scholarly journals Temperature-dependent Self assembly of biofilaments during red blood cell sickling

2021 ◽  
Author(s):  
Arabinda Behera ◽  
Oshin Sharma ◽  
Debjani Paul ◽  
Anirban Sain
Keyword(s):  
Self Assembly ◽  
Kinetic Monte Carlo ◽  
Lag Time ◽  
Vital Role ◽  
Temperature Dependent ◽  
Opposite Case ◽  
Assembly Kinetics ◽  
The Mean ◽  
Kinetics Of

Molecular self-assembly plays vital role in various biological functions. However, when aberrant molecules self-assemble to form large aggregates, it can give rise to various diseases. For example, the sickle cell disease and Alzheimer’s disease are caused by self-assembled hemoglobin fibers and amyloid plaques, respectively. Here we study the assembly kinetics of such fibers using kinetic Monte-Carlo simulation. We focus on the initial lag time of these highly stochastic processes, during which self-assembly is very slow. The lag time distributions turn out to be similar for two very different regimes of polymerization, namely, a) when polymerization is slow and depolymerization is fast, and b) the opposite case, when polymerization is fast and depolymerization is slow. Using temperature dependent on- and off-rates for hemoglobin fiber growth, reported in recent in-vitro experiments, we show that the mean lag time can exhibit non-monotonic behaviour with respect to change of temperature.

scholarly journals Measurements of the Self-Assembly Kinetics of Individual Viral Capsids Around Their RNA Genome

2018 ◽  
Author(s):  
Rees F. Garmann ◽  
Aaron M. Goldfain ◽  
Vinothan N. Manoharan
Keyword(s):  
Self Assembly ◽  
Structural Complexity ◽  
High Yield ◽  
Growth Time ◽  
Coat Proteins ◽  
Viral Capsids ◽  
Assembly Kinetics ◽  
Pathogenic Viruses ◽  
Kinetics Of

The formation of a viral capsid-the highly—ordered protein shell that surrounds the genome of a virus—is the canonical example of self-assembly1. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro mixtures of the coat protein and RNA2. The high yield of proper capsids that assemble is remarkable, given their structural complexity: 180 identical proteins must arrange into three distinct local configurations to form an icosahedral capsid with a triangulation number of 3 (T = 3)1. Despite a wealth of data from structural studies3–5 and simulations6–10, even the most fundamental questions about how these structures assemble remain unresolved. Experiments have not determined whether the assembly pathway involves aggregation or nucleation, or how the RNA controls the process. Here we use interferometric scattering microscopy11,12 to directly observe the in vitro assembly kinetics of individual, unlabeled capsids of bacteriophage MS2. By measuring how many coat proteins bind to each of many individual MS2 RNA strands on time scales from 1 ms to 900 s, we find that the start of assembly is broadly distributed in time and is followed by a rapid increase in the number of bound proteins. These measurements provide strong evidence for a nucleation-and-growth pathway. We also find that malformed structures assemble when multiple nuclei appear on the same RNA before the first nucleus has finished growing. Our measurements reveal the complex assembly pathways for viral capsids around RNA in quantitative detail, including the nucleation threshold, nucleation time, growth time, and constraints on the critical nucleus size. These results may inform strategies for engineering synthetic capsids13 or for derailing the assembly of pathogenic viruses14.

scholarly journals The assembly of microtubule protein in vitro. The kinetic role in microtubule elongation of oligomeric fragments containing microtubule-associated proteins

1985 ◽  
Vol 227 (2) ◽  
pp. 439-455 ◽  
Author(s):  
P M Bayley ◽  
F M M Butler ◽  
D C Clark ◽  
E J Manser ◽  
S R Martin
Keyword(s):  
Self Assembly ◽  
Protein Concentration ◽  
Wavelength Dependence ◽  
Electrophoretic Analysis ◽  
Slow Phase ◽  
Condensation Polymerization ◽  
Fast Phase ◽  
Microtubule Protein ◽  
Kinetics Of

The kinetics of assembly were studied for bovine and pig microtubule protein in vitro over a range of conditions of pH, temperature, nucleotide and protein concentration. The kinetics are in general biphasic with two major processes of similar amplitude but separated in rate by one order of magnitude. Rates and amplitudes are complex functions of solution conditions. The rates of the fast phase and the slow phase attain limiting values as a function of increasing protein concentration, and are more stringently limited at pH 6.5 than pH 6.95. Such behaviour indicates that mechanisms other than the condensation polymerization of tubulin dimer become rate-limiting at higher protein concentration. The constancy of the wavelength-dependence of light-scattering and ultrastructural criteria indicate that microtubules of normal morphology are formed in both phases of the assembly process. Electrophoretic analysis of assembling microtubule protein shows that MAP- (microtubule-associated-protein-)rich microtubules are formed during the fast phase. The rate of dissociation of oligomeric species on dilution of microtubule protein closely parallels the fast-phase rate in magnitude and temperature-dependence. We propose that the rate of this process constitutes an upper limit to the rate of the fast phase of assembly. The kinetics of redistribution of MAPs from MAP-rich microtubules may be a factor limiting the slow-phase rate. A working model is derived for the self-assembly of microtubule protein incorporating the dissociation and redistribution mechanisms that impose upper limits to the rates of assembly attainable by bimolecular addition reactions. Key roles are assigned to MAP-containing fragments in both phases of microtubule elongation. Variations in kinetic behaviour with solution conditions are inferred to derive from the nature and properties of fragments formed from oligomeric species after the rapid temperature jump. The model accounts for the limiting rate behaviour and indicates experimental criteria to be applied in evaluating the relative contributions of alternative pathways.

scholarly journals Temperature Dependent Seed Germination of Dalbergia nigra Allem (Leguminosae)

2001 ◽  
Vol 44 (4) ◽  
pp. 401-404 ◽  
Author(s):  
Fernanda G. A. Ferraz-Grande ◽  
Massanori Takaki
Keyword(s):  
Seed Germination ◽  
Endangered Species ◽  
High Temperatures ◽  
Broad Temperature Range ◽  
Optimum Temperature ◽  
Temperature Dependent ◽  
Temperature Range ◽  
Dalbergia Nigra ◽  
The Mean ◽  
Kinetics Of

The germination of endangered species Dalbergia nigra was studied and 30.5° C was found as optimum temperature, although the species presented a broad temperature range where germination occurs and light had no effect. The analysis of kinetics of seed germination confirmed the asynchronized germination below and above the optimum temperature. The light insensitive seed and germination also at high temperatures indicated that D. nigra could occur both in understories and gaps where the mean temperature was high.

Fast Self-Assembly Kinetics of Quantum Dots and a Dendrimeric Peptide Ligand

Langmuir ◽  
2012 ◽  
Vol 28 (21) ◽  
pp. 7962-7966 ◽  
Author(s):  
Jianhao Wang ◽  
Pengju Jiang ◽  
Zuoyan Han ◽  
Lin Qiu ◽  
Cheli Wang ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Self Assembly ◽  
Peptide Ligand ◽  
Assembly Kinetics ◽  
Kinetics Of

The role of sucrose concentration in self-assembly kinetics of high methoxyl pectin

2018 ◽  
Vol 112 ◽  
pp. 1183-1190 ◽  
Author(s):  
Daniela Giacomazza ◽  
Donatella Bulone ◽  
Pier Luigi San Biagio ◽  
Rosamaria Marino ◽  
Romano Lapasin
Keyword(s):  
Self Assembly ◽  
Sucrose Concentration ◽  
Assembly Kinetics ◽  
Kinetics Of

scholarly journals Self-Assembly Kinetics of Amphiphilic Dendritic Copolymers

2017 ◽  
Vol 50 (4) ◽  
pp. 1657-1665 ◽  
Author(s):  
Cuiyun Zhang ◽  
You Fan ◽  
Yunyi Zhang ◽  
Cong Yu ◽  
Hongfei Li ◽  
...  
Keyword(s):  
Self Assembly ◽  
Assembly Kinetics ◽  
Kinetics Of

Enhancing the Directed Self-assembly Kinetics of Block Copolymers Using Binary Solvent Mixtures

2015 ◽  
Vol 7 (46) ◽  
pp. 25843-25850 ◽  
Author(s):  
Woon Ik Park ◽  
Young Joong Choi ◽  
Je Moon Yun ◽  
Suck Won Hong ◽  
Yeon Sik Jung ◽  
...  
Keyword(s):  
Block Copolymers ◽  
Self Assembly ◽  
Binary Solvent ◽  
Solvent Mixtures ◽  
Binary Solvent Mixtures ◽  
Assembly Kinetics ◽  
Kinetics Of

scholarly journals Small-Molecule Effectors of Hepatitis B Virus Capsid Assembly Give Insight into Virus Life Cycle

2008 ◽  
Vol 82 (20) ◽  
pp. 10262-10270 ◽  
Author(s):  
Christina Bourne ◽  
Sejin Lee ◽  
Bollu Venkataiah ◽  
Angela Lee ◽  
Brent Korba ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Small Molecule ◽  
Self Assembly ◽  
Binding Pocket ◽  
Hbv Replication ◽  
B Virus ◽  
In Vitro Assembly ◽  
Kinetics Of

ABSTRACT The relationship between the physical chemistry and biology of self-assembly is poorly understood, but it will be critical to quantitatively understand infection and for the design of antivirals that target virus genesis. Here we take advantage of heteroaryldihydropyrimidines (HAPs), which affect hepatitis B virus (HBV) assembly, to gain insight and correlate in vitro assembly with HBV replication in culture. Based on a low-resolution crystal structure of a capsid-HAP complex, a closely related series of HAPs were designed and synthesized. These differentially strengthen the association between neighboring capsid proteins, alter the kinetics of assembly, and give rise to aberrant structures incompatible with a functional capsid. The chemical nature of the HAP variants correlated well with the structure of the HAP binding pocket. The thermodynamics and kinetics of in vitro assembly had strong and predictable effects on product morphology. However, only the kinetics of in vitro assembly had a strong correlation with inhibition of HBV replication in HepG2.2.15 cells; there was at best a weak correlation between assembly thermodynamics and replication. The correlation between assembly kinetics and virus suppression implies a competition between successful assembly and misassembly, small molecule induced or otherwise. This is a predictive and testable model for the mechanism of action of assembly effectors.

scholarly journals The release of toxic oligomers from α-synuclein fibrils induces dysfunction in neuronal cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Roberta Cascella ◽  
Serene W. Chen ◽  
Alessandra Bigi ◽  
José D. Camino ◽  
Catherine K. Xu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Inclusion Bodies ◽  
Neuronal Damage ◽  
Cellular Systems ◽  
The Self ◽  
Brain Areas ◽  
Rapid Release ◽  
Neuronal Membranes ◽  
Kinetics Of

AbstractThe self-assembly of α-synuclein (αS) into intraneuronal inclusion bodies is a key characteristic of Parkinson’s disease. To define the nature of the species giving rise to neuronal damage, we have investigated the mechanism of action of the main αS populations that have been observed to form progressively during fibril growth. The αS fibrils release soluble prefibrillar oligomeric species with cross-β structure and solvent-exposed hydrophobic clusters. αS prefibrillar oligomers are efficient in crossing and permeabilize neuronal membranes, causing cellular insults. Short fibrils are more neurotoxic than long fibrils due to the higher proportion of fibrillar ends, resulting in a rapid release of oligomers. The kinetics of released αS oligomers match the observed kinetics of toxicity in cellular systems. In addition to previous evidence that αS fibrils can spread in different brain areas, our in vitro results reveal that αS fibrils can also release oligomeric species responsible for an immediate dysfunction of the neurons in the vicinity of these species.

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