scholarly journals Loops linking secondary structure elements affect the stability of molten globule intermediate state of apomyoglobin

2019 ◽  
Author(s):  
M.A. Majorina ◽  
B.S. Melnik
Keyword(s):  
Protein Folding ◽  
Secondary Structure ◽  
Rate Constant ◽  
Intermediate State ◽  
Molten Globule ◽  
Protein Secondary Structure ◽  
Free Energies ◽  
Real Effect ◽  
Unfolded State ◽  
The Stability

AbstractApomyoglobin is a protein widely used as a model for studying globular protein folding. This work aimed to test the hypothesis on influence of rigidity and length of loops linking protein secondary structure elements on the stability of molten globule intermediate state. For this purpose, we studied folding/unfolding of mutant apomyoglobin forms with substitutions of proline residues to glycine and with loops elongated by three and six glycine residues. For all the protein forms, denaturation/renaturation kinetic curves at different urea concentrations were obtained, folding/unfolding constants were calculated and dependencies of rate constant logarithms on urea concentrations were plotted. All the data gave an opportunity to calculate free energies of different apomyoglobin states. As a result, the mutations in apomyoglobin loops were demonstrated to have a real effect on intermediate state stability compared to unfolded state.

scholarly journals Loops linking secondary structure elements affect the stability of the molten globule intermediate state of apomyoglobin

FEBS Letters ◽  
2020 ◽  
Vol 594 (20) ◽  
pp. 3293-3304
Author(s):  
Maria A. Majorina ◽  
Vitaly A. Balobanov ◽  
Vladimir N Uversky ◽  
Bogdan S. Melnik
Keyword(s):  
Secondary Structure ◽  
Intermediate State ◽  
Molten Globule ◽  
The Stability

scholarly journals Protein secondary structure prediction (PSSP) using different machine algorithms

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Heba M. Afify ◽  
Mohamed B. Abdelhalim ◽  
Mai S. Mabrouk ◽  
Ahmed Y. Sayed
Keyword(s):  
Secondary Structure ◽  
Decision Tree ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Protein Secondary Structure ◽  
Support Vector ◽  
Protein Secondary Structure Prediction ◽  
The Stability ◽  
Protein Datasets ◽  
Future Work

Abstract Background The computational biology approach has advanced exponentially in protein secondary structure prediction (PSSP), which is vital for the pharmaceutical industry. Extracting protein structure from the laboratory has insufficient information for PSSP that is used in bioinformatics studies. In this paper, the support vector machine (SVM) model and decision tree are presented on the RS126 dataset to address the problem of PSSP. A decision tree is applied for the SVM outcome to obtain the relevant guidelines possible for PSSP. Furthermore, the number of produced rules was fairly small, and they show a greater degree of comprehensibility compared to other rules. Several of the proposed principles have compelling and relevant biological clarification. Results The results confirmed that the existence of a particular amino acid in a protein sequence increases the stability for the forecast of protein secondary structure. The suggested algorithm achieved 85% accuracy for the E|~E classifier. Conclusions The proposed rules can be very important in managing wet laboratory experiments intended at determining protein secondary structure. Lastly, future work will focus mainly on large protein datasets without overfitting and expand the amount of extracted regulations for PSSP.

PROTEIN FOLDING ON THE HEXAGONAL LATTICE IN THE HP MODEL

2005 ◽  
Vol 03 (01) ◽  
pp. 19-34 ◽  
Author(s):  
MINGHUI JIANG ◽  
BINHAI ZHU
Keyword(s):  
Monte Carlo ◽  
Protein Folding ◽  
Secondary Structure ◽  
Hexagonal Lattice ◽  
Protein Secondary Structure ◽  
Square Lattice ◽  
Enumeration Algorithm ◽  
Hp Model ◽  
Sharp Turn ◽  
Partial Enumeration

In this paper, we introduce the 2D hexagonal lattice as a biologically meaningful alternative to the standard square lattice for the study of protein folding in the HP model. We show that the hexagonal lattice alleviates the "sharp turn" problem and models certain aspects of the protein secondary structure more realistically. We present a ⅙-approximation and a clustering heuristic for protein folding on the hexagonal lattice. In addition to these two algorithms, we also implement a Monte Carlo Metropolis algorithm and a branch-and-bound partial enumeration algorithm, and conduct experiments to compare their effectiveness.

Study of the ?molten globule? intermediate state in protein folding by a hydrophobic fluorescent probe

Biopolymers ◽  
1991 ◽  
Vol 31 (1) ◽  
pp. 119-128 ◽  
Author(s):  
G. V. Semisotnov ◽  
N. A. Rodionova ◽  
O. I. Razgulyaev ◽  
V. N. Uversky ◽  
A. F. Gripas' ◽  
...  
Keyword(s):  
Protein Folding ◽  
Fluorescent Probe ◽  
Intermediate State ◽  
Molten Globule

Stability and Folding of the Unusually Stable Hemoglobin from Synechocystis is Subtly Optimized and Dependent on the Key Heme Pocket Residues.

2020 ◽  
Vol 27 ◽  
Author(s):  
Sheetal Uppal ◽  
Mohd. Asim Khan ◽  
Suman Kundu
Keyword(s):  
Molten Globule ◽  
Life Forms ◽  
Model System ◽  
Heme Pocket ◽  
The Past ◽  
Specific Manner ◽  
Delivery Vehicles ◽  
The Stability ◽  
Key Residues ◽  
Synechocystis Sp

Aims: The aim of our study is to understand the biophysical traits that govern the stability and folding of Synechocystis hemoglobin, a unique cyanobacterial globin that displays unusual traits not observed in any of the other globins discovered so far. Background: For the past few decades, classical hemoglobins such as vertebrate hemoglobin and myoglobin have been extensively studied to unravel the stability and folding mechanisms of hemoglobins. However, the expanding wealth of hemoglobins identified in all life forms with novel properties, like heme coordination chemistry and globin fold, have added complexity and challenges to the understanding of hemoglobin stability, which has not been adequately addressed. Here, we explored the unique truncated and hexacoordinate hemoglobin from the freshwater cyanobacterium Synechocystis sp. PCC 6803 known as “Synechocystis hemoglobin (SynHb)”. The “three histidines” linkages to heme are novel to this cyanobacterial hemoglobin. Objective: Mutational studies were employed to decipher the residues within the heme pocket that dictate the stability and folding of SynHb. Methods: Site-directed mutants of SynHb were generated and analyzed using a repertoire of spectroscopic and calorimetric tools. Result: The results revealed that the heme was stably associated to the protein under all denaturing conditions with His117 playing the anchoring role. The studies also highlighted the possibility of existence of a “molten globule” like intermediate at acidic pH in this exceptionally thermostable globin. His117 and other key residues in the heme pocket play an indispensable role in imparting significant polypeptide stability. Conclusion: Synechocystis hemoglobin presents an important model system for investigations of protein folding and stability in general. The heme pocket residues influenced the folding and stability of SynHb in a very subtle and specific manner and may have been optimized to make this Hb the most stable known as of date. Other: The knowledge gained hereby about the influence of heme pocket amino acid side chains on stability and expression is currently being utilized to improve the stability of recombinant human Hbs for efficient use as oxygen delivery vehicles.

A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

2019 ◽  
Vol 16 (2) ◽  
pp. 159-172 ◽  
Author(s):  
Elaheh Kashani-Amin ◽  
Ozra Tabatabaei-Malazy ◽  
Amirhossein Sakhteman ◽  
Bagher Larijani ◽  
Azadeh Ebrahim-Habibi
Keyword(s):  
Systematic Review ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Web Of Science ◽  
Secondary Structure Prediction ◽  
Structural Information ◽  
Protein Secondary Structure ◽  
Structural Features ◽  
Prediction Tools ◽  
Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

scholarly journals Complexes of Copper and Iron with Pyridoxamine, Ascorbic Acid, and a Model Amadori Compound: Exploring Pyridoxamine’s Secondary Antioxidant Activity

Antioxidants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 208
Author(s):  
Guillermo García-Díez ◽  
Roger Monreal-Corona ◽  
Nelaine Mora-Diez
Keyword(s):  
Antioxidant Activity ◽  
Ascorbic Acid ◽  
Rate Constant ◽  
Stable Complex ◽  
Aqueous Environment ◽  
Oh Radicals ◽  
Bidentate Ligands ◽  
Superoxide Radical Anion ◽  
Amadori Compound ◽  
The Stability

The thermodynamic stability of 11 complexes of Cu(II) and 26 complexes of Fe(III) is studied, comprising the ligands pyridoxamine (PM), ascorbic acid (ASC), and a model Amadori compound (AMD). In addition, the secondary antioxidant activity of PM is analyzed when chelating both Cu(II) and Fe(III), relative to the rate constant of the first step of the Haber-Weiss cycle, in the presence of the superoxide radical anion (O2•−) or ascorbate (ASC−). Calculations are performed at the M05(SMD)/6-311+G(d,p) level of theory. The aqueous environment is modeled by making use of the SMD solvation method in all calculations. This level of theory accurately reproduces the experimental data available. When put in perspective with the stability of various complexes of aminoguanidine (AG) (which we have previously studied), the following stability trends can be found for the Cu(II) and Fe(III) complexes, respectively: ASC < AG < AMD < PM and AG < ASC < AMD < PM. The most stable complex of Cu(II) with PM (with two bidentate ligands) presents a ΔGf0 value of −35.8 kcal/mol, whereas the Fe(III) complex with the highest stability (with three bidentate ligands) possesses a ΔGf0 of −58.9 kcal/mol. These complexes can significantly reduce the rate constant of the first step of the Haber-Weiss cycle with both O2•− and ASC−. In the case of the copper-containing reaction, the rates are reduced up to 9.70 × 103 and 4.09 × 1013 times, respectively. With iron, the rates become 1.78 × 103 and 4.45 × 1015 times smaller, respectively. Thus, PM presents significant secondary antioxidant activity since it is able to inhibit the production of ·OH radicals. This work concludes a series of studies on secondary antioxidant activity and allows potentially new glycation inhibitors to be investigated and compared relative to both PM and AG.

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