The Influence of Dipeptide Composition on Protein Folding Rates

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.378-379.157 ◽

2011 ◽

Vol 378-379 ◽

pp. 157-160

Author(s):

Jian Xiu Guo ◽

Ni Ni Rao

Keyword(s):

Protein Folding ◽

Amino Acid ◽

Amino Acid Sequences ◽

Dipeptide Composition ◽

Coupling Effects ◽

Jackknife Test ◽

Folding Rates ◽

Important Challenge ◽

The Relationship

Understanding the relationship between amino acid sequences and folding rates of proteins is an important challenge in computational and molecular biology. All existing algorithms for predicting protein folding rates have never taken into account the sequence coupling effects. In this work, a novel algorithm was developed for predicting the protein folding rates from amino acid sequences. The prediction was achieved on the basis of dipeptide composition, in which the sequence coupling effects are explicitly included through a series of conditional probability elements. Based on a non-redundant dataset of 99 proteins, the proposed method was found to provide an excellent agreement between the predicted and experimental folding rates of proteins when evaluated with the jackknife test. The correlation coefficient was 87.7% and the standard error was 2.04, which indicated the important contribution from sequence coupling effects to the determination of protein folding rates.

Download Full-text

PREDICTING PROTEIN FOLDING RATE FROM AMINO ACID SEQUENCE

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720011005306 ◽

2011 ◽

Vol 09 (01) ◽

pp. 1-13 ◽

Cited By ~ 8

Author(s):

JIANXIU GUO ◽

NINI RAO

Keyword(s):

Protein Folding ◽

Amino Acid ◽

Amino Acid Sequence ◽

Structural Information ◽

Protein Structures ◽

Amino Acid Sequences ◽

Folding Rate ◽

Jackknife Test ◽

Folding Rates ◽

Protein Folding Rate

Predicting protein folding rate from amino acid sequence is an important challenge in computational and molecular biology. Over the past few years, many methods have been developed to reflect the correlation between the folding rates and protein structures and sequences. In this paper, we present an effective method, a combined neural network — genetic algorithm approach, to predict protein folding rates only from amino acid sequences, without any explicit structural information. The originality of this paper is that, for the first time, it tackles the effect of sequence order. The proposed method provides a good correlation between the predicted and experimental folding rates. The correlation coefficient is 0.80 and the standard error is 2.65 for 93 proteins, the largest such databases of proteins yet studied, when evaluated with leave-one-out jackknife test. The comparative results demonstrate that this correlation is better than most of other methods, and suggest the important contribution of sequence order information to the determination of protein folding rates.

Download Full-text

Study on the Influence of mRNA, the Genetic Language, on Protein Folding Rates

Frontiers in Genetics ◽

10.3389/fgene.2021.635250 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ruifang Li ◽

Hong Li ◽

Xue Feng ◽

Ruifeng Zhao ◽

Yongxia Cheng

Keyword(s):

Protein Folding ◽

Amino Acid ◽

Protein Structures ◽

Gc Content ◽

Amino Acid Sequences ◽

Information Redundancy ◽

Folding Rate ◽

Folding Rates ◽

Related Information ◽

Linear Regressions

Many works have reported that protein folding rates are influenced by the characteristics of amino acid sequences and protein structures. However, few reports on the problem of whether the corresponding mRNA sequences are related to the protein folding rates can be found. An mRNA sequence is regarded as a kind of genetic language, and its vocabulary and phraseology must provide influential information regarding the protein folding rate. In the present work, linear regressions on the parameters of the vocabulary and phraseology of mRNA sequences and the corresponding protein folding rates were analyzed. The results indicated that D2 (the adjacent base-related information redundancy) values and the GC content values of the corresponding mRNA sequences exhibit significant negative relations with the protein folding rates, but D1 (the single base information redundancy) values exhibit significant positive relations with the protein folding rates. In addition, the results show that the relationships between the parameters of the genetic language and the corresponding protein folding rates are obviously different for different protein groups. Some useful parameters that are related to protein folding rates were found. The results indicate that when predicting protein folding rates, the information from protein structures and their amino acid sequences is insufficient, and some information for regulating the protein folding rates must be derived from the mRNA sequences.

Download Full-text

The Influences of Palindromes in mRNA on Protein Folding Rates

Protein and Peptide Letters ◽

10.2174/0929866526666191014144015 ◽

2020 ◽

Vol 27 (4) ◽

pp. 303-312 ◽

Cited By ~ 1

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.

Download Full-text

A head-activator binding protein is present in hydra in a soluble and a membrane-anchored form

Development ◽

10.1242/dev.126.18.4077 ◽

1999 ◽

Vol 126 (18) ◽

pp. 4077-4086 ◽

Cited By ~ 3

Author(s):

W. Hampe ◽

J. Urny ◽

I. Franke ◽

S.A. Hoffmeister-Ullerich ◽

D. Herrmann ◽

...

Keyword(s):

Stem Cells ◽

Amino Acid ◽

Transmembrane Domain ◽

Binding Protein ◽

Amino Acid Sequences ◽

Secreted Protein ◽

Specific Antibodies ◽

Head Activator ◽

Carboxy Terminal

The neuropeptide head activator plays an important role for proliferation and determination of stem cells in hydra. By affinity chromatography a 200 kDa head-activator binding protein, HAB, was isolated from the multiheaded mutant of Chlorohydra viridissima. Partial amino acid sequences were used to clone the HAB cDNA which coded for a receptor with a unique alignment of extracellular modules, a transmembrane domain, and a short carboxy-terminal cytoplasmic tail. A mammalian HAB homologue with identical alignment of these modules is expressed early in brain development. Specific antibodies revealed the presence of HAB in hydra as a transmembrane receptor, but also as secreted protein, both capable of binding head activator. Secretion of HAB during regeneration and expression in regions of high determination potential hint at a role for HAB in regulating the concentration and range of action of head activator.

Download Full-text

Pepsinogens and Pepsins from House Musk Shrew, Suncus murinus: Purification, Characterization, Determination of the Amino-Acid Sequences of the Activation Segments, and Analysis of Proteolytic Specificities

The Journal of Biochemistry ◽

10.1093/oxfordjournals.jbchem.a021687 ◽

1997 ◽

Vol 121 (6) ◽

pp. 1010-1017 ◽

Cited By ~ 12

Author(s):

Y. Narita ◽

S.-i. Oda ◽

A. Moriyama ◽

O. Takenaka ◽

T. Kageyama

Keyword(s):

Amino Acid ◽

Amino Acid Sequences ◽

Suncus Murinus ◽

Musk Shrew

Download Full-text

Structure and function of voltage-dependent sodium channels: comparison of brain II and cardiac isoforms

Physiological Reviews ◽

10.1152/physrev.1996.76.3.887 ◽

1996 ◽

Vol 76 (3) ◽

pp. 887-926 ◽

Cited By ~ 193

Author(s):

H. A. Fozzard ◽

D. A. Hanck

Keyword(s):

Amino Acid ◽

Three Dimensional ◽

Point Mutations ◽

Amino Acid Sequences ◽

Na Channel ◽

Na Channels ◽

Voltage Dependent ◽

And Function ◽

Relationship Of ◽

The Relationship

Cardiac and nerve Na channels have broadly similar functional properties and amino acid sequences, but they demonstrate specific differences in gating, permeation, ionic block, modulation, and pharmacology. Resolution of three-dimensional structures of Na channels is unlikely in the near future, but a number of amino acid sequences from a variety of species and isoforms are known so that channel differences can be exploited to gain insight into the relationship of structure to function. The combination of molecular biology to create chimeras and channels with point mutations and high-resolution electrophysiological techniques to study function encourage the idea that predictions of structure from function are possible. With the goal of understanding the special properties of the cardiac Na channel, this review examines the structural (sequence) similarities between the cardiac and nerve channels and considers what is known about the relationship of structure to function for voltage-dependent Na channels in general and for the cardiac Na channels in particular.

Download Full-text

Determination of Factor Xa Activity by Means of Chromogenic Substrates Based on the Primary Structure of Prothrombin

10.1055/s-0039-1689426 ◽

1975 ◽

Cited By ~ 1

Author(s):

L. Aurell ◽

A. Olausson ◽

G. Claeson

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Primary Structure ◽

Serine Proteases ◽

Factor Xa ◽

Amino Acid Sequences ◽

Peptide Substrate ◽

Chromogenic Substrates ◽

Special Regard

Through the work of Magnusson and co-workers leading to the elucidation of the primary structure of prothrombin including the amino acid sequences around the two bonds split by factor Xa it has been possible to design a synthetic chromogenic peptide substrate. Bz-Ile-Glu-Gly-Arg-pNA, specifically intended for the determination of factor Xa. Furthermore, additional substrates have been synthezised with various alterations in the amino acid sequence. The activity of factor Xa and other serine proteases within the coagulation and fibrinolytic systems towards these substrates will be discussed with special regard to their possible use in coagulation studies.

Download Full-text