Effects of pH on structural and functional properties of porin from the outer membrane of Yersinia pseudotuberculosis. II. Characterization of pH-induced conformational intermediates of yersinin

Novikova, O. D.; Kim, N. Yu.; Lukyanov, Pavel; Likhatskaya, G. N.; Emelyanenko, V. I.; Соловьева, Т. Ф.

doi:10.1134/s1990747807020080

Cited by 4 publications

(5 citation statements)

References 23 publications

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“…Both residues have a hydrophobic microenvironment, but Trp56 is more hydrophobic. Trp106 residues localized in L3 loops and inside the pore cavity manifest a higher accessibility for solvent molecules [1].…”

Section: Discussionmentioning

confidence: 99%

“…The OmpF-like porin of the Gram-negative bacteria Yersinia pseudotuberculosis (YOmpF) is a cylinder-shaped homotrimeric protein that forms a non-specific transmembrane channel, allowing passive diffusion of hydrophilic low-molecular-mass substances across the bacterial outer membrane [1]. Thus, the protein-lipid interactions are crucial for cellular functions of this protein.…”

Section: Introductionmentioning

confidence: 99%

“…The lipid bilayer of biological membranes is characterized by complex structural and dynamical properties, which are important for the structural organization and function of membrane proteins and for many cell functions. The OmpF-like porin of the Gram-negative bacteria Yersinia pseudotuberculosis (YOmpF) is a cylinder-shaped homotrimeric protein that forms a non-specific transmembrane channel, allowing passive diffusion of hydrophilic low-molecular-mass substances across the bacterial outer membrane [1]. Thus, the protein-lipid interactions are crucial for cellular functions of this protein.…”

Section: Introductionmentioning

confidence: 99%

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Effect of phenol‐induced changes in lipid composition on conformation of OmpF‐like porin of Yersinia pseudotuberculosis

et al. 2013

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a b s t r a c tThe present work aimed to compare the effects of different lysophosphatidylethanolamine (LPE) content in lipids derived from Yersinia pseudotuberculosis cells exposed and not exposed to phenol on the conformation of OmpF-like porin of these bacteria. Differential scanning calorimetry and intrinsic protein fluorescence showed that the 2.5-fold increase of LPE content and the corresponding increase in the phase transition temperature of bacterial lipids were accompanied by enhanced protein thermostability. Integral conformational rearrangement of protein was supported by drastic changes in the microenvironment of the tryptophan residues, likely resulting in a convergence of monomers in trimeric porin and exposure of outer tryptophan residues to the water environment. These conformational changes may impede the porin channel permeability under stress conditions in bacteria.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Effect of phenol‐induced changes in lipid composition on conformation of OmpF‐like porin of Yersinia pseudotuberculosis

et al. 2013

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“…A wide range of pH stability provides plasticity to proteins. Porin from Yersinia pseudotuberculosis was studied for its wide pH range (2.0 to 8.0) for its plasticity and structural rearrangement 39 , 40 . β-barrel proteins show a blue-shift and a few folds less intensity in Trp fluorescence spectra upon unfolding 41 .…”

Section: Discussionmentioning

confidence: 99%

Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori

Tamrakar

Singh

Kumar

et al. 2021

Sci Rep

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Helicobacter pylori is a Gram-negative bacterium that causes chronic inflammations in the stomach area and is involved in ulcers, which can develop into gastric malignancies. H. pylori attaches and colonizes to the human epithelium using some of their outer membrane proteins (OMPs). HomB and HomA are the most studied OMPs from H. pylori as they play a crucial role in adherence, hyper biofilm formation, antibiotic resistance and are also associated with severe gastric malignancies. The role of HomA and HomB in pathogenesis concerning their structure and function has not been evaluated yet. In the present study, we explored the structural aspect of HomA and HomB proteins using various computational, biophysical and small-angle X-ray scattering (SAXS) techniques. Interestingly, the in-silico analysis revealed that HomA/B consists of 8 discontinuous N and C terminal β-strands forming a small β-barrel, along with a large surface-exposed globular domain. Further, biophysical experiments suggested that HomA and HomB are dimeric and most likely the cysteine residues present on surface-exposed loops participate in protein–protein interactions. Our study provides essential structural information of unexplored proteins of the Hom family that can help in a better understanding of H. pylori pathogenesis.

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“…By some estimates, over a third of all mammalian proteins participate in two or more protein–protein interactions,4 each of which may be modeled as a distinct structural state. Moreover, many proteins are highly sensitive to cellular conditions (e.g., pH,5 ion concentration,6 oxidative state,7 temperature8), the presence of small molecules,9 and post‐translational covalent modifications (e.g., phosphorylation10, 11). Perturbations in these conditions can induce moderate to large conformational changes, and some proteins have multiple well‐defined structural states that depend on such conditions12–14 or protein–protein interactions 15.…”

Section: Introductionmentioning

confidence: 99%

Design of multispecific protein sequences using probabilistic graphical modeling

2009

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In nature, proteins partake in numerous protein- protein interactions that mediate their functions. Moreover, proteins have been shown to be physically stable in multiple structures, induced by cellular conditions, small ligands, or covalent modifications. Understanding how protein sequences achieve this structural promiscuity at the atomic level is a fundamental step in the drug design pipeline and a critical question in protein physics. One way to investigate this subject is to computationally predict protein sequences that are compatible with multiple states, i.e., multiple target structures or binding to distinct partners. The goal of engineering such proteins has been termed multispecific protein design. We develop a novel computational framework to efficiently and accurately perform multispecific protein design. This framework utilizes recent advances in probabilistic graphical modeling to predict sequences with low energies in multiple target states. Furthermore, it is also geared to specifically yield positional amino acid probability profiles compatible with these target states. Such profiles can be used as input to randomly bias high-throughput experimental sequence screening techniques, such as phage display, thus providing an alternative avenue for elucidating the multispecificity of natural proteins and the synthesis of novel proteins with specific functionalities. We prove the utility of such multispecific design techniques in better recovering amino acid sequence diversities similar to those resulting from millions of years of evolution. We then compare the approaches of prediction of low energy ensembles and of amino acid profiles and demonstrate their complementarity in providing more robust predictions for protein design.

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Effects of pH on structural and functional properties of porin from the outer membrane of Yersinia pseudotuberculosis. II. Characterization of pH-induced conformational intermediates of yersinin

Cited by 4 publications

References 23 publications

Effect of phenol‐induced changes in lipid composition on conformation of OmpF‐like porin of Yersinia pseudotuberculosis

Effect of phenol‐induced changes in lipid composition on conformation of OmpF‐like porin of Yersinia pseudotuberculosis

Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori

Design of multispecific protein sequences using probabilistic graphical modeling

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