Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank

Chwastyk, Mateusz; Panek, Ewa; Malinowski, J.; Jaskólski, M.; Cieplak, Marek

doi:10.3389/fmolb.2020.591381

Cited by 20 publications

(10 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Such a cavity has been described for the insect allergen repeat domain, which contains two repeats of a domain of 5 helices, forming two hemispheres with one lipid inside (Mueller et al, 2013). The Lec1 cavity is uniquely large for a globular protein, at 29 nm 3 almost 10-fold larger than any known cavity with a predominantly hydrophobic surface (Chwastyk et al, 2020). Since Lec1 is associated with membranes, lipid droplets and also with lipid modifying enzymes, we consider it possible that it encloses hydrophobic molecules such as lipids or intermediates of lipid synthesis.…”

Section: Discussionmentioning

confidence: 99%

Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution

Castro

Shortill

Dziurdzik

et al. 2022

eLife

View full text Add to dashboard Cite

Actively maintained close appositions between organelle membranes, also known as contact sites, enable the efficient transfer of biomolecules between cellular compartments. Several such sites have been described as well as their tethering machineries. Despite these advances we are still far from a comprehensive understanding of the function and regulation of most contact sites. To systematically characterize contact site proteomes, we established a high-throughput screening approach in Saccharomyces cerevisiae based on co-localization imaging. We imaged split fluorescence reporters for six different contact sites, several of which are poorly characterized, on the background of 1165 strains expressing a mCherry-tagged yeast protein that has a cellular punctate distribution (a hallmark of contact sites), under regulation of the strong TEF2 promoter. By scoring both co-localization events and effects on reporter size and abundance, we discovered over 100 new potential contact site residents and effectors in yeast. Focusing on several of the newly identified residents, we identified three homologs of Vps13 and Atg2 that are residents of multiple contact sites. These proteins share their lipid transport domain, thus expanding this family of lipid transporters. Analysis of another candidate, Ypr097w, which we now call Lec1 (Lipid-droplet Ergosterol Cortex 1), revealed that this previously uncharacterized protein dynamically shifts between lipid droplets and the cell cortex, and plays a role in regulation of ergosterol distribution in the cell. Overall, our analysis expands the universe of contact site residents and effectors and creates a rich database to mine for new functions, tethers, and regulators.

show abstract

Section: Discussionmentioning

confidence: 99%

Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution

Castro

Shortill

Dziurdzik

et al. 2022

eLife

View full text Add to dashboard Cite

show abstract

“…The algorithm uses two parameters: the lattice constant a and the probe radius r. The former value was set based on a number of tests (Chwastyk et al, 2020;Chwastyk & Cieplak, 2021). The probe radius was set to 1.42 A ˚, which is close to the size of a water molecule.…”

Section: Detection and Volume Calculation Of Protein Cavitiesmentioning

confidence: 99%

Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center

Loch

Worsztynowicz

Sliwiak

et al. 2023

Acta Cryst Sect D Struct Biol

View full text Add to dashboard Cite

The genome of Rhizobium etli, a nitrogen-fixing bacterial symbiont of legume plants, encodes two L-asparaginases, ReAIV and ReAV, that have no similarity to the well characterized enzymes of class 1 (bacterial type) and class 2 (plant type). It has been hypothesized that ReAIV and ReAV might belong to the same structural class 3 despite their low level of sequence identity. When the crystal structure of the inducible and thermolabile protein ReAV was solved, this hypothesis gained a stronger footing because the key residues of ReAV are also present in the sequence of the constitutive and thermostable ReAIV protein. High-resolution crystal structures of ReAIV now confirm that it is a class 3 L-asparaginase that is structurally similar to ReAV but with important differences. The most striking differences concern the peculiar hydration patterns of the two proteins, the presence of three internal cavities in ReAIV and the behavior of the zinc-binding site. ReAIV has a high pH optimum (9–11) and a substrate affinity of ∼1.3 mM at pH 9.0. These parameters are not suitable for the direct application of ReAIV as an antileukemic drug, although its thermal stability and lack of glutaminase activity would be of considerable advantage. The five crystal structures of ReAIV presented in this work allow a possible enzymatic scenario to be postulated in which the zinc ion coordinated in the active site is a dispensable element. The catalytic nucleophile seems to be Ser47, which is part of two Ser–Lys tandems in the active site. The structures of ReAIV presented here may provide a basis for future enzyme-engineering experiments to improve the kinetic parameters for medicinal applications.

show abstract

“…Still, they exclude the effects of bound charges within the microstructure [31]. EM waves in hydrophobic protein cavities [32] and mitochondria [33] represent EM cavities [32] and mitochondria [33] represent EM resonances. They are the origin of the endogenous EM field in aromatic studies of amino acids and organelles.…”

Section: Introductionmentioning

confidence: 99%

The archetypal molecular patterns of conscious experience are quantum analogs

Tuszyński¹,

Poznanski²,

Cacha³

2022

J. Multiscale Neurosci.

View full text Add to dashboard Cite

We define quantum analogs as vibrational excitations of quasi-particles coupled to electromagnetically-mediated resonance energy transfer in water (a crystal lattice). This paper addresses how neural magnetic resonance spectra of the brain’s magnetic field influence dipolar oscillation waves in crystal lattices of interfacial water molecules to produce correlates of phenomenal consciousness. We explore dipolar oscillation waves in hydrophobic protein cavities of aromatic amino acids as a conduit for coherent propagation of vibrational excitation and hydrogen bond distortion associated with phase coherence present in the magnetic field intensity oscillations at a frequency at which the energy switches from its trapped form as excited phonon states to free, cavity-mode magnetic field energy states. A quasi-polaritons that reflect “hydro-ionic waves” is a macroscopic quantum effect of crystal lattice vibrations, consisting of vibron polaritons coupled to ions across the neocortex, except the cerebellum, due to the absence of protein-protein interactions. They are quantum-like at the core and hence can exhibit quantum-like signaling properties when resonant energy is transferred as dipolar waves in hydrophobic protein cavities of aromatic amino acids. This is due to aromatic residue flexibility in molecular electromagnetic resonances. Finally, the archetypal molecular patterning of conscious experiences, which carries an inherent ambiguity necessary for non-contextually applying ‘meaning’ that encompasses cognitive signatures of conscious experience, satisfies the nature of quantum analogs and their transmutative properties.

show abstract

Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank

Cited by 20 publications

References 51 publications

Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution

Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution

Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center

The archetypal molecular patterns of conscious experience are quantum analogs

Contact Info

Product

Resources

About