scholarly journals A simple model for calculating the kinetics of protein folding from three-dimensional structures

1999 ◽  
Vol 96 (20) ◽  
pp. 11311-11316 ◽  
Author(s):  
V. Munoz ◽  
W. A. Eaton
Keyword(s):  
Protein Folding ◽  
Simple Model ◽  
Three Dimensional ◽  
Kinetics Of

Description of a Simple Model for the Study of Bone Calcium Metabolism

1980 ◽  
Vol 19 (01) ◽  
pp. 11-15
Author(s):  
G. Roncari ◽  
L. Rapisardi ◽  
L. Conte ◽  
G. Pedroli
Keyword(s):  
Simple Model ◽  
Calcium Metabolism ◽  
Good Description ◽  
Radioactive Tracer ◽  
Normal Subjects ◽  
Bone Diseases ◽  
Compartment System ◽  
Bone Calcium ◽  
Finite Period ◽  
Kinetics Of

A simple model for the study of bone calcium metabolism is proposed. It describes the kinetics of a radioactive tracer in terms of an open single compartment system with an expanding volume for a finite period of time. In addition to the simplicity of the hypotheses introduced, the model is able to give a good description of the biological processes which regulate calcium kinetics. Moreover the functional parameters can be easily calculated, even just graphically. 15 normal subjects and 22 patients affected by various bone diseases were studied. The results were compared with those obtained by using the model proposed by Burkinshaw et al. and the method described by Reeve et al.

From Levinthal’s Paradox to the Effects of Cell Environmental Perturbation on Protein Folding

2020 ◽  
Vol 26 (42) ◽  
pp. 7537-7554 ◽  
Author(s):  
Juan Zeng ◽  
Zunnan Huang
Keyword(s):  
Protein Folding ◽  
Posttranslational Modifications ◽  
Three Dimensional ◽  
Rational Drug Design ◽  
Basic Knowledge ◽  
Sequence Evolution ◽  
3D Structures ◽  
Folding Mechanism ◽  
Cellular Environment ◽  
Environment Temperature

Background: The rapidly increasing number of known protein sequences calls for more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus providing basic knowledge for rational drug design. Understanding the folding mechanism of proteins is valuable for predicting their 3D structures and for designing proteins with new functions and medicinal applications. Levinthal’s paradox is that although the astronomical number of conformations possible even for proteins as small as 100 residues cannot be fully sampled, proteins in nature normally fold into the native state within timescales ranging from microseconds to hours. These conflicting results reveal that there are factors in organisms that can assist in protein folding. Methods: In this paper, we selected a crowded cell-like environment and temperature, and the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal’s paradox does not reflect the folding mechanism of proteins. We then revealed the effects of these factors on protein folding. Results: The results summarized in this review indicate that a crowded cell-like environment, temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins, thereby regulating the folding process. The balance between entropy and enthalpy is the key to understanding the effect of the crowded cell-like environment and PTMs on protein folding. In addition, the stability/flexibility of proteins is regulated by temperature. Conclusion: This paper concludes that the cellular environment could directly intervene in protein folding. The long-term interactions of the cellular environment and sequence evolution may enable proteins to fold efficiently. Therefore, to correctly understand the folding mechanism of proteins, the effect of the cellular environment on protein folding should be considered.

scholarly journals A Novel Pseudomonas geniculata AGE Family Epimerase/Isomerase and Its Application in d-Mannose Synthesis

Foods ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1809
Author(s):  
Zhanzhi Liu ◽  
Ying Li ◽  
Jing Wu ◽  
Sheng Chen
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Optimal Temperature ◽  
Reaction Conditions ◽  
Enzymatic Production ◽  
Physiological Properties ◽  
Potential Applications ◽  
Kinetics Of ◽  
Optimal Reaction ◽  
Gene Age

d-mannose has exhibited excellent physiological properties in the food, pharmaceutical, and feed industries. Therefore, emerging attention has been applied to enzymatic production of d-mannose due to its advantage over chemical synthesis. The gene age of N-acetyl-d-glucosamine 2-epimerase family epimerase/isomerase (AGEase) derived from Pseudomonas geniculata was amplified, and the recombinant P. geniculata AGEase was characterized. The optimal temperature and pH of P. geniculata AGEase were 60 °C and 7.5, respectively. The Km, kcat, and kcat/Km of P. geniculata AGEase for d-mannose were 49.2 ± 8.5 mM, 476.3 ± 4.0 s−1, and 9.7 ± 0.5 s−1·mM−1, respectively. The recombinant P. geniculata AGEase was classified into the YihS enzyme subfamily in the AGE enzyme family by analyzing its substrate specificity and active center of the three-dimensional (3D) structure. Further studies on the kinetics of different substrates showed that the P. geniculata AGEase belongs to the d-mannose isomerase of the YihS enzyme. The P. geniculata AGEase catalyzed the synthesis of d-mannose with d-fructose as a substrate, and the conversion rate was as high as 39.3% with the d-mannose yield of 78.6 g·L−1 under optimal reaction conditions of 200 g·L−1d-fructose and 2.5 U·mL−1P. geniculata AGEase. This novel P. geniculata AGEase has potential applications in the industrial production of d-mannose.

Chaos in a simple model of the three-dimensional, salt-dominated ocean circulation

1998 ◽  
Vol 14 (7-8) ◽  
pp. 489-502 ◽  
Author(s):  
G. van der Schrier ◽  
L. R. M. Maas
Keyword(s):  
Simple Model ◽  
Ocean Circulation ◽  
Three Dimensional

When rDNA transcription is arrested during mitosis, UBF is still associated with non-condensed rDNA

1997 ◽  
Vol 110 (19) ◽  
pp. 2429-2440 ◽  
Author(s):  
J. Gebrane-Younes ◽  
N. Fomproix ◽  
D. Hernandez-Verdun
Keyword(s):  
Secondary Constriction ◽  
Three Dimensional ◽  
Ribosomal Gene ◽  
Rdna Transcription ◽  
Transcription Machinery ◽  
Late Anaphase ◽  
Early Anaphase ◽  
Dimensional Distribution ◽  
Open Question ◽  
Kinetics Of

The mechanisms that control inactivation of ribosomal gene (rDNA) transcription during mitosis is still an open question. To investigate this fundamental question, the precise timing of mitotic arrest was established. In PtK1 cells, rDNA transcription was still active in prophase, stopped in prometaphase until early anaphase, and activated in late anaphase. Because rDNA transcription can still occur in prophase and late anaphase chromosomes, the kinetics of rDNA condensation during mitosis was questioned. The conformation of the rDNA was analyzed by electron microscopy from the G2/M transition to late anaphase in the secondary constriction, the chromosome regions where the rDNAs are clustered. Whether at transcribing or non-transcribing stages, non-condensed rDNA was observed in addition to axial condensed rDNA. Thus, the persistence of this non-condensed rDNA during inactive transcription argues in favor of the fact that mitotic inactivation is not the consequence of rDNA condensation. Analysis of the three-dimensional distribution of the rDNA transcription factor, UBF, revealed that it was similar at each stage of mitosis in the secondary constriction. In addition, the colocalization of UBF with non-condensed rDNA was demonstrated. This is the first visual evidence of the association of UBF with non-condensed rDNA. As we previously reported that the rDNA transcription machinery remained assembled during mitosis, the colocalization of rDNA fibers with UBF argues in favor of the association of the transcription machinery with certain rDNA copies even in the absence of transcription. If this hypothesis is correct, it can be assumed that condensation of rDNA as well as dissociation of the transcription machinery from rDNA cannot explain the arrest of rDNA transcription during mitosis. It is proposed that modifications of the transcription machinery occurring in prometaphase could explain the arrest of transcription, while reverse modifications in late anaphase could explain activation.

scholarly journals Protein Folding: Search for Basic Physical Models

2003 ◽  
Vol 3 ◽  
pp. 623-635 ◽  
Author(s):  
Ivan Y. Torshin ◽  
Robert W. Harrison
Keyword(s):  
Protein Folding ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Physical Models ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Linear Sequence ◽  
Physical Forces

How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context ofin vivoprotein folding (which has been studied only for a few proteins), the roles of the fundamental physical forces in thein vitrofolding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces). Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

scholarly journals Thermal Properties and Non-Isothermal Crystallization Kinetics of Poly (δ-Valerolactone) and Poly (δ-Valerolactone)/Titanium Dioxide Nanocomposites

Crystals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 452 ◽  
Author(s):  
Waseem Saeed ◽  
Abdel-Basit Al-Odayni ◽  
Abdulaziz Alghamdi ◽  
Ali Alrahlah ◽  
Taieb Aouak
Keyword(s):  
Titanium Dioxide ◽  
Crystallization Kinetics ◽  
Isothermal Crystallization ◽  
Three Dimensional ◽  
Degree Of Crystallinity ◽  
Simultaneous Occurrence ◽  
Scanning Calorimetry ◽  
Isothermal Crystallization Kinetics ◽  
The Stability ◽  
Kinetics Of

New poly (δ-valerolactone)/titanium dioxide (PDVL/TiO2) nanocomposites with different TiO2 nanoparticle loadings were prepared by the solvent-casting method and characterized by Fourier transform infra-red, differential scanning calorimetry, X-ray diffraction and scanning electron microscopy, and thermogravimetry analyses. The results obtained reveal good dispersion of TiO2 nanoparticles in the polymer matrix and non-formation of new crystalline structures indicating the stability of the crystallinity of TiO2 in the composite. A significant increase in the degree of crystallinity was observed with increasing TiO2 content. The non-isothermal crystallization kinetics of the PDVL/TiO2 system indicate that the crystallization process involves the simultaneous occurrence of two- and three-dimensional spherulitic growths. The thermal degradation analysis of this nanocomposite reveals a significant improvement in the thermal stability with increasing TiO2 loading.

A simple model describing the kinetics of the xanthophyll cycle

1991 ◽  
Vol 41 (2) ◽  
pp. 125-129 ◽  
Author(s):  
Jan Sielewiesiuk ◽  
Wiesław I. Gruszecki
Keyword(s):  
Simple Model ◽  
Xanthophyll Cycle ◽  
Kinetics Of

GROWTH OF OXIDE LAYER ON GERMANIUM (011) SUBSTRATE UNDER DRY AND WET ATMOSPHERES

1999 ◽  
Vol 06 (06) ◽  
pp. 1053-1060 ◽  
Author(s):  
N. TABET ◽  
J. AL-SADAH ◽  
M. SALIM
Keyword(s):  
Simple Model ◽  
Oxide Film ◽  
Growth Kinetics ◽  
Photoelectron Spectroscopy ◽  
Early Stage ◽  
X Ray ◽  
Apparent Thickness ◽  
Different Temperatures ◽  
Kinetics Of

X-ray Photoelectron Spectroscopy (XPS) has been used to investigate the oxidation of (011) Ge substrates. The sample surfaces were CP4-etched, then annealed in situ, at different temperatures, for various durations. Dry and wet atmospheres were used. The oxidation rate during the early stage was increased by the presence of moisture in the atmosphere. A simple model was used to define and determine an apparent thickness of the oxide film from XPS measurements. The time dependence of the apparent thickness is consistent with a partial coverage of the surface by oxide islands. The growth kinetics of the oxide islands obeys a nearly cubic law.

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