scholarly journals Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL

Biochemistry ◽  
2021 ◽  
Vol 60 (6) ◽  
pp. 460-464
Author(s):  
Eda Koculi ◽  
D. Thirumalai
Keyword(s):  
Folding Rates ◽  
Substrate Proteins

scholarly journals Retardation of folding rates of substrate proteins in the nanocage of GroEL

2020 ◽  
Author(s):  
Eda Koculi ◽  
D. Thirumalai
Keyword(s):  
Short Duration ◽  
Time Scale ◽  
Folding Rate ◽  
E Coli ◽  
Biological Time ◽  
Folding Rates ◽  
Substrate Proteins ◽  
Do So

AbstractThe E. Coli. ATP-consuming chaperonin machinery, a complex between GroEL and GroES, has evolved to facilitate folding of substrate proteins (SPs) that cannot do so spontaneously. A series of kinetic experiments show that the SPs are encapsulated in the GroEL/ES nano cage for a short duration. If confining the SPs in the predominantly polar cage of GroEL in order to help folding, the assisted folding rate, relative to the bulk value, should always be enhanced. Here, we show that this is not the case for the folding of rhodanese in the presence of the full machinery of GroEL/ES and ATP. The assisted folding rate of rhodanese decreases. Based on our finding and those reported in other studies, we suggest that the ATP-consuming chaperonin machinery has evolved to optimize the product of the folding rate and the yield of the folded SPs on the biological time scale. Neither the rate nor the yield is separately maximized.

An Effective Cumulative Torsion Angles Model for Prediction of Protein Folding Rates

2020 ◽  
Vol 27 (4) ◽  
pp. 321-328 ◽  
Author(s):  
Yanru Li ◽  
Ying Zhang ◽  
Jun Lv
Keyword(s):  
Protein Folding ◽  
Size Structure ◽  
Conformational Space ◽  
Coefficient Of Determination ◽  
Folding Rate ◽  
Torsion Angles ◽  
Folding Rates ◽  
Protein Folding Rate ◽  
Optimal Set ◽  
Conformation Space

Background: Protein folding rate is mainly determined by the size of the conformational space to search, which in turn is dictated by factors such as size, structure and amino-acid sequence in a protein. It is important to integrate these factors effectively to form a more precisely description of conformation space. But there is no general paradigm to answer this question except some intuitions and empirical rules. Therefore, at the present stage, predictions of the folding rate can be improved through finding new factors, and some insights are given to the above question. Objective: Its purpose is to propose a new parameter that can describe the size of the conformational space to improve the prediction accuracy of protein folding rate. Method: Based on the optimal set of amino acids in a protein, an effective cumulative backbone torsion angles (CBTAeff) was proposed to describe the size of the conformational space. Linear regression model was used to predict protein folding rate with CBTAeff as a parameter. The degree of correlation was described by the coefficient of determination and the mean absolute error MAE between the predicted folding rates and experimental observations. Results: It achieved a high correlation (with the coefficient of determination of 0.70 and MAE of 1.88) between the logarithm of folding rates and the (CBTAeff)0.5 with experimental over 112 twoand multi-state folding proteins. Conclusion: The remarkable performance of our simplistic model demonstrates that CBTA based on optimal set was the major determinants of the conformation space of natural proteins.

The Influences of Palindromes in mRNA on Protein Folding Rates

2020 ◽  
Vol 27 (4) ◽  
pp. 303-312 ◽  
Author(s):  
Ruifang Li ◽  
Hong Li ◽  
Sarula Yang ◽  
Xue Feng
Keyword(s):  
Protein Folding ◽  
Regression Analysis ◽  
Linear Regression ◽  
Linear Regression Analysis ◽  
Folding Rate ◽  
Folding Rates ◽  
Negative Linear Correlation ◽  
Protein Folding Rate ◽  
The Relationship ◽  
Structure Environment

Background: It is currently believed that protein folding rates are influenced by protein structure, environment and temperature, amino acid sequence and so on. We have been working for long to determine whether and in what ways mRNA affects the protein folding rate. A large number of palindromes aroused our attention in our previous research. Whether these palindromes do have important influences on protein folding rates and what’s the mechanism? Very few related studies are focused on these problems. Objective: In this article, our motivation is to find out if palindromes have important influences on protein folding rates and what’s the mechanism. Method: In this article, the parameters of the palindromes were defined and calculated, the linear regression analysis between the values of each parameter and the experimental protein folding rates were done. Furthermore, to compare the results of different kinds of proteins, proteins were classified into the two-state proteins and the multi-state proteins. For the two kinds of proteins, the above linear regression analysis were performed respectively. Results : Protein folding rates were negatively correlated to the palindrome frequencies for all proteins. An extremely significant negative linear correlation appeared in the relationship between palindrome densities and protein folding rates. And the repeatedly used bases by different palindromes simultaneously have an important effect on the relationship between palindrome density and protein folding rate. Conclusion: The palindromes have important influences on protein folding rates, and the repeatedly used bases in different palindromes simultaneously play a key role in influencing the protein folding rates.

scholarly journals Mechanism of the small ATP-independent chaperone Spy is substrate specific

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rishav Mitra ◽  
Varun V. Gadkari ◽  
Ben A. Meinen ◽  
Carlo P. M. van Mierlo ◽  
Brandon T. Ruotolo ◽  
...  
Keyword(s):  
Relative Affinity ◽  
Complex Protein ◽  
Partially Unfolded ◽  
Substrate Proteins ◽  
Partially Unfolded States

AbstractATP-independent chaperones are usually considered to be holdases that rapidly bind to non-native states of substrate proteins and prevent their aggregation. These chaperones are thought to release their substrate proteins prior to their folding. Spy is an ATP-independent chaperone that acts as an aggregation inhibiting holdase but does so by allowing its substrate proteins to fold while they remain continuously chaperone bound, thus acting as a foldase as well. The attributes that allow such dual chaperoning behavior are unclear. Here, we used the topologically complex protein apoflavodoxin to show that the outcome of Spy’s action is substrate specific and depends on its relative affinity for different folding states. Tighter binding of Spy to partially unfolded states of apoflavodoxin limits the possibility of folding while bound, converting Spy to a holdase chaperone. Our results highlight the central role of the substrate in determining the mechanism of chaperone action.

scholarly journals Protein lysine crotonylation: past, present, perspective

2021 ◽  
Vol 12 (7) ◽  
Author(s):  
Gaoyue Jiang ◽  
Chunxia Li ◽  
Meng Lu ◽  
Kefeng Lu ◽  
Huihui Li
Keyword(s):  
Cross Talk ◽  
Tissue Injury ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Histone Proteins ◽  
Physiological Functions ◽  
Neuropsychiatric Disease ◽  
Enzymatic Mechanisms ◽  
Substrate Proteins ◽  
Tools And Methods

AbstractLysine crotonylation has been discovered in histone and non-histone proteins and found to be involved in diverse diseases and biological processes, such as neuropsychiatric disease, carcinogenesis, spermatogenesis, tissue injury, and inflammation. The unique carbon–carbon π-bond structure indicates that lysine crotonylation may use distinct regulatory mechanisms from the widely studied other types of lysine acylation. In this review, we discussed the regulation of lysine crotonylation by enzymatic and non-enzymatic mechanisms, the recognition of substrate proteins, the physiological functions of lysine crotonylation and its cross-talk with other types of modification. The tools and methods for prediction and detection of lysine crotonylation were also described.

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