a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.112698
更新日期:2007-11-15 00:00:00
abstract::Proteins must be stable to accomplish their biological function and to avoid enzymatic degradation. Constitutive proteolysis, however, is the main source of free amino acids used for de novo protein synthesis. In this paper the delicate balance of protein stability and degradability is discussed in the context of func...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76476-9
更新日期:2000-11-01 00:00:00
abstract::We investigated whether the cysteine residues in Shaker potassium (K+) channels are essential for activation and inactivation gating or for modulation of activation gating by external zinc (Zn2+). Mutants of the Shaker K+ channel were prepared in which all seven cysteine residues were replaced (C-less). These changes ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(94)80843-4
更新日期:1994-03-01 00:00:00
abstract::The E5 oncoprotein is the major transforming protein of bovine papillomavirus type 1. This 44-residue transmembrane protein can interact with the platelet-derived growth factor receptor β, leading to ligand-independent activation and cell transformation. For productive interaction, E5 needs to dimerize via a C-termina...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.06.073
更新日期:2010-09-22 00:00:00
abstract::Computer simulations suggest that the translocation of arginine through the hydrocarbon core of a lipid membrane proceeds by the formation of a water-filled defect that keeps the arginine molecule hydrated even at the center of the bilayer. We show here that adding additional arginine molecules into one of these water...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.05.038
更新日期:2011-07-06 00:00:00