scholarly journals Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures

2007 ◽  
Vol 16 (6) ◽  
pp. 1032-1041 ◽  
Author(s):  
M. Jack Borrok ◽  
Laura L. Kiessling ◽  
Katrina T. Forest
Keyword(s):  
High Resolution ◽  
Conformational Changes ◽  
Binding Protein

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

A high-resolution 1H-NMR investigation of the histidine-binding protein J of Salmonella Typhimurium

1984 ◽  
Vol 19 (4) ◽  
pp. 279-287 ◽  
Author(s):  
Thomas E. Cedel ◽  
Patricia F. Cottam ◽  
Michael D. Meadows ◽  
Chien Ho
Keyword(s):  
High Resolution ◽  
Salmonella Typhimurium ◽  
1H Nmr ◽  
Binding Protein

scholarly journals The EF-Hand Ca2+-binding Protein p22 Plays a Role in Microtubule and Endoplasmic Reticulum Organization and Dynamics with Distinct Ca2+-binding Requirements

2004 ◽  
Vol 15 (2) ◽  
pp. 481-496 ◽  
Author(s):  
Josefa Andrade ◽  
Hu Zhao ◽  
Brian Titus ◽  
Sandra Timm Pearce ◽  
Margarida Barroso
Keyword(s):  
Endoplasmic Reticulum ◽  
Conformational Changes ◽  
Membrane Trafficking ◽  
Secretory Pathway ◽  
Network Formation ◽  
Binding Protein ◽  
Dependent Manner ◽  
Microtubule Depolymerization ◽  
Independent Manner ◽  
Ef Hand

We have reported that p22, an N-myristoylated EF-hand Ca2+-binding protein, associates with microtubules and plays a role in membrane trafficking. Here, we show that p22 also associates with membranes of the early secretory pathway membranes, in particular endoplasmic reticulum (ER). On binding of Ca2+, p22's ability to associate with membranes increases in an N-myristoylation-dependent manner, which is suggestive of a nonclassical Ca2+-myristoyl switch mechanism. To address the intracellular functions of p22, a digitonin-based “bulk microinjection” assay was developed to load cells with anti-p22, wild-type, or mutant p22 proteins. Antibodies against a p22 peptide induce microtubule depolymerization and ER fragmentation; this antibody-mediated effect is overcome by preincubation with the respective p22 peptide. In contrast, N-myristoylated p22 induces the formation of microtubule bundles, the accumulation of ER structures along the bundles as well as an increase in ER network formation. An N-myristoylated Ca2+-binding p22 mutant, which is unable to undergo Ca2+-mediated conformational changes, induces microtubule bundling and accumulation of ER structures along the bundles but does not increase ER network formation. Together, these data strongly suggest that p22 modulates the organization and dynamics of microtubule cytoskeleton in a Ca2+-independent manner and affects ER network assembly in a Ca2+-dependent manner.

Solution Structure and Conformational Changes of theStreptomycesChitin-Binding Protein (CHB1)†

Biochemistry ◽  
2000 ◽  
Vol 39 (35) ◽  
pp. 10677-10683 ◽  
Author(s):  
Dmitri I. Svergun ◽  
Ardina Bećirević ◽  
Hildgund Schrempf ◽  
Michel H. J. Koch ◽  
Gerhard Grüber
Keyword(s):  
Conformational Changes ◽  
Solution Structure ◽  
Binding Protein

Overlap of IGF- and heparin-binding sites in rat IGF-binding protein-5

2000 ◽  
Vol 24 (1) ◽  
pp. 43-51 ◽  
Author(s):  
H Song ◽  
J Beattie ◽  
IW Campbell ◽  
GJ Allan
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Binding Protein ◽  
Binding Activity ◽  
Binding Domain ◽  
Site Directed Mutagenesis ◽  
Heparin Binding ◽  
Igf I ◽  
Heparin Binding Domain ◽  
Igf Binding

Using site-directed mutagenesis, we have undertaken a study of a potential IGF-binding site in the C-terminal domain of rat IGFBP-5, lying close to or within a previously described heparin-binding domain (residues 201-218) in this protein. After analysis of binding activity using three different methods - ligand blotting, solution phase equilibrium binding and biosensor measurement of real-time on- and off-rates - we report that the mutation of two highly conserved residues within this region (glycine 203 and glutamine 209) reduces the affinity of the binding protein for both IGF-I and IGF-II, while having no effect on heparin binding. In addition, we confirm that mutation of basic residues within the heparin-binding domain (R201L, K202E, K206Q and R214A) results in a protein that has attenuated heparin binding but shows only a small reduction in affinity for IGF-I and -II. Previous findings have described the reduction in affinity of IGFBP-5 for IGFs that occurs after complexation of the binding protein with heparin or other components of the extracellular matrix (ECM) and have postulated that such an interaction may result in conformational changes in protein structure, affecting subsequent IGF interaction. Our data suggesting potential overlap of heparin- and IGF-binding domains argue for a more direct effect of ECM modulation of the affinity of IGFBP-5 for ligand by partial occlusion of the IGF-binding site after interaction with ECM.

scholarly journals Substrate recognition and ATPase activity of the E. coli cysteine/cystine ABC transporter YecSC-FliY

2020 ◽  
Vol 295 (16) ◽  
pp. 5245-5256 ◽  
Author(s):  
Siwar Sabrialabed ◽  
Janet G. Yang ◽  
Elon Yariv ◽  
Nir Ben-Tal ◽  
Oded Lewinson
Keyword(s):  
Atpase Activity ◽  
Abc Transporter ◽  
Conformational Changes ◽  
Binding Protein ◽  
Substrate Binding ◽  
Transporter Family ◽  
Wide Range ◽  
Substrate Binding Protein ◽  
Sulfur Containing ◽  
Sulfur Containing Compounds

Sulfur is essential for biological processes such as amino acid biogenesis, iron–sulfur cluster formation, and redox homeostasis. To acquire sulfur-containing compounds from the environment, bacteria have evolved high-affinity uptake systems, predominant among which is the ABC transporter family. Theses membrane-embedded enzymes use the energy of ATP hydrolysis for transmembrane transport of a wide range of biomolecules against concentration gradients. Three distinct bacterial ABC import systems of sulfur-containing compounds have been identified, but the molecular details of their transport mechanism remain poorly characterized. Here we provide results from a biochemical analysis of the purified Escherichia coli YecSC-FliY cysteine/cystine import system. We found that the substrate-binding protein FliY binds l-cystine, l-cysteine, and d-cysteine with micromolar affinities. However, binding of the l- and d-enantiomers induced different conformational changes of FliY, where the l- enantiomer–substrate-binding protein complex interacted more efficiently with the YecSC transporter. YecSC had low basal ATPase activity that was moderately stimulated by apo FliY, more strongly by d-cysteine–bound FliY, and maximally by l-cysteine– or l-cystine–bound FliY. However, at high FliY concentrations, YecSC reached maximal ATPase rates independent of the presence or nature of the substrate. These results suggest that FliY exists in a conformational equilibrium between an open, unliganded form that does not bind to the YecSC transporter and closed, unliganded and closed, liganded forms that bind this transporter with variable affinities but equally stimulate its ATPase activity. These findings differ from previous observations for similar ABC transporters, highlighting the extent of mechanistic diversity in this large protein family.

scholarly journals Binding partner- and force-promoted changes in αE-catenin conformation probed by native cysteine labeling

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ksenia Terekhova ◽  
Sabine Pokutta ◽  
Yee S. Kee ◽  
Jing Li ◽  
Emad Tajkhorshid ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Binding Protein ◽  
Binding Domain ◽  
Actin Binding ◽  
Titration Calorimetry ◽  
Allosteric Coupling ◽  
Actin Binding Protein ◽  
Binding Partners ◽  
Actin Binding Domain ◽  
Cysteine Labeling

Abstract Adherens Junctions (AJs) are cell-cell adhesion complexes that sense and propagate mechanical forces by coupling cadherins to the actin cytoskeleton via β-catenin and the F-actin binding protein αE-catenin. When subjected to mechanical force, the cadherin•catenin complex can tightly link to F-actin through αE-catenin, and also recruits the F-actin-binding protein vinculin. In this study, labeling of native cysteines combined with mass spectrometry revealed conformational changes in αE-catenin upon binding to the E-cadherin•β-catenin complex, vinculin and F-actin. A method to apply physiologically meaningful forces in solution revealed force-induced conformational changes in αE-catenin when bound to F-actin. Comparisons of wild-type αE-catenin and a mutant with enhanced vinculin affinity using cysteine labeling and isothermal titration calorimetry provide evidence for allosteric coupling of the N-terminal β-catenin-binding and the middle (M) vinculin-binding domain of αE-catenin. Cysteine labeling also revealed possible crosstalk between the actin-binding domain and the rest of the protein. The data provide insight into how binding partners and mechanical stress can regulate the conformation of full-length αE-catenin, and identify the M domain as a key transmitter of conformational changes.

Binding of Radiolabeled Folate and 5-Methyltetrahydrofolate to Cow's Milk Folate Binding Protein at pH 7.4 and 5.0. Relationship to Concentration and Polymerization Equilibrium of the Purified Protein

2001 ◽  
Vol 21 (6) ◽  
pp. 733-743 ◽  
Author(s):  
Jan Holm ◽  
Steen Ingemann Hansen
Keyword(s):  
Ligand Binding ◽  
Binding Affinity ◽  
Conformational Changes ◽  
Protein Conformation ◽  
Binding Protein ◽  
Cow’S Milk ◽  
Folate Binding Protein ◽  
Cow's Milk ◽  
Polymerization Equilibrium ◽  
Methyl Tetrahydrofolate

Binding of folate (pteroylglutamate) and 5-methyltetrahydrofolate, the major endogenous form of folate, to folate binding protein purified from cow's milk was studied at 7°C to avoid degradation of 5-methyltetrahydrofolate. Both folates dissociate rapidly from the protein at pH 3.5, but extremely slowly at pH 7.4, most likely due to drastic changes in protein conformation occurring after folate binding. Dissociation of 5-methyltetrahydrofolate showed no increase at 37°C suggesting that protein-bound-5-methyltetrahydrofolate is protected against degradation. Binding displayed two characteristics, positive cooperativity and a binding affinity that increased with decreasing concentrations of the protein. The binding affinity of folate was somewhat greater than that of 5-methyl tetrahydrofolate, in particular at pH 5.0. Ligand-bound protein exhibited concentration-dependent polymerization (8-mers formed at 13 μM) at pH 7.4. At pH 5.0, only folate-bound forms showed noticeable polymerization. The fact that folate at pH 5.0 surpasses 5-methyltetrahydrofolate both with regard to binding affinity and ability to induce polymerization suggests that ligand binding is associated with conformational changes of the protein which favor polymerization.

Conformational changes in humic acids in aqueous solutions

2012 ◽  
Vol 66 (9) ◽  
Author(s):  
Martina Klučáková ◽  
Andrea Kargerová ◽  
Kristýna Nováčková
Keyword(s):  
High Resolution ◽  
Aqueous Solutions ◽  
Humic Acids ◽  
Conformational Changes ◽  
Ultrasonic Waves ◽  
Binding Ability ◽  
Molecular Arrangement ◽  
Velocity Of Ultrasound ◽  
Minimal Velocity ◽  
Minimum Velocity

AbstractConformational changes in humic acids in two different aqueous solutions (NaCl and NaOH) are studied by means of high resolution ultrasound spectrometry. The method is based on the measurement of parameters of ultrasonic waves propagating through the sample. The attenuation describes the decay of the amplitude of the ultrasonic wave with the distance travelled. The velocity is the speed of this wave and is related to the wavelength and the frequency of oscillation of the deformation. It is determined by the density and elasticity of the sample, which is strongly influenced by the molecular arrangement. The minimal velocity of ultrasound was observed at 1 g dm−3 for lignitic humic acids and at 0.5 g dm−3 for IHSS Leonardite standard. The values of compressibility as computed are almost constant up to humic acids’ content corresponding to the minimum velocity of ultrasound and then decrease with the increase in concentration. This shows that the organisation of particles in diluted and concentrated humic acids sols is different. The decrease in compressibility points to the formation of a more rigid structure, which could lead to the decrease in humic acids’ binding ability. It was confirmed that the method employed was very sensitive and could be utilised as an indicator of conformational changes in humic acids in solutions with varying concentrations.

Effector‐induced self‐association and conformational changes in the enhancer‐binding protein NTRC

1996 ◽  
Vol 22 (5) ◽  
pp. 779-788 ◽  
Author(s):  
M. Esther Farez‐Vidal ◽  
Timothy J. Wilson ◽  
Barrie E. Davidson ◽  
Geoffrey J. Howlett ◽  
Sara Austin ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Binding Protein ◽  
Enhancer Binding Protein ◽  
Self Association
Sign in / Sign up

Export Citation Format

Share Document