Carbodome: Linking Carbon Distribution to Protein Stability and Function | Chapter 5 | Recent Developments in Chemistry and Biochemistry Research Vol. 10

A novel metric Carbodome quantifies the carbon content of amino acid residues, offering insights into their hydrophobic or hydrophilic tendencies and their profound effects on protein stability and function. This study highlights key findings, demonstrating that amino acids with higher Carbodome values, such as tryptophan and phenylalanine, contribute to hydrophobic core stability, while lower Carbodome residues like arginine enhance solubility and surface interactions. The implications of carbon distribution extend to protein folding dynamics, structural integrity, and interactions, providing a foundation for advances in protein engineering, therapeutic design, and disease understanding. These findings underscore the pivotal role of carbon in shaping protein structure and functionality.

 

Author (s) Details

Rajasekaran Ekambaram
V.S.B. Engineering College, Karur-639111, TN, India.

 

Please see the book here:- https://doi.org/10.9734/bpi/rdcbr/v10/3791

How Altered Folding Enables Protein Stability in Aqueous Environments | Chapter 5 | Chemistry and Biochemistry: Research Progress Vol. 3

 Knowledge of the spatial structure of a protein is essential for determining its biological activity and critical for the design of drugs using In Silico techniques. Despite the significant advances in protein structure prediction based on a specific amino acid sequence achieved by the AlphaFold technique based on artificial intelligence through the introduction of artificial intelligence (deep learning) methods in 3D structure prediction methodology, the question concerning the mechanism of the folding process remains unanswered. In the current work, achieving an appropriate ordering of the hydrophobicity distribution in the 3D structure was identified as a determining factor for protein structuring. This paper discusses the structuring process as dependent on two factors: external (environment like water or membrane for example) and internal force field (non-bonding interaction in protein body). The objects of the analysis are proteins with a single mutation showing a different secondary structure and an example of the chameleon sequence, where certain segments with an identical sequence adopt different forms of secondary structure. The paper presents a theoretical model with appreciation to Protein Data Bank and ChSeq databases. The analysis used the fuzzy oil drop model in its modified version (FOD-M). The analysis was performed with In Silico techniques using software of open access status. The importance of the environmental contribution was demonstrated by four proteins with targeted single mutations leading to a change in secondary structure from helical to β. It has also been demonstrated in the example of chameleon sequences with segments of 7 amino acids of identical sequence take adopt different forms of secondary structure. The role of environmental conditions in the folding process was demonstrated quantitatively with a mathematical function, the optimization of which should lead to a structure with a defined biological function. The application of the discussed model introduces the possibility of controlling the folding process. The analysis supports the hypothesis of the folding process as the effect of consensus between the internal force field (non-bonding interaction in the protein body) and external force field which directs the process toward the structure appropriate for environment specificity (water/membrane).

 

Author (s) Details

 

Roterman I
Department of Bioinformatics and Telemedicine, Jagiellonian University – Medical College, 30-688 Krakow, Medyczna 7, Poland.

 

Dulak D
ABB Business Services Sp. z o.o., ul. Zeganska 1, 04-713 Warszawa, Poland.

 

Slupina M
ALSTOM ZWUS Sp. z o.o., Modelarska 12, 40-142, Katowice, Poland.

 

Stapor K
Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland.

 

Konieczny L
Chair of Medical Biochemistry, Jagiellonian University – Medical College, 31-034 Krakow, Kopernika 7, Poland.

 

Please see the book here:- https://doi.org/10.9734/bpi/cbrp/v3/4436

Study on the Characteristics of α-Chymotrypsin Folding Intermediates by Hydrophobic Interaction Chromatography (HIC) | Chapter 2 | Current Advances in Chemistry and Biochemistry Vol. 7

The study of protein folding intermediates is crucial for understanding the folding mechanism of denatured proteins and enhancing protein folding efficiency. A new methodology to define the intermediate of urea-denatured -chymotrypsin (-Chy) was established in this study by using some of the linear parameters of the stoichiometric displacement theory of retention of solute (SDT-R) of hydrophobic interaction chromatography (HIC). As urea concentration (Curea) fluctuates, the contact surface region (Z, S), affinity (logI), and character of interaction force (j) of the -Chy to the stationary phase of HIC (STHIC) between the intermediate (M) and native (N) states were shown to be considerably different. With modifications in Curea, a linear relationship between logI and Z was discovered only for its N state, not for its M state, implying that the interaction force between -Chy in N state and the STHIC is non-selective in N state but selective in M state. In addition, the magnitude of both logI and Z measured in the M state is only a fifth of that in the N state. To discriminate between proteins in the N and M states, all three parameters were used. This finding could be used to distinguish any non-functional protein with a correct three- or four-dimensional molecular structure from their stable M state of any kind of protein, and/or other proteins, in proteome research, protein separation, and a thorough understanding of the intrinsic rule of protein folding in molecular biology.

Author (s) Details

Congyu Ke
College of Chemistry and Chemical Engineering, Xi’an Shiyou University, Xi,’an 710065, China.

Wei Tuo
Schol of Foreign Languages, Xi’an Shiyou University, Xi’an 710065, China.

Wujuan Sun
College of Chemistry and Chemical Engineering, Xi’an Shiyou University, Xi,’an 710065, China.

Jianjun Li
Institute of Modern Separation Science, Shaanxi Key Laboratory of Modern Separation Science, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Northwest University, 710069 Xi’an, P.R. China.

Zhenling Liu
Xinxiang Medical College, Xinxiang, 453003, Henan Province, P.R. China.

Xindu Geng
Institute of Modern Separation Science, Shaanxi Key Laboratory of Modern Separation Science, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Northwest University, 710069 Xi’an, P.R. China.

View Book :- https://stm.bookpi.org/CACB-V7/article/view/1188

Effect of Size of Crowder on Protein Stabilization | Chapter 10 | Recent Research Advances in Biology Vol. 3

 There are a large number of biomolecules responsible for the extremely crowded intracellular environment, which, i.e. the idealised conditions, are entirely different from the dilute solutions. Owing to the existence of macromolecules of various sizes, shapes, and composition, such a crowded environment governs the degree of crowding within a cell. The effect of different sizes and shapes of crowders (ficoll 70, dextran 70, and dextran 40), which are polysaccharides in nature, on the thermodynamic stability of two models of UV-Vis spectroscopy proteins has therefore been investigated. We found that due to the excluded volume effect and the small-sized and rod-shaped crowder, i.e., the level of stabilisation of alpha-lactalbumin and lysozyme increases with the increasing concentration of the crowding agents. In addition to dextran 70 and ficoll 70, dextran 40 resulted in greater stability of both proteins. Because different osmolytes have a functional and structural effect on IDPs, they can help to improve the pathology of different human diseases (such as amyloidosis, neurodegeneration, cancer, and diabetes), with the common hallmark being the aggregation of IDPs. The crowders (sugar osmolyte polymers) used in our research may therefore have clinical implications for diseases, including IDPs.

Author(s) Details

Sumra Shahid
Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.

Ikramul Hasan
Department of Basic Medical Science, Faculty of applied Medical Sciences, Al-Baha University, PO Box: 1988- Al-Baha 65411, Kingdom of Saudi Arabia.

Faizan Ahmad
Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.

Md. Imtaiyaz Hassan
Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.

Asimul Islam

Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.

View Book :- https://bp.bookpi.org/index.php/bpi/catalog/book/343