scholarly journals Adhesion mechanisms of curli subunit CsgA to abiotic surfaces

2016 ◽  
Vol 2 (11) ◽  
pp. e1600998 ◽  
Author(s):  
Elizabeth P. DeBenedictis ◽  
Jenny Liu ◽  
Sinan Keten
Keyword(s):  
Collective Motion ◽  
Point Mutations ◽  
Structural Features ◽  
Strong Interactions ◽  
Surface Attachment ◽  
Silica Surfaces ◽  
Abiotic Surfaces ◽  
Correlated Motion ◽  
Functional Amyloids ◽  
The Stability

Curli fibers are functional amyloids that play a key role in biofilm structure and adhesion to various surfaces. Strong bioinspired adhesives comprising curli fibers have recently been created; however, the mechanisms curli uses to attach onto abiotic surfaces are still uncharacterized. Toward a materials-by-design approach for curli-based adhesives and multifunctional materials, we examine curli subunit adsorption onto graphene and silica surfaces through atomistic simulation. We find that both structural features and sequence influence adhesive strength, enabling the CsgA subunit to adhere strongly to both polar and nonpolar surfaces. Specifically, flexible regions facilitate adhesion to both surfaces, charged and polar residues (Arg, Lys, and Gln) enable strong interactions with silica, and six-carbon aromatic rings (Tyr and Phe) adsorb strongly to graphene. We find that adsorption not only lowers molecular mobility but also leads to loss of secondary structure, factors that must be well balanced for effective surface attachment. Both events appear to propagate through the CsgA structure as correlated motion between clusters of residues, often H-bonded between rows on adjacent β strands. To quantify this, we present a correlation analysis approach to detecting collective motion between residue groups. We find that certain clusters of residues have a higher impact on the stability of the rest of the protein structure, often polar and bulky groups within the helix core. These findings lend insight into bacterial adhesion mechanisms and reveal strategies for theory-driven design of engineered curli fibers that harness point mutations and conjugates for stronger adhesion.

scholarly journals Superconducting edge states in a topological insulator

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
I. V. Yurkevich ◽  
V. Kagalovsky
Keyword(s):  
Topological Insulator ◽  
Time Reversal ◽  
Collective Motion ◽  
Effective Theory ◽  
Strong Interactions ◽  
Time Reversal Symmetry ◽  
Edge States ◽  
Translation Invariant ◽  
Clean System ◽  
The Stability

AbstractWe study the stability of multiple conducting edge states in a topological insulator against perturbations allowed by the time-reversal symmetry. A system is modeled as a multi-channel Luttinger liquid, with the number of channels equal to the number of Kramers doublets at the edge. Assuming strong interactions and weak disorder, we first formulate a low-energy effective theory for a clean translation invariant system and then include the disorder terms allowed by the time-reversal symmetry. In a clean system with N Kramers doublets, N − 1 edge states are gapped by Josephson couplings and the single remaining gapless mode describes collective motion of Cooper pairs synchronous across the channels. Disorder perturbation in this regime, allowed by the time reversal symmetry is a simultaneous backscattering of particles in all N channels. Its relevance depends strongly on the parity if the number of channel N is not very large. Our main result is that disorder becomes irrelevant with the increase of the number of edge modes leading to the stability of the edge states superconducting regime even for repulsive interactions.

scholarly journals Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region

2017 ◽  
Vol 114 (42) ◽  
pp. 11115-11120 ◽  
Author(s):  
Binnu Gangadharan ◽  
Margaret S. Sunitha ◽  
Souhrid Mukherjee ◽  
Ritu Roy Chowdhury ◽  
Farah Haque ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Troponin T ◽  
Point Mutations ◽  
Structural Features ◽  
Sarcomeric Proteins ◽  
Binding Assays ◽  
Genes Encoding ◽  
The Stability ◽  
Insight Into

Point mutations in genes encoding sarcomeric proteins are the leading cause of inherited primary cardiomyopathies. Among them are mutations in the TNNT2 gene that encodes cardiac troponin T (TnT). These mutations are clustered in the tropomyosin (Tm) binding region of TnT, TNT1 (residues 80–180). To understand the mechanistic changes caused by pathogenic mutations in the TNT1 region, six hypertrophic cardiomyopathy (HCM) and two dilated cardiomyopathy (DCM) mutants were studied by biochemical approaches. Binding assays in the absence and presence of actin revealed changes in the affinity of some, but not all, TnT mutants for Tm relative to WT TnT. HCM mutants were hypersensitive and DCM mutants were hyposensitive to Ca2+ in regulated actomyosin ATPase activities. To gain better insight into the disease mechanism, we modeled the structure of TNT1 and its interactions with Tm. The stability predictions made by the model correlated well with the affinity changes observed in vitro of TnT mutants for Tm. The changes in Ca2+ sensitivity showed a strong correlation with the changes in binding affinity. We suggest the primary reason by which these TNNT2 mutations between residues 92 and 144 cause cardiomyopathy is by changing the affinity of TnT for Tm within the TNT1 region.

Exo-bonded six-membered heterocycle in the crystal structures of RE7Co2Ge4(RE = La–Nd)

2016 ◽  
Vol 45 (46) ◽  
pp. 18522-18531 ◽  
Author(s):  
Siméon Ponou ◽  
Sven Lidin
Keyword(s):  
Crystal Structures ◽  
Strong Interactions ◽  
The Stability ◽  
Membered Heterocycle

The stability of the heterocyclic {Co4Ge6} clusters in RE7Co2Ge4(RE = La–Nd) is determined by strong interactions with the surrounding RE atoms in the structures.

scholarly journals Promiscuous Cross-seeding between Bacterial Amyloids Promotes Interspecies Biofilms

2012 ◽  
Vol 287 (42) ◽  
pp. 35092-35103 ◽  
Author(s):  
Yizhou Zhou ◽  
Daniel Smith ◽  
Bryan J. Leong ◽  
Kristoffer Brännström ◽  
Fredrik Almqvist ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shewanella Oneidensis ◽  
Bacterial Attachment ◽  
Surface Attachment ◽  
E Coli ◽  
Amyloid Aggregates ◽  
Functional Amyloids ◽  
Biofilm Development ◽  
Distant Homolog

Amyloids are highly aggregated proteinaceous fibers historically associated with neurodegenerative conditions including Alzheimers, Parkinsons, and prion-based encephalopathies. Polymerization of amyloidogenic proteins into ordered fibers can be accelerated by preformed amyloid aggregates derived from the same protein in a process called seeding. Seeding of disease-associated amyloids and prions is highly specific and cross-seeding is usually limited or prevented. Here we describe the first study on the cross-seeding potential of bacterial functional amyloids. Curli are produced on the surface of many Gram-negative bacteria where they facilitate surface attachment and biofilm development. Curli fibers are composed of the major subunit CsgA and the nucleator CsgB, which templates CsgA into fibers. Our results showed that curli subunit homologs from Escherichia coli, Salmonella typhimurium LT2, and Citrobacter koseri were able to cross-seed in vitro. The polymerization of Escherichia coli CsgA was also accelerated by fibers derived from a distant homolog in Shewanella oneidensis that shares less than 30% identity in primary sequence. Cross-seeding of curli proteins was also observed in mixed colony biofilms with E. coli and S. typhimurium. CsgA was secreted from E. coli csgB− mutants assembled into fibers on adjacent S. typhimurium that presented CsgB on its surfaces. Similarly, CsgA was secreted by S. typhimurium csgB− mutants formed curli on CsgB-presenting E. coli. This interspecies curli assembly enhanced bacterial attachment to agar surfaces and supported pellicle biofilm formation. Collectively, this work suggests that the seeding specificity among curli homologs is relaxed and that heterogeneous curli fibers can facilitate multispecies biofilm development.

FABRICATION OF NANOPOROUS CHITOSAN MEMBRANES

NANO ◽  
2010 ◽  
Vol 05 (01) ◽  
pp. 53-60 ◽  
Author(s):  
XIAOLIANG WANG ◽  
XIANG LI ◽  
ELEANOR STRIDE ◽  
MOHAN EDIRISINGHE
Keyword(s):  
Low Frequency ◽  
Drug Carriers ◽  
Structural Features ◽  
Wound Dressings ◽  
Ftir Analysis ◽  
Tissue Engineering Scaffolds ◽  
Nanoscale Structures ◽  
Low Frequency Ultrasound ◽  
Chitosan Membranes ◽  
The Stability

Naturally derived biopolymers have been widely used for biomedical applications such as drug carriers, wound dressings, and tissue engineering scaffolds. Chitosan is a typical polysaccharide of great interest due to its biocompatibility and film-formability. Chitosan membranes with controllable porous structures also have significant potential in membrane chromatography. Thus, the processing of membranes with porous nanoscale structures is of great importance, but it is also challenging and this has limited the application of these membranes to date. In this study, with the aid of a carefully selected surfactant, polyethyleneglycol stearate-40, chitosan membranes with a well controlled nanoscale structure were successfully prepared. Additional control over the membrane structure was obtained by exposing the suspension to high intensity, low frequency ultrasound. It was found that the concentration of chitosan/surfactant ratio and the ultrasound exposure conditions affect the structural features of the membranes. The stability of nanopores in the membrane was improved by intensive ultrasonication. Furthermore, the stability of the blended suspensions and the intermolecular interactions between chitosan and the surfactant were investigated using scanning electron microscope and Fourier transform infrared spectroscopy (FTIR) analysis, respectively. Hydrogen bonds and possible reaction sites for molecular interactions in the two polymers were also confirmed by FTIR analysis.

Invited review: Importance of animal health and welfare for the stability of the three pillars of sustainability of livestock systems

2016 ◽  
Vol 7 (2) ◽  
pp. 208-214
Author(s):  
P. Chemineau
Keyword(s):  
Animal Welfare ◽  
Production Systems ◽  
Animal Health ◽  
Holistic Approach ◽  
Population Increase ◽  
Strong Interactions ◽  
Essential Components ◽  
The Future ◽  
The Stability ◽  
Livestock Systems

The future livestock systems at the world level will have to produce more in the perspective of the population increase in the next 30 years, whereas reducing their environmental footprint and addressing societal concerns. In that perspective, we may wonder if animal health and animal welfare, which are two essential components of production systems, may play an important role in the stability of the three pillars of sustainability of the livestock systems. We already know that objectives driven by economy, environment and society may modify animal welfare and animal health, but is the reverse true? The answer is yes and in 11 cases out of 12 of the matrix health-welfare×3 pillars of sustainability×positive or negative change, we have many examples indicating that animal health and animal welfare are able to modify, positively or negatively, the three pillars of sustainability. Moreover, we also have good examples of strong interactions between health and welfare. These elements play in favour of an holistic approach at the farm level and of a multicriterial definition of what could be the sustainable systems of animal production in the future which will respect animal welfare and maintain a good animal health.

scholarly journals Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain

2020 ◽  
Author(s):  
Mohamed Raef Smaoui ◽  
Hamdi Yahyaoui
Keyword(s):  
Receptor Binding ◽  
Single Point ◽  
Protein Structures ◽  
Point Mutations ◽  
Binding Domain ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Point Mutant ◽  
The Stability ◽  
Spike Proteins

Abstract The interaction between the receptor-binding domain of the SARS-CoV-2 spike glycoprotein and the ACE2 enzyme is believed to be the entry point of the virus into various cells in the body, including the lungs, heart, liver, and kidneys. The current focus of several therapeutic design efforts explore attempts at affecting the binding interaction between the two proteins to limit the activity of the virus and disease progression. In this work, we analyze the stability of the spike protein under all possible single-point mutations in the receptor-binding domain and computationally explore mutations that can affect the binding with the ACE2 enzyme. We unravel the mutation landscape of the receptor region and assess the toxicity potential of single and multi-point mutations, generating insights for future vaccine efforts on potential mutations that might further stabilize the spike protein and increase its infectivity. We developed a tool, called SpikeMutator, to construct full atomic protein structures of the mutant spike proteins and shared a database of 3,800 single-point mutant structures. We analyzed the recent 65,000 reported spike sequences across the globe and observed the emergence of stable multi-point mutant structures. Using the landscape, we searched through 7.5 million possible 2-point mutation combinations and report that the (R355D K424E) mutation produces one of the strongest spike proteins that therapeutic efforts should investigate for the sake of developing an effective vaccine.

scholarly journals Surface-Tension-Confined Channel with Biomimetic Microstructures for Unidirectional Liquid Spreading

Micromachines ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 978
Author(s):  
Yi Zhang ◽  
Yang Gan ◽  
Liwen Zhang ◽  
Deyuan Zhang ◽  
Huawei Chen
Keyword(s):  
Surface Tension ◽  
Underlying Mechanism ◽  
Structural Features ◽  
Liquid Motion ◽  
Water Separation ◽  
Lab On Chip ◽  
Liquid Spreading ◽  
Oil Water Separation ◽  
On Chip ◽  
The Stability

Unidirectional liquid spreading without energy input is of significant interest for the broad applications in diverse fields such as water harvesting, drop transfer, oil–water separation and microfluidic devices. However, the controllability of liquid motion and the simplification of manufacturing process remain challenges. Inspired by the peristome of Nepenthes alata, a surface-tension-confined (STC) channel with biomimetic microcavities was fabricated facilely through UV exposure photolithography and partial plasma treatment. Perfect asymmetric liquid spreading was achieved by combination of microcavities and hydrophobic boundary, and the stability of pinning effect was demonstrated. The influences of structural features of microcavities on both liquid spreading and liquid pinning were investigated and the underlying mechanism was revealed. We also demonstrated the spontaneous unidirectional transport of liquid in 3D space and on tilting slope. In addition, through changing pits arrangement and wettability pattern, complex liquid motion paths and microreactors were realized. This work will open a new way for liquid manipulation and lab-on-chip applications.

Crystallographic analysis and biochemical applications of a novel penicillin-binding protein/β-lactamase homologue from a metagenomic library

2014 ◽  
Vol 70 (9) ◽  
pp. 2455-2466 ◽  
Author(s):  
Tri Duc Ngo ◽  
Bum Han Ryu ◽  
Hansol Ju ◽  
Eun Jin Jang ◽  
Kyeong Kyu Kim ◽  
...  
Keyword(s):  
Metagenomic Library ◽  
Structural Features ◽  
Crystallographic Analysis ◽  
Penicillin Binding Protein ◽  
Hydrophobic Residues ◽  
Penicillin Binding Proteins ◽  
Hydrophobic Compounds ◽  
Nitrophenyl Phosphate ◽  
Biophysical Studies ◽  
The Stability

Interest in penicillin-binding proteins and β-lactamases (the PBP-βL family) is increasing owing to their biological and clinical significance. In this study, the crystal structure of Est-Y29, a metagenomic homologue of the PBP-βL family, was determined at 1.7 Å resolution. In addition, complex structures of Est-Y29 with 4-nitrophenyl phosphate (4NP) and with diethyl phosphonate (DEP) at 2.0 Å resolution were also elucidated. Structural analyses showed that Est-Y29 is composed of two domains: a β-lactamase fold and an insertion domain. A deep hydrophobic patch between these domains defines a wide active site, and a nucleophilic serine (Ser58) residue is located in a groove defined primarily by hydrophobic residues between the two domains. In addition, three hydrophobic motifs, which make up the substrate-binding site, allow this enzyme to hydrolyze a wide variety of hydrophobic compounds, including fish and olive oils. Furthermore, cross-linked Est-Y29 aggregates (CLEA-Est-Y29) significantly increase the stability of the enzyme as well as its potential for extensive reuse in various deactivating conditions. The structural features of Est-Y29, together with biochemical and biophysical studies, could provide a molecular basis for understanding the properties and regulatory mechanisms of the PBP-βL family and their potential for use in industrial biocatalysts.

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