scholarly journals High-resolution structures of mitochondrial glutaminase C tetramers indicate conformational changes upon phosphate binding

2022 ◽  
pp. 101564
Author(s):  
Thuy-Tien T. Nguyen ◽  
Sekar Ramachandran ◽  
Matthew J. Hill ◽  
Richard A. Cerione
Keyword(s):  
High Resolution ◽  
Conformational Changes ◽  
Phosphate Binding

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.

Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding

2018 ◽  
Vol 74 (5) ◽  
pp. 480-489 ◽  
Author(s):  
Marina Plaza-Garrido ◽  
M. Carmen Salinas-Garcia ◽  
Ana Camara-Artigas
Keyword(s):  
Conformational Changes ◽  
Protein Function ◽  
Protein Crystallization ◽  
Amyloid Formation ◽  
Acidic Ph ◽  
Phosphate Binding ◽  
Cell Parameters ◽  
Ph Values ◽  
Phosphate Ion ◽  
Α Helix

The structure of orthorhombic lysozyme has been obtained at 298 K and pH 4.5 using sodium chloride as the precipitant and in the presence of sodium phosphate at a concentration as low as 5 mM. Crystals belonging to space groupP212121(unit-cell parametersa= 30,b= 56,c= 73 Å, α = β = γ = 90.00°) diffracted to a resolution higher than 1 Å, and the high quality of these crystals permitted the identification of a phosphate ion bound to Arg14 and His15. The binding of this ion produces long-range conformational changes affecting the loop containing Ser60–Asn74. The negatively charged phosphate ion shields the electrostatic repulsion of the positively charged arginine and histidine residues, resulting in higher stability of the phosphate-bound lysozyme. Additionally, a low-humidity orthorhombic variant was obtained at pH 4.5, and comparison with those previously obtained at pH 6.5 and 9.5 shows a 1.5 Å displacement of the fifth α-helix towards the active-site cavity, which might be relevant to protein function. Since lysozyme is broadly used as a model protein in studies related to protein crystallization and amyloid formation, these results indicate that the interaction of some anions must be considered when analysing experiments performed at acidic pH values.

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.

scholarly journals High Resolution Crystal Structures of Human Rab5a and Five Mutants with Substitutions in the Catalytically Important Phosphate-binding Loop

2002 ◽  
Vol 278 (4) ◽  
pp. 2452-2460 ◽  
Author(s):  
Guangyu Zhu ◽  
Jian Liu ◽  
Simon Terzyan ◽  
Peng Zhai ◽  
Guangpu Li ◽  
...  
Keyword(s):  
High Resolution ◽  
Crystal Structures ◽  
Phosphate Binding ◽  
Binding Loop

scholarly journals MD simulation of high-resolution X-ray structures reveals post-translational modification dependent conformational changes in HSF-DNA interaction

2016 ◽  
Vol 7 (12) ◽  
pp. 916-920 ◽  
Author(s):  
Han Feng ◽  
Sheng Wang ◽  
Ling Guo ◽  
Avinash S. Punekar ◽  
Rudolf Ladenstein ◽  
...  
Keyword(s):  
High Resolution ◽  
Conformational Changes ◽  
Md Simulation ◽  
Dna Interaction ◽  
Post Translational Modification ◽  
X Ray

scholarly journals Allosteric interactions of glycogen phosphorylase b. A crystallographic study of glucose 6-phosphate and inorganic phosphate binding to di-imidate-cross-linked phosphorylase b

1984 ◽  
Vol 218 (1) ◽  
pp. 45-60 ◽  
Author(s):  
A Lorek ◽  
K S Wilson ◽  
M S P Sansom ◽  
D I Stuart ◽  
E A Stura ◽  
...  
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Inorganic Phosphate ◽  
Glycogen Phosphorylase ◽  
Phosphate Binding ◽  
Binding Studies ◽  
Structural Explanation ◽  
Alpha Helices ◽  
Allosteric Effector ◽  
Glycogen Phosphorylase B

The binding to glycogen phosphorylase b of glucose 6-phosphate and inorganic phosphate (respectively allosteric inhibitor and substrate/activator of the enzyme) were studied in the crystal at 0.3 nm (3A) resolution. Glucose 6-phosphate binds in the alpha-configuration at a site that is close to the AMP allosteric effector site at the subunit-subunit interface and promotes several conformational changes. The phosphate-binding site of the enzyme for glucose 6-phosphate involves contacts to two cationic residues, Arg-309 and Lys-247. This site is also occupied in the inorganic-phosphate-binding studies and is therefore identified as a high-affinity phosphate-binding site. It is distinct from the weaker phosphate-binding site of the enzyme for AMP, which is 0.27 nm (2.7A) away. The glucose moiety of glucose 6-phosphate and the adenosine moiety of AMP do not overlap. The results provide a structural explanation for the kinetic observations that glucose 6-phosphate inhibition of AMP activation of phosphorylase b is partially competitive and highly co-operative. The results suggest that the transmission of allosteric conformational changes involves an increase in affinity at phosphate-binding sites and relative movements of alpha-helices. In order to study glucose 6-phosphate and phosphate binding it was necessary to cross-link the crystals. The use of dimethyl malondi-imidate as a new cross-linking reagent in protein crystallography is discussed.

High resolution nuclear magnetic resonance studies of platinum(II) – guanosine-5′-monophosphate interactions in aqueous solutions

1981 ◽  
Vol 59 (23) ◽  
pp. 3297-3302 ◽  
Author(s):  
Moschos Polissiou ◽  
Minh Tan Phan Viet ◽  
Maurice St-Jacques ◽  
Theophile Theophanides
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
High Resolution ◽  
Aqueous Solutions ◽  
Conformational Changes ◽  
Coupling Constant ◽  
Magnetic Resonance Studies ◽  
H Nmr ◽  
Nmr Study ◽  
Ribose Moiety

A detailed 400 MHz 1H nmr study was carried out on platinum complexation products of GMP by K2PtCl4. Coupling constant values show that platination on N7 induces a conformational change on the ribose moiety: the 3E form of the ring and the gt conformer about the C(4′)—C(5′) bond are favoured upon complexation. The results are compared to the conformational changes induced by N7 protonation and methylation.

scholarly journals Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes

2020 ◽  
Author(s):  
Karolina Michalska ◽  
Youngchang Kim ◽  
Robert Jedrzejczak ◽  
Natalia I. Maltseva ◽  
Lucy Stols ◽  
...  
Keyword(s):  
Immune Response ◽  
High Resolution ◽  
Water Molecule ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Molecular Targets ◽  
Nonstructural Proteins ◽  
Phosphatase Domain ◽  
Ethanesulfonic Acid ◽  
Precise Role

ABSTRACTAmong 15 nonstructural proteins (Nsps), the newly emerging SARS-CoV-2 encodes a large, multidomain Nsp3. One of its units is ADP-ribose phosphatase domain (ADRP, also known as macrodomain) which is believed to interfere with the host immune response. Such a function appears to be linked to the protein’s ability to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remains unknown. Here, we have determined five, high resolution (1.07 - 2.01 Å) crystal structures corresponding to the apo form of the protein and complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADPr. We show that the protein undergoes conformational changes to adapt to the ligand in a manner previously observed before for in close homologs from other viruses. We also identify a conserved water molecule that may participate in hydrolysis. This work builds foundations for future structure-based research of the ADRP, including search for potential antiviral therapeutics.

Structures of the deoxy and CO forms of haemoglobin from Dasyatis akajei, a cartilaginous fish

1999 ◽  
Vol 55 (7) ◽  
pp. 1291-1300 ◽  
Author(s):  
Khoon Tee Chong ◽  
Gentaro Miyazaki ◽  
Hideki Morimoto ◽  
Yutaka Oda ◽  
Sam-Yong Park
Keyword(s):  
Conformational Changes ◽  
Main Chain ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Oxygen Affinity ◽  
Organic Phosphate ◽  
Phosphate Binding ◽  
Phosphate Effect ◽  
Structural Differences ◽  
Dasyatis Akajei

The three-dimensional structures of the deoxy- and carbonmonoxyhaemoglobin (Hb) from Dasyatis akajei, a stingray, have been determined at 1.6 and 1.9 Å resolution, respectively. This is one of the most distantly related vertebrate Hbs to human HbA. Both structures resemble the respective forms of HbA, indicating that the α2β2-type tetramer and the mode of the quaternary structure change are common to Hbs of jawed vertebrates. Larger deviations between D. akajei Hb and human HbA are observed in various parts of the molecule, even in the E and F helices. Significant mutations and/or conformational changes are also observed around the haems, in the C-terminal region of the β subunit, in the α1β2 interface and in the organic phosphate-binding site of HbA. Despite these structural differences, the oxygen affinity, haem–haem interaction, Bohr effect and organic phosphate effect of D. akajei Hb are all only moderately reduced. Compared with human HbA, the overall r.m.s. deviation of main-chain atoms in the helical regions of bony fish Hbs is smaller than that of D. akajei Hb.

Sign in / Sign up

Export Citation Format

Share Document