Insights into stabilizing interactions in the distorted domain-swapped dimer ofSalmonella typhimuriumsurvival protein

2015 ◽  
Vol 71 (9) ◽  
pp. 1812-1823 ◽  
Author(s):  
Yamuna Kalyani Mathiharan ◽  
H. S. Savithri ◽  
M. R. N. Murthy
Keyword(s):  
Hydrogen Bond ◽  
Catalytic Activity ◽  
Salt Bridge ◽  
Salt Bridges ◽  
X Ray ◽  
Dimeric Interface ◽  
Distorted Structure ◽  
Dimeric Protein ◽  
The Stability

The survival protein SurE fromSalmonella typhimurium(StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of β-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167°. New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11° between theBchains upon superposition of theAchains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.

Cu0.8Mg1.2Si2O6 : a copper-bearing silicate with the low-clinopyroxene structure

2016 ◽  
Vol 80 (2) ◽  
pp. 325-335 ◽  
Author(s):  
Lei Ding ◽  
Céline Darie ◽  
Claire V. Colin ◽  
Pierre Bordet
Keyword(s):  
X Ray Diffraction ◽  
Soft Chemistry ◽  
X Ray ◽  
Cu Content ◽  
Distorted Structure ◽  
Mechanisms Of Formation ◽  
Jahn Teller ◽  
The Stability ◽  
Insight Into

AbstractThe Cu0.8Mg1.2Si2O6 pyroxene has been synthesized using a soft chemistry method. Its crystal structure was determined from powder X-ray diffraction data. Cu0.8Mg1.2Si2O6 crystallizes with the lowclinopyroxene monoclinic structure (space group P21/c). The role of the Jahn-Teller-distorted Cu2+ cation on the stability of this strongly distorted structure is investigated. Cu2+ shows a strong preference for the M2 site, attributed to a better adaptation of its JT-distorted coordination polyhedron to this already distorted and more flexible site. Comparison with previously reported compounds indicates that increasing the Cu content enhances the M2 site distortion, eventually leading to symmetry lowering from orthorhombic Pbca to monoclinic P21/c. These observations bring new insight into the mechanisms of formation and chemical composition of pyroxene minerals in the presence of JT cations.

scholarly journals Intrinsic basis of thermostability of prolyl oligopeptidase from Pyrococcus furiosus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sahini Banerjee ◽  
Parth Sarthi Sen Gupta ◽  
Rifat Nawaz Ul Islam ◽  
Amal Kumar Bandyopadhyay
Keyword(s):  
Pyrococcus Furiosus ◽  
Intrinsic Property ◽  
Salt Bridge ◽  
Primary Role ◽  
Salt Bridges ◽  
Energy Contribution ◽  
Desolvation Energy ◽  
The Stability ◽  
Intrinsic Basis

AbstractSalt-bridges play a key role in the thermostability of proteins adapted in stress environments whose intrinsic basis remains to be understood. We find that the higher hydrophilicity of PfP than that of HuP is due to the charged but not the polar residues. The primary role of these residues is to enhance the salt-bridges and their ME. Unlike HuP, PfP has made many changes in its intrinsic property to strengthen the salt-bridge. First, the desolvation energy is reduced by directing the salt-bridge towards the surface. Second, it has made bridge-energy more favorable by recruiting energetically advantageous partners with high helix-propensity among the six possible salt-bridge pairs. Third, ME-residues that perform intricate interactions have increased their energy contribution by making major changes in their binary properties. The use of salt-bridge partners as ME-residues, and ME-residues' overlapping usage, predominant in helices, and energetically favorable substitution are some of the favorable features of PfP compared to HuP. These changes in PfP reduce the unfavorable, increase the favorable ME-energy. Thus, the per salt-bridge stability of PfP is greater than that of HuP. Further, unfavorable target ME-residues can be identified whose mutation can increase the stability of salt-bridge. The study applies to other similar systems.

Factors affecting the amplitude of the τ angle in proteins: a revisitation

2017 ◽  
Vol 73 (7) ◽  
pp. 618-625 ◽  
Author(s):  
Nicole Balasco ◽  
Luciana Esposito ◽  
Luigi Vitagliano
Keyword(s):  
Protein Structures ◽  
Factors Affecting ◽  
X Ray ◽  
Backbone Conformation ◽  
Potential Factors ◽  
The Stability ◽  
Major Factors ◽  
The Impact ◽  
Open Issues

The protein folded state is the result of the fine balance of a variety of different forces. Even minor structural perturbations may have a significant impact on the stability of these macromolecules. Studies carried out in recent decades have led to the convergent view that proteins are endowed with a flexible spine. One of the open issues related to protein local backbone geometry is the identification of the factors that influence the amplitude of the τ (N—Cα—C) angle. Here, statistical analyses performed on an updated ensemble of X-ray protein structures by dissecting the contribution of the major factors that can potentially influence the local backbone geometry of proteins are reported. The data clearly indicate that the local backbone conformation has a prominent impact on the modulation of the τ angle. Therefore, a proper assessment of the impact of the other potential factors can only be appropriately evaluated when small (φ, ψ) regions are considered. Here, it is shown that when the contribution of the backbone conformation is removed by considering small (φ, ψ) areas, an impact of secondary structure, as defined byDSSP, and/or the residue type on τ is still detectable, although to a limited extent. Indeed, distinct τ-value distributions are detected for Pro/Gly and β-branched (Ile/Val) residues. The key role of the local backbone conformation highlighted here supports the use of variable local backbone geometry in protein refinement protocols.

scholarly journals Synthesis and Complexation Properties of 2-Hydroxy-5-methoxyphenylphosphonic Acid (H3L1). Crystal Structure of the [Cu(H2L1)2(Н2О)2] Complex

2021 ◽  
Vol 91 (11) ◽  
pp. 2176-2186
Author(s):  
G. S. Tsebrikova ◽  
Yu. I. Rogacheva ◽  
I. S. Ivanova ◽  
A. B. Ilyukhin ◽  
V. P. Soloviev ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Methoxy Group ◽  
Protonation Constants ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Stability ◽  
Intramolecular Hydrogen ◽  
Oxygen Atoms

Abstract 2-Hydroxy-5-methoxyphenylphosphonic acid (H3L1) and the complex [Cu(H2L1)2(H2O)2] were synthesized and characterized by IR spectroscopy, thermogravimetry, and X-ray diffraction analysis. The polyhedron of the copper atom is an axially elongated square bipyramid with oxygen atoms of phenolic and of monodeprotonated phosphonic groups at the base and oxygen atoms of water molecules at the vertices. The protonation constants of the H3L1 acid and the stability constants of its Cu2+ complexes in water were determined by potentiometric titration. The protonation constants of the acid in water are significantly influenced by the intramolecular hydrogen bond and the methoxy group. The H3L1 acid forms complexes CuL‒ and CuL24‒ with Cu2+ in water.

Investigation of ZnO/CuO/Nanographene Platelets Composites Catalyst for the Degradation of Methylene Blue from Aqueous Solution

2016 ◽  
Vol 864 ◽  
pp. 117-122 ◽  
Author(s):  
Hesni Shabrany ◽  
Hendry Tju ◽  
Ardiansyah Taufik ◽  
Rosari Saleh
Keyword(s):  
Aqueous Solution ◽  
Methylene Blue ◽  
Catalytic Activity ◽  
Visible Light ◽  
Sol Gel ◽  
Nitrogen Adsorption ◽  
Ultrasound Irradiation ◽  
X Ray Diffraction ◽  
X Ray

This paper discusses the catalytic activity of ZnO/CuO/nanographene platelets composites under visible light and ultrasound irradiation separately. The ZnO/CuO/nanographene platelets composites were synthesized using a sol-gel method. X-ray diffraction and nitrogen adsorption spectroscopy were employed to investigate the structural and surface area of the catalyst. The catalytic activity results showed that the presence of nanographene platelets in ZnO/CuO nanocomposites improved its efficiency in degrading methylene blue. A scavenger method was also used to understand the role of charged carriers and the active radical involved in the catalytic activity.

scholarly journals Electrostatics in the stability and misfolding of the prion protein: salt bridges, self energy, and solvationThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 371-381 ◽  
Author(s):  
Will C. Guest ◽  
Neil R. Cashman ◽  
Steven S. Plotkin
Keyword(s):  
Prion Protein ◽  
Electrostatic Potential ◽  
Peer Review Process ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Self Energy ◽  
Low Dielectric ◽  
The Stability ◽  
Α Helix ◽  
Electrostatic Potential Energy

Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectric amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self energies play key roles in stabilizing secondary and tertiary structural elements of the prion protein. The total electrostatic potential energy of each residue was found to be invariably stabilizing. Residues frequently found to be mutated in familial prion disease were among those with the largest electrostatic energies. The large barrier to charged group desolvation imposes regional constraints on involvement of the prion protein in an amyloid aggregate, resulting in an electrostatic amyloid recruitment profile that favours regions of sequence between α helix 1 and β strand 2, the middles of helices 2 and 3, and the region N-terminal to α helix 1. We found that the stabilization due to salt bridges is minimal among the proteins studied for disease-susceptible human mutants of prion protein.

scholarly journals CHEMISORPTION OF ENROFLOXACIN ON RUTILE-TIO2 (110) SURFACE: A THEORETICAL INVESTIGATION

2019 ◽  
Vol 57 (4) ◽  
pp. 449
Author(s):  
Trung Tien Nguyen ◽  
Tri Ngoc Nguyen ◽  
Dai Quoc Ho
Keyword(s):  
Hydrogen Bond ◽  
Chemical Analysis ◽  
Dft Calculations ◽  
Quantum Chemical ◽  
Adsorption Process ◽  
Stable Configuration ◽  
Quantum Chemical Analysis ◽  
Rutile Tio2 ◽  
The Stability

We investigated the adsorption of enrofloxacin (ENR) antibiotic on rutile-TiO2 (r-TiO2­) (110) surface using DFT calculations. Stable configurations of the adsorption of ENR on r-TiO2 (110) were observed. The origin and role of interactions in stablizing the configurations are thoroughly analyzed using NBO and AIM analyses. Obtained results indicate that the adsorption process is characterized as a strong chemisorption with an associated energy of ca. -35.1 kcal.mol-1 for the most stable configuration. Quantum chemical analysis shows that the stability of configurations is mainly determined by >C=O∙∙∙Ti5f electrostatic interaction along with supplement of H∙∙∙Ob hydrogen bond.

scholarly journals How well do force fields capture the strength of salt bridges in proteins?

2018 ◽  
Author(s):  
Mustapha Carab Ahmed ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Enhanced Sampling ◽  
Important Interaction ◽  
Close Proximity ◽  
The Stability ◽  
Dynamics Simulations

AbstractSalt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulations is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depend on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is slightly overestimated in simulations of GB1 using six commonly used combinations of force fields and water models. We therefore conclude that further work is needed to refine our ability to model quantitatively the stability of salt bridges through simulations, and that comparisons between experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

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