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Wyniki wyszukiwania dla: PROTEIN–STRUCTURE PREDICTION.
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Review of Research into Enterprise Bankruptcy Prediction in Selected Central and Eastern European Countries
PublikacjaIn developed countries, the first studies on forecasting bankruptcy date to the early 20th century. In Central and Eastern Europe, due to, among other factors, the geopolitical situation and the introduced economic system, this issue became the subject of researcher interest only in the 1990s. Therefore, it is worthwhile to analyze whether these countries conduct bankruptcy risk assessments and what their level of advancement is....
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In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies
PublikacjaDespite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding...
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublikacjaUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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Chemometrics for Selection, Prediction, and Classification of Sustainable Solutions for Green Chemistry—A Review
PublikacjaIn this review, we present the applications of chemometric techniques for green and sustainable chemistry. The techniques, such as cluster analysis, principal component analysis, artificial neural networks, and multivariate ranking techniques, are applied for dealing with missing data, grouping or classification purposes, selection of green material, or processes. The areas of application are mainly finding sustainable solutions...
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Structure and thermal expansion of liquid bismuth
PublikacjaExperimental structural data for liquid Bi were used for estimation of the main structure parameters as well as the thermal expansion coefficient both in supercooled and superheated temperature ranges. It was shown that the equilibrium melt had a positive thermal expansion coefficient within a temperature range upon melting and a negative one at higher temperatures. The former was related to structure changes upon melting, whereas...
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Estimation and Prediction of Vertical Deformations of Random Surfaces, Applying the Total Least Squares Collocation Method
PublikacjaThis paper proposes a method for determining the vertical deformations treated as random fields. It is assumed that the monitored surfaces are subject not only to deterministic deformations, but also to random fluctuations. Furthermore, the existence of random noise coming from surface’s vibrations is also assumed. Such noise disturbs the deformation’s functional models. Surface monitoring with the use of the geodetic levelling...
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Age Prediction from Low Resolution, Dual-Energy X-ray Images Using Convolutional Neural Networks
PublikacjaAge prediction from X-rays is an interesting research topic important for clinical applications such as biological maturity assessment. It is also useful in many other practical applications, including sports or forensic investigations for age verification purposes. Research on these issues is usually carried out using high-resolution X-ray scans of parts of the body, such as images of the hands or images of the chest. In this...
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Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublikacjaIn order to obtain a potential chemotherapeutic which is not affected on the normal BALB/3T3 cell line, a new arene ruthenium(II) complex {[RuCl(L1)(η6-p-cymene)]PF6}2 · H2O has been synthesized by a direct reaction of precursor, [{(η6-p-cymene)Ru(μ-Cl)}2Cl2], with N,N-chelating ligand (L1 - 2,2′-bis(4,5-dimethylimidazole). The compound has been fully characterized by elemental analysis, X-ray diffraction, IR, UV–Vis and 1H, 13C...
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Forewarned Is Forearmed: Machine Learning Algorithms for the Prediction of Catheter-Induced Coronary and Aortic Injuries
PublikacjaCatheter-induced dissections (CID) of coronary arteries and/or the aorta are among the most dangerous complications of percutaneous coronary procedures, yet the data on their risk factors are anecdotal. Logistic regression and five more advanced machine learning techniques were applied to determine the most significant predictors of dissection. Model performance comparison and feature importance ranking were evaluated. We identified...
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Wideband crossover structure with double ring resonators
PublikacjaThe structure of a four-port microstrip crossover is presented. The device is composed of two ring resonators, one circular and one built from meander lines, connected by four straight lines. The equivalent circuit model of the crossover is derived. The structure is designed on thin and flexible substrate to allow it to bend. The possibility of applying the device on curved surfaces is tested experimentally.
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Electrochemical simulation of metabolism for antitumor-active imidazoacridinone C-1311 and in silico prediction of drug metabolic reactions
PublikacjaThe metabolism of antitumor-active 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) has been investigated widely over the last decade but some aspects of molecular mechanisms of its metabolic transformation are still not explained. In the current work, we have reported a direct and rapid analytical tool for better prediction of C-1311 metabolism which is based on electrochemistry (EC) coupled on-line with electrospray...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublikacjaThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Prediction of coking dynamics for wet coal charge
PublikacjaA one-dimensional transient mathematical model describing thermal and flow phenomena during coal coking in an oven chamber was studied in the paper. It also accounts for heat conduction in the ceramic oven wall when assuming a constant temperature at the heating channel side. The model was solved numerically using partly implicit methods for gas flow and heat transfer problems. The histories of temperature, gas evolution and internal...
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Prediction of Deflagrative Explosions in Variety of Closed Vessels
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Creep failure prediction of pipelines in elevated temperature
PublikacjaW pracy omówiono zastoswanie modelu konstytutytwnego pełzania pozwalającego na analizę trwałości metalowych ruruciągów pracujących w wysokich temperaturach. Zaprezentowano wyniki obliczeń opartych na metodzie elementów skończonych (MES) wykonanych z wykorzystaniem procedur użytkownika w komercyjnym programie MES. Porównano wyniki dla dwóch typów 4-węzłowych elementów powłokowych.
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A Stand for Measurement and Prediction of Scattering Properties of Diffusers
PublikacjaIn this paper we present a set of solutions which may be used for prototyping and simulation of acoustic scattering devices. A system proposed is capable of measuring sound field. Also a way to use an open source solution for simulation of scattering phenomena occurring in proximity of acoustic diffusers is shown. The result of our work are measurement procedure and a prototype of the simulation script based on FEniCS - an open source...
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On Bayesian Tracking and Prediction of Radar Cross Section
PublikacjaWe consider the problem of Bayesian tracking of radar cross section. The adopted observation model employs the gamma family, which covers all Swerling cases in a unified framework. State dynamics are modeled using a nonstationary autoregressive gamma process. The principal component of the proposed solution is a nontrivial gamma approximation, applied during the time update recursion. The superior performance of the proposed approach...
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Prediction of Weld Deformations by Numerical Methods - Review
PublikacjaThe welding process is the basic technique of joining in the shipbuilding industry. This method generates welding distortions that cause a lot of problems during the manufacturing process due to both the time and cost of straightening as well as their influence on later stages of production. Proper preparation of welding processes plays a growing role in the shipbuilding industry and the development of calculating tools is being...
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Pitch etection enhancement employing music prediction.
PublikacjaW artykule przedstawiono przegląd metod detekcji częstotliwości podstawowej we frazach muzycznych. Wskazano też główne problemy występujące w procesie estymacji dźwięków muzycznych. W celu zmniejszenia błędów oktawowych zaproponowano uwzględnienie w systemie predyktora neuronalnego. Opracowana przez Autorów metoda predykcji zdarzeń muzycznych wykorzystywana jest jako moduł wspomagający pracę systemu. Proponowane podejście pozwala...
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Highly selective impedimetric determination of Haemophilus influenzae protein D using maze-like boron-doped carbon nanowall electrodes
PublikacjaThis study reports a novel impedimetric immunosensor for protein D detection in purified and bacterial (Haemophilus influenzae, Hi) samples. The detection was based on antigen recognition by anti-protein D antibodies (apD) immobilised at the maze-like boron-doped carbon nanowall electrodes (B:CNW). The B:CNW electrodes were synthesised, and their surface was characterised by scanning electron microscopy (SEM) and X-ray photoelectron...
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Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode
PublikacjaThis work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10−18 to 10−8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10−14 M for PD-L1 (S/N = 3.3) and at a concentration of 10−14...
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Structure and paramagnetism in weakly correlated Y8Co5
PublikacjaWe report the basic physical properties of monoclinic Y8Co5 determined by means of magnetic susceptibility, electrical resistivity, and specific heat measurements. The crystal structure of Y8Co5 is monoclinic (P21/c) with lattice parameters a = 7.0582(6) Å, b = 7.2894(6) Å, c = 24.2234(19) Å, and β = 102.112(6)° as refined by using synchrotron powder x-ray diffraction data. The compound shows temperature independent paramagnetism...
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublikacjaMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Surface Structure of Components Created by Stereolitography
PublikacjaStereolithography is an additive rapid prototyping method. This method is based on the principle of solidifying a liquid photopolymer (resin) by laser radiation. Models obtained with this method are characterized by a specific surface structure called “stairstep effect”. It causes that, the surface should be processed by additional finishing (postprocessing). To minimize the additional machining process, the model should be set...
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Prediction of flow boiling heat transfer data for R134a, R600a and R290 in minichannels
PublikacjaIn the paper presented is the analysis of the results of calculations using a model to predict flow boiling of refrigerants such as R134a, R600a and R290. The latter two fluids were not used in development of model semiempirical correction. For that reason the model was verified with present experimental data. The experimental research was conducted for a full range of quality variation and a relatively wide range of mass velocity....
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Heterogeneity of quaternary structure of glucosamine-6-phosphate deaminase from Giardia lamblia
PublikacjaThe oligoHis-tagged versions of glucosamine-6- phosphate deaminase from Giardia lamblia (GlmNagB-HisN, GlmNagB-HisC) were constructed and purified to hear homogeneity, and their kinetic and structural properties were compared to those of the wild-type enzyme (GlmNagB). Introduction of the oligoHis tag at the GlmNagB C-terminus resulted in almost complete loss of the catalytic activity, while the catalytic properties of GlmNagB-HisN...
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Apple pectin complexes with whey protein isolate
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Some applications of thermophiles and their enzymes for protein processing
PublikacjaPrzedstawiono charakterystykę, właściwości oraz możliwości zastosowań enzymów proteolitycznych wytwarzanych przez termofile. Zaletą tych biokatalizatorów jest między innymi duża odporność na działanie rozpuszczalników organicznych, detergentów i innych czynników denaturujących białka oraz mała wrażliwość na zmiany pH. Dokonano też przeglądu czynników powodujących dużą stabilność proteaz z termofili.
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Pea Protein for Hempseed Oil Nanoemulsion Stabilization
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ANALYSIS OF THE p53 PROTEIN GENE EXPRESSION MODEL
PublikacjaWe study the asymptotic behaviour of the solutions of the p53-Mdm2 model proposed by Monk (2003). The p53 gene is crucial for cellular inhibition of the angiogenesis process, while Mdm2 is a negative regulator of the p53 tumor-suppressor. We investigate the stability of the positive steady state and perform some numerical experiments.
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Polysaccharide–Protein Complexes in a Coarse-Grained Model
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Construction and development of IT Competence Centers - organizational structure
PublikacjaThe author presents the situation of the current units working between academic environment and business. the paper presents the possibility of using a dynamic structure to develop UCC.
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Ontology-based text convolution neural network (TextCNN) for prediction of construction accidents
PublikacjaThe construction industry suffers from workplace accidents, including injuries and fatalities, which represent a significant economic and social burden for employers, workers, and society as a whole.The existing research on construction accidents heavily relies on expert evaluations,which often suffer from issues such as low efficiency, insufficient intelligence, and subjectivity.However, expert opinions provided in construction...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublikacjaA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
PublikacjaControlled ovarian stimulation is tailored to the patient based on clinical parameters but estimating the number of retrieved metaphase II (MII) oocytes is a challenge. Here, we have developed a model that takes advantage of the patient’s genetic and clinical characteristics simultaneously for predicting the stimulation outcome. Sequence variants in reproduction-related genes identified by next-generation sequencing were matched...
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Software modules and application layer's security structure of RSMAD
PublikacjaThe paper discusses the software modules of Radio System for Monitoring and Acquisition of Data from Traffic Enforcement Cameras (in short RSMAD). The structure of the application layer of the system has also been analysed in details, including: purpose, structure and principles of operation of software modules constituting this system. In addition, the paper presents and discusses the structure of security of application layer...
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Sequence variants of p21 gene of the MRL/MpJ mouse: a possible association with the deficit of p21 protein and regenerative phenotype.
PublikacjaThe MRL/MpJ mouse is known for its enhanced regeneration abilities that manifested themselves by scarless ear-hole wound closure. The deficit of p21 found in the MRL is associated with the regenerative capacity as the p21 gene knockout in a mouse strain unrelated to the MRL mouse results in an ear-hole closure effect, similar to that observed in the MRL mouse. Cdkn1a gene encodes p21 protein, a cyclin-dependent kinase inhibitor,...
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Why is the cubic structure preferred in newly formed ice?
PublikacjaMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
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FFT analysis of temperature modulated semiconductor gas sensor response for the prediction of ammonia concentration under humidity interference
PublikacjaThe increasing environmental contamination forces the need to design reliable devices for detecting of the volatile compounds present in the air. For this purpose semiconductor gas sensors, which have been widely used for years, are often utilized. Although they have many advantages such as low price and quite long life time, they still lack of long term stability and selectivity. Namely, environmental conditions have significant...
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Fatigue life prediction of notched components under size effect using strain energy reformulated critical distance theory
PublikacjaNotch and size effects show significant impact on the fatigue performance of engineering components, which deserves special attention. In this work, a strain energy reformulated critical distance theory was developed for fatigue life prediction of notched components under size effect. Experimental data of different notched specimens manufactured from GH4169, TC4, TC11 alloys and low carbon steel En3B were used for model validation...
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Influence of dopants on structure of polycrystalline bismuth niobate
PublikacjaBismuth niobate (BiNbO4) has attracted attention as a low-fired ceramics with promising microwave application potential. BiNbO4 ceramics was fabricated by mixed oxide method and sintered at temperature T<1000˚C. As the sintering aids a small amount of CuO oxide was used. The crystalline structure of the ceramic samples was examined by X-ray diffraction method at room temperature. The Rietveld refinement method was used for analysis...
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Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease
PublikacjaWe previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation...
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Ultrasound assisted synthesis of 3-alkynyl substituted 2-chloroquinoxaline derivatives: Their in silico assessment as potential ligands for N-protein of SARS-CoV-2
PublikacjaIn view of recent global pandemic the 3-alkynyl substituted 2-chloroquinoxaline framework has been explored as a potential template for the design of molecules targeting COVID-19. Initial in silico studies of representative compounds to assess their binding affinities via docking into the N-terminal RNA-binding domain (NTD) of N-protein of SARS-CoV-2 prompted further study of these molecules. Thus building of a small library of...
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublikacjaThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein
PublikacjaThe environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy...
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Prediction of flow boiling heat transfer coefficient for carbon dioxide in minichannels and conventional channels
PublikacjaIn the paper are presented the results of calculations using authors own model to predict heat transfer coefficient during flow boiling for carbon dioxide. The experimental data from various researches were scrutinised conducted for a full range of quality variation and wide range of mass velocity. The aim of the study was to test the sensitivity of the in-house model. The work shows the importance of taking into account surface...
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Effect of chemical structure on complexation efficiency of aromatic drugs with cyclodextrins: The example of dibenzazepine derivatives
PublikacjaIt is widely believed that the hydrophobic effect governs the binding of guest molecules to cyclodextrins (CDs). However, it is also known that high hydrophobicity of guest molecules does not always translate to the formation of stable inclusion complexes with CDs. Indeed, a plethora of other factors can play a role in the efficiency of guest–CD interactions, rendering structure-based prediction of the complexation efficiency with...
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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublikacjaHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...