scholarly journals Allosteric pathway selection in templated assembly

2019 ◽  
Vol 5 (10) ◽  
pp. eaaw3353 ◽  
Author(s):  
Martijn van Galen ◽  
Ruben Higler ◽  
Joris Sprakel
Keyword(s):  
Building Blocks ◽  
Supramolecular Interactions ◽  
High Fidelity ◽  
Self Assembling ◽  
Molecular Building Blocks ◽  
Large Numbers ◽  
Solution Aggregation ◽  
Allosteric Pathway ◽  
Insight Into ◽  
Selection Of

Assembling large numbers of molecular building blocks into functional nanostructures is no trivial task. It relies on guiding building blocks through complex energy landscapes shaped by synergistic and antagonistic supramolecular interactions. In nature, the use of molecular templates is a potent strategy to navigate the process to the desired structure with high fidelity. Yet, nature’s templating strategy remains to be fully exploited in man-made nanomaterials. Designing effective template-guided self-assembling systems can only be realized through precise insight into how the chemical design of building blocks and the resulting balance of repulsive and attractive forces give rise to pathway selection and suppression of trapped states. We develop a minimal model to unravel the kinetic pathways and pathway selection of the templated assembly of molecular building blocks on a template. We show how allosteric activation of the associative interactions can suppress undesired solution-aggregation pathways and gives rise to a true template-assembly path.

scholarly journals Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals

2021 ◽  
Author(s):  
Elaine C. Chen ◽  
Pavlo Gilchuk ◽  
Seth J. Zost ◽  
Naveenchandra Suryadevara ◽  
Emma S. Winkler ◽  
...  
Keyword(s):  
Antibody Responses ◽  
Viral Escape ◽  
Spike Protein ◽  
Heptad Repeat ◽  
Healthy Individuals ◽  
Large Numbers ◽  
Escape Mutants ◽  
Insight Into ◽  
Selection Of

Unrelated individuals can produce genetically similar clones of antibodies, known as public clonotypes, which have been seen in responses to different infectious diseases as well as healthy individuals. Here we identify 37 public clonotypes in memory B cells from convalescent survivors of SARS-CoV-2 infection or in plasmablasts from an individual after vaccination with mRNA-encoded spike protein. We identified 29 public clonotypes, including clones recognizing the receptor-binding domain (RBD) in the spike protein S1 subunit (including a neutralizing, ACE2-blocking clone that protects in vivo), and others recognizing non-RBD epitopes that bound the heptad repeat 1 region of the S2 domain. Germline-revertant forms of some public clonotypes bound efficiently to spike protein, suggesting these common germline-encoded antibodies are preconfigured for avid recognition. Identification of large numbers of public clonotypes provides insight into the molecular basis of efficacy of SARS-CoV-2 vaccines and sheds light on the immune pressures driving the selection of common viral escape mutants.

scholarly journals Redox Activity as a Powerful Strategy to Tune Magnetic and/or Conducting Properties in Benzoquinone-Based Metal-Organic Frameworks

2021 ◽  
Vol 7 (8) ◽  
pp. 109
Author(s):  
Noemi Monni ◽  
Mariangela Oggianu ◽  
Suchithra Ashoka Sahadevan ◽  
Maria Laura Mercuri
Keyword(s):  
Electrode Materials ◽  
Metal Organic Frameworks ◽  
Future Generation ◽  
Building Blocks ◽  
Redox Activity ◽  
Semiquinone Radical ◽  
Molecular Building Blocks ◽  
Redox Active ◽  
Metal Organic ◽  
Selection Of

Multifunctional molecular materials have attracted material scientists for several years as they are promising materials for the future generation of electronic devices. Careful selection of their molecular building blocks allows for the combination and/or even interplay of different physical properties in the same crystal lattice. Incorporation of redox activity in these networks is one of the most appealing and recent synthetic strategies used to enhance magnetic and/or conducting and/or optical properties. Quinone derivatives are excellent redox-active linkers, widely used for various applications such as electrode materials, flow batteries, pseudo-capacitors, etc. Quinones undergo a reversible two-electron redox reaction to form hydroquinone dianions via intermediate semiquinone radical formation. Moreover, the possibility to functionalize the six-membered ring of the quinone by various substituents/functional groups make them excellent molecular building blocks for the construction of multifunctional tunable metal-organic frameworks (MOFs). An overview of the recent advances on benzoquinone-based MOFs, with a particular focus on key examples where magnetic and/or conducting properties are tuned/switched, even simultaneously, by playing with redox activity, is herein envisioned.

α-Hemolysin: A Self-Assembling Protein Pore With Potential Applications In The Synthesis of New Materials

1991 ◽  
Vol 255 ◽  
Author(s):  
Hagan Bayley ◽  
Musti Krishnasastry ◽  
Barbara Walker ◽  
John Kasianowicz
Keyword(s):  
Genetic Manipulation ◽  
Internal Diameter ◽  
New Materials ◽  
Membrane Pores ◽  
Self Assembling ◽  
Assembly Mechanism ◽  
Potential Applications ◽  
Membrane Bound ◽  
Insight Into ◽  
Selection Of

AbstractA selection of nanoscale membrane pores is being constructed by genetic manipulation of α-hemolysin (αHL), a 33.2 kDa polypeptide secreted by the bacterium Staphylococcus aureus, which can self-assemble into hexameric cylindrical channels -1 to 2 nm In Internal diameter. Ultimately, the new pores will be used to confer novel permeability properties upon materials such as thin films utilizing, for example, monolayer sheets of the hexamer. Recombinant αHL (r-αHL) has now been obtained in multimilligram amounts and purified to homogeneity after overexpression of the αHL gene in Escherichia coli. The properties of r-αHL are closely similar to those of αHL purified from S. aureus. Recent deletion mutagenesis experiments have given us new insight into the assembly mechanism of the pore. Three intermediates have been identified: a membrane-bound monomer; an oligomeric pore precursor; and the hexameric pore itself. Currently, point mutogenesis combined with chemical modification is being used to produce new pores of different internal diameter, with selectivity for the passage of molecules and Ions, and with gating properties (the ability to open and close in response to a physical stimulus, e.g. an electric field or light).

scholarly journals Chemical engineering of quasicrystal approximants in lanthanide-based coordination solids

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Laura Voigt ◽  
Mariusz Kubus ◽  
Kasper S. Pedersen
Keyword(s):  
Chemical Engineering ◽  
Organic Materials ◽  
Building Blocks ◽  
Lanthanide Ions ◽  
Two Dimensional ◽  
Ionic Radii ◽  
Coordination Solids ◽  
Self Assembling ◽  
Molecular Building Blocks ◽  
Metal Organic

Abstract Tessellation of self-assembling molecular building blocks is a promising strategy to design metal-organic materials exhibiting geometrical frustration and ensuing frustrated physical properties. Appearing in two-dimensional quasiperiodic phases, tilings consisting of five-vertex nodes are regarded as approximants for quasicrystals. Unfortunately, these structural motifs are exceedingly rare due to the complications of acquiring five-fold coordination confined to the plane. Lanthanide ions display the sufficient coordinative plasticity, and large ionic radii, to allow their incorporation into irregular molecule-based arrays. We herein present the use of ytterbium(II) as a five-vertex node in a two-dimensional coordination solid, YbI2(4,4′-bipyridine)2.5. The semi-regular Archimedean tessellation structure verges on quasicrystallinity and paves the way for lanthanide-based metal-organic materials with interesting photonic and magnetic properties.

Combinatorial Peptide Libraries for Selecting Inorganic-Binding Proteins: A Step in Molecular Biomimetics

2003 ◽  
Vol 773 ◽  
Author(s):  
C. Tamerler ◽  
S. Dinçer ◽  
D. Heidel ◽  
N. Karagûler ◽  
M. Sarikaya
Keyword(s):  
Binding Proteins ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Inorganic Materials ◽  
Combinatorial Peptide Libraries ◽  
Self Assembling ◽  
Complex Functions ◽  
Recent Developments ◽  
Specific Proteins ◽  
Molecular Biomimetics

AbstractProteins, one of the building blocks in organisms, not only control the assembly in biological systems but also provide most of their complex functions. It may be possible to assemble materials for practical technological applications utilizing the unique advantages provided by proteins. Here we discuss molecular biomimetic pathways in the quest for imitating biology at the molecular scale via protein engineering. We use combinatorial biology protocols to select short polypeptides that have affinity to inorganic materials and use them in assembling novel hybrid materials. We give an overview of some of the recent developments of molecular engineering towards this goal. Inorganic surface specific proteins were identified by using cell surface and phage display technologies. Examples of metal and metal oxide specific polypeptides were represented with an emphasis on certain level of specificities. The recognition and self assembling characteristics of these inorganic-binding proteins would be employed in develeopment of hybrid multifunctional materials for novel bio- and nano-technological applications.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

A First Principles Approach for Partitioning Linear Response Properties into Additive and Cooperative Contributions

2018 ◽  
Author(s):  
Daniel Lambrecht ◽  
Eric Berquist
Keyword(s):  
First Principles ◽  
Linear Response ◽  
Building Blocks ◽  
Field Method ◽  
Response Property ◽  
Response Properties ◽  
Consistent Field ◽  
Molecular Building Blocks ◽  
Self Consistent ◽  
Self Consistent Field

We present a first principles approach for decomposing molecular linear response properties into orthogonal (additive) plus non-orthogonal/cooperative contributions. This approach enables one to 1) identify the contributions of molecular building blocks like functional groups or monomer units to a given response property and 2) quantify cooperativity between these contributions. In analogy to the self consistent field method for molecular interactions, SCF(MI), we term our approach LR(MI). The theory, implementation and pilot data are described in detail in the manuscript and supporting information.

Language, procedures, and the non-perceptual origin of natural number concepts

2016 ◽  
Author(s):  
David Barner
Keyword(s):  
General Framework ◽  
Ad Hoc ◽  
Building Blocks ◽  
Number Words ◽  
Linguistic Markers ◽  
Logical Foundations ◽  
Large Numbers ◽  
Perceptual Representations ◽  
Positive Integers ◽  
Perceptual Systems

Perceptual representations – e.g., of objects or approximate magnitudes –are often invoked as building blocks that children combine with linguisticsymbols when they acquire the positive integers. Systems of numericalperception are either assumed to contain the logical foundations ofarithmetic innately, or to supply the basis for their induction. Here Ipropose an alternative to this general framework, and argue that theintegers are not learned from perceptual systems, but instead arise toexplain perception as part of language acquisition. Drawing oncross-linguistic data and developmental data, I show that small numbers(1-4) and large numbers (~5+) arise both historically and in individualchildren via entirely distinct mechanisms, constituting independentlearning problems, neither of which begins with perceptual building blocks.Specifically, I propose that children begin by learning small numbers(i.e., *one, two, three*) using the same logical resources that supportother linguistic markers of number (e.g., singular, plural). Several yearslater, children discover the logic of counting by inferring the logicalrelations between larger number words from their roles in blind countingprocedures, and only incidentally associate number words with perception ofapproximate magnitudes, in an *ad hoc* and highly malleable fashion.Counting provides a form of explanation for perception but is not causallyderived from perceptual systems.

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

Sign in / Sign up

Export Citation Format

Share Document