The Role of Water in the Responsive Properties in Lipid Interphase of Biomimetic Systems

Disalvo, Anibal; Frías, María de los Ángeles

doi:10.5772/intechopen.85811

Cited by 5 publications

(4 citation statements)

References 73 publications

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“…For the fully hydrated DMPC lipid bilayer (∼50% by weight), it was calculated to have about 40 water molecules per lipid, most of them in the bulk aqueous environment, i.e., between the lipid headgroups of opposing lipid bilayers. Thus, the 17 O signals are dominated by the bulk water that is highly mobile, resulting in a smaller residual quadrupolar coupling (RQC) , than the typical applied radio-frequency (RF) amplitude. , On the contrary, for those water molecules directly interacting with the lipid headgroups, especially those buried deep in this environment next to the fatty acyl carbonyl oxygens, they would retain a large quadrupolar coupling that is much greater than the RF amplitude. Consequently, these sites with different magnitudes for the quadrupolar couplings respond to the RF pulses differently.…”

Section: Results and Discussionmentioning

confidence: 99%

“…Such short-lived water states − make it difficult to understand the important biological function and structural aspects associated with these waters that have been reported extensively. − It has not been recognized until recently that water’s mobility in constrained biological systems can be a lot slower than what had been anticipated (nano- to picosecond timescale). , For example, the water exchange rate between different bound water sites in the gA pore had been thought to be on the sub-nanosecond timescale; however, recent results based on 17 O spectroscopy of the gA carbonyl oxygens found it to be on the millisecond timescale when an ion gradient across the membrane was not presenta difference of 6 orders of magnitude . Since much of what is known about the waters in the phospholipid headgroup environment is known from MD simulations and fast-timescale experimental methods, the unique capability of NMR technology to characterize slow dynamics (milli- to nanosecond) allows for the opportunity to identify additional water species on a slower timescale that may have important biological significance.…”

Section: Introductionmentioning

confidence: 99%

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Surprising Rigidity of Functionally Important Water Molecules Buried in the Lipid Headgroup Region

et al. 2022

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Understanding water dynamics and structure is an important topic in biological systems. It is generally held in the literature that the interfacial water of hydrated phospholipids is highly mobile, in fast exchange with the bulk water ranging from the nano- to femtosecond timescale. Although nuclear magnetic resonance (NMR) is a powerful tool for structural and dynamic studies, direct probing of interfacial water in hydrated phospholipids is formidably challenging due to the extreme population difference between bulk and interfacial water. We developed a novel 17O solid-state NMR technique in combination with an ultra-high-field magnet (35.2 T) to directly probe the functionally important interfacial water. By selectively suppressing the dominant bulk water signal, we observed two distinct water species in the headgroup region of hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayers for the first time. One water species denoted as “confined water” is chemically and dynamically different from the bulk water (∼0.17 ppm downfield and a slightly shorter spin-lattice relaxation time). Another water species denoted as “bound water” has severely restricted motion and a distinct chemical shift (∼12 ppm upfield). Additionally, the bulk water is not as “free” as pure water, resulting from the fast exchange with the water molecules that weakly and transiently interact with the lipid choline groups. These new discoveries clearly indicate the existence of the interfacial water molecules that are relatively stable over the NMR timescale (on the order of milliseconds), providing an opportunity to characterize water dynamics on the millisecond or slower timescale in biomacromolecules.

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Section: Results and Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Surprising Rigidity of Functionally Important Water Molecules Buried in the Lipid Headgroup Region

et al. 2022

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“…That is not to say that water was (or would be) found in these structures, but the possibility does exist. Water is known to associate with the lipid head groups and with attached methylenes ( Disalvo and de los Angeles Frias, 2019 ).…”

Section: Resultsmentioning

confidence: 99%

3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins

Mughram

Catalano

Herrington

et al. 2023

Front. Mol. Biosci.

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The aliphatic hydrophobic amino acid residues—alanine, isoleucine, leucine, proline and valine—are among the most common found in proteins. Their structural role in proteins is seemingly obvious: engage in hydrophobic interactions to stabilize secondary, and to a lesser extent, tertiary and quaternary structure. However, favorable hydrophobic interactions involving the sidechains of these residue types are generally less significant than the unfavorable set arising from interactions with polar atoms. Importantly, the constellation of interactions between residue sidechains and their environments can be recorded as three-dimensional maps that, in turn, can be clustered. The clustered average map sets compose a library of interaction profiles encoding interaction strengths, interaction types and the optimal 3D position for the interacting partners. This library is backbone angle-dependent and suggests solvent and lipid accessibility for each unique interaction profile. In this work, in addition to analysis of soluble proteins, a large set of membrane proteins that contained optimized artificial lipids were evaluated by parsing the structures into three distinct components: soluble extramembrane domain, lipid facing transmembrane domain, core transmembrane domain. The aliphatic residues were extracted from each of these sets and passed through our calculation protocol. Notable observations include: the roles of aliphatic residues in soluble proteins and in the membrane protein’s soluble domains are nearly identical, although the latter are slightly more solvent accessible; by comparing maps calculated with sidechain-lipid interactions to maps ignoring those interactions, the potential extent of residue-lipid and residue-interactions can be assessed and likely exploited in structure prediction and modeling; amongst these residue types, the levels of lipid engagement show isoleucine as the most engaged, while the other residues are largely interacting with neighboring helical residues.

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“…This important component of glycoconjugates found on cell walls has multiple functions including concentrating water on cell surfaces [95] and regulating membrane permeability [96]. It can also enable the regulation of the thickness of the hydration layer surrounding the cell membrane [97], which could prevent system volume change and stabilize membrane protein complexes and membrane structure under pressure [97,98], while also regulating membrane permeability [96]. Modification of the hydration layer properties has also been identified as a specific adaptation mechanism of the piezophilic archaeon Thermococcus barophilus [99].…”

Section: Adaptations To Low Energy and High Pressure Environmentsmentioning

confidence: 99%

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Kerou

Ponce‐Toledo

Zhao

et al. 2020

Preprint

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26Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing 27 archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored 28 inhabitants, that seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. 29We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores 30 obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic 31 placement reveals three independently evolved clades within the order Ca. Nitrosopumilales, of which 32 no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon 33 fixation known from other AOA, all genomes encode an extended capacity for the conversion of 34 fermentation products that can be channeled into the central carbon metabolism, as well as uptake of 35 amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of gene repair systems that may allow to overcome 37 challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine 38 sediments occurred more than once in evolution and resulted in three distinct lineages with particular 39 adaptations to this extremely energy limiting and high-pressure environment. 40 41 42 Introduction 43 44 Ammonia oxidizing archaea (AOA) comprise one of the most successful archaeal phyla having 45 colonized almost every imaginable oxic environment of the planet where they emerge as key players in 46 the nitrogen cycle [1-6]. This includes the marine environment where they dominate archaeal 47 communities associated with oxic sediments ranging from shallow estuaries to the open ocean [7-12], 48and from the surface layers all the way into the deep oceanic crust [13][14][15]. In these ecosystems they 49 seem to play a critical role in the transformation of nitrogen compounds and control its partitioning into 50 the bottom ocean and the underlying oceanic crust [12,[14][15][16][17][18][19]). 52Studies from the North Atlantic and Pacific show that the composition of the sedimentary AOA 53 population differs drastically from that in the overlying water suggesting distinct ecophysiological 54 potential to colonise sedimentary environments, albeit all were found to belong to the order 55 Nitrosopumilales (NP) [20]. Whereas the amoA-NP-gamma clade seems to be dominant and 56 omnipresent in these oceans, irrespective of water depths, the amoA-NP-alpha clade represents the most 57 abundant ecotypes in deep ocean waters [6, 7,[21][22][23][24][25][26][27] (nomenclature based amoA gene classification 58 [28]). In contrast, dominant phylotypes in deep-sea sediments belong to the amoA-NP-theta and amoA-59 NP-delta clades [11, 12]. In addition, in cases of oligotrophic oceanic regions, these were detected 60 throughout the sediment column and further into the underlying basaltic crust, even at depth where 61 oxygen is below detection [7, ...

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The Role of Water in the Responsive Properties in Lipid Interphase of Biomimetic Systems

Cited by 5 publications

References 73 publications

Surprising Rigidity of Functionally Important Water Molecules Buried in the Lipid Headgroup Region

Surprising Rigidity of Functionally Important Water Molecules Buried in the Lipid Headgroup Region

3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

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