scholarly journals A comparison of the secondary structure of human brain mitochondrial and cytosolic ‘malic’ enzyme investigated by Fourier-transform infrared spectroscopy

1995 ◽  
Vol 309 (2) ◽  
pp. 607-611 ◽  
Author(s):  
Z Kochan ◽  
J Karbowska ◽  
G Bukato ◽  
M M Zydowo ◽  
E Bertoli ◽  
...  
Keyword(s):  
Fourier Transform ◽  
Secondary Structure ◽  
Human Brain ◽  
Ir Spectra ◽  
Conformational Changes ◽  
Malic Enzyme ◽  
Tertiary Structure ◽  
Alpha Helix ◽  
Random Structure ◽  
Mitochondrial Enzymes

The secondary structure of human brain cytosolic and mitochondrial ‘malic’ enzymes purified to homogeneity has been investigated by Fourier-transform IR spectroscopy. The absorbance IR spectra of these two isoenzymes were slightly different, but calculated secondary-structure compositions were essentially similar (38% alpha-helix, 38-39% beta-sheet, 14% beta-turn and 9-10% random structure). These proportions were not affected by succinate, a positive effector of mitochondrial ‘malic’ enzyme activity. IR spectra indicate that the tertiary structures of human brain cytosolic and mitochondrial ‘malic’ enzymes are slightly different, and addition of succinate does not cause conformational changes to the tertiary structure of the mitochondrial enzyme. Thermal-denaturation patterns of the cytosolic and mitochondrial enzymes, obtained from spectra recorded at different temperatures in the absence or presence of Mg2+, suggest that the tertiary structure of both isoenzymes is stabilized by bivalent cations and that the cytosolic enzyme possesses a more compact tertiary structure.

scholarly journals Conformational changes in gastric H+/K+-ATPase monitored by difference Fourier-transform infrared spectroscopy and hydrogen/deuterium exchange

2004 ◽  
Vol 382 (1) ◽  
pp. 121-129 ◽  
Author(s):  
Frantz SCHEIRLINCKX ◽  
Vincent RAUSSENS ◽  
Jean-Marie RUYSSCHAERT ◽  
Erik GOORMAGHTIGH
Keyword(s):  
Fourier Transform ◽  
Secondary Structure ◽  
Conformational Changes ◽  
Tertiary Structure ◽  
Structural Information ◽  
Deuterium Exchange ◽  
Attenuated Total Reflection ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium ◽  
Difference Fourier

Gastric H+/K+-ATPase is a P-type ATPase responsible for acid secretion in the stomach. This protein adopts mainly two conformations called E1 and E2. Even though two high-resolution structures for a P-ATPase in these conformations are available, little structural information is available about the transition between these two conformations. In the present study, we used two experimental approaches to investigate the structural differences that occur when gastric ATPase is placed in the presence of various ligands and ligand combinations. We used attenuated total reflection–Fourier-transform IR experiments under a flowing buffer to modify the environment of the protein inside the measurement cell. The high accuracy of the results allowed us to demonstrate that the E1–E2 transition induces a net change in the secondary structure that concerns 10–15 amino acid residues of a total of 1324 in the proteins. The E2.K+ structure is characterized by a decreased β-sheet content and an increase in the disordered structure content with respect to the E1 form of the enzyme. Modifications in the absorption of the side chain of amino acids are also suggested. By using hydrogen/deuterium-exchange kinetics, we show that tertiary-structure modifications occurred in the presence of the same ligands, but these changes involved several hundreds of residues. The present study suggests that conformational changes in the catalytic cycle imply secondary-structure rearrangements of small hinge regions that have an impact on large domain re-organizations.

In Silico Study of Secondary Structure of Hemoglobin Protein

2021 ◽  
pp. 6245-6249
Author(s):  
Roma Chandra
Keyword(s):  
Secondary Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Prediction Methods ◽  
Protein Secondary Structures

Protein structure prediction is one of the important goals in the area of bioinformatics and biotechnology. Prediction methods include structure prediction of both secondary and tertiary structures of protein. Protein secondary structure prediction infers knowledge related to presence of helixes, sheets and coils in a polypeptide chain whereas protein tertiary structure prediction infers knowledge related to three dimensional structures of proteins. Protein secondary structures represent the possible motifs or regular expressions represented as patterns that are predicted from primary protein sequence in the form of alpha helix, betastr and and coils. The secondary structure prediction is useful as it infers information related to the structure and function of unknown protein sequence. There are various secondary structure prediction methods used to predict about helixes, sheets and coils. Based on these methods there are various prediction tools under study. This study includes prediction of hemoglobin using various tools. The results produced inferred knowledge with reference to percentage of amino acids participating to produce helices, sheets and coils. PHD and DSC produced the best of the results out of all the tools used.

Fourier-transform infrared and circular dichroism studies on temperature dependence of the secondary structure of troponin C from bullfrog skeletal muscle

1991 ◽  
Vol 69 (11) ◽  
pp. 1679-1684 ◽  
Author(s):  
Tatsuyuki Yamamoto ◽  
Mitsuo Tasumi ◽  
Masaru Tanokura
Keyword(s):  
Skeletal Muscle ◽  
Fourier Transform ◽  
Circular Dichroism ◽  
Secondary Structure ◽  
Tertiary Structure ◽  
Fourier Transform Infrared ◽  
Difference Spectrum ◽  
Troponin C ◽  
Free Protein ◽  
Circular Dichroïsm

The infrared spectra and circular dichroism of bullfrog (Rana catesbeiana) skeletal muscle troponin C with and without Ca2+ have been measured in aqueous solution at temperatures between 24 and 80 °C at pH 7.0. Infrared spectral changes with increasing temperature, particularly in the amide I region, have been extensively examined by using the techniques of thermal difference spectrum and deconvolution. Ca2+-free troponin C seems to be denatured at about 70 °C, but its denaturation proceeds gradually without an abrupt structural change. Ca2+ binding causes a considerable change in the secondary structure of the whole protein. Consequently, Ca2+-bound troponin C has a higher α-helix content and is thermally more stable than the Ca2+-free protein. Both the deconvolved amide I bands and circular dichroism data indicate that there are similarities between the secondary structure (and probably the tertiary structure as well) of the Ca2+-bound protein at 80 °C and that of the Ca2+-free protein at room temperature. Key words: bullfrog skeletal muscle troponin C, Fourier transform infrared and circular dichroism studies.

scholarly journals Prediction and Fourier-transform infrared-spectroscopy estimation of the secondary structure of a recombinant β-glucosidase from Streptomyces sp. (ATCC 11238)

1995 ◽  
Vol 308 (3) ◽  
pp. 791-794 ◽  
Author(s):  
J A Perez-Pons ◽  
E Padros ◽  
E Querol
Keyword(s):  
Fourier Transform ◽  
Secondary Structure ◽  
Alpha Helix ◽  
Beta Sheet ◽  
Computer Algorithms ◽  
Computer Prediction ◽  
Ordered Structures ◽  
Streptomyces Sp ◽  
Helix 23 ◽  
Beta Glucosidase

The secondary structure of a recombinant beta-glucosidase (EC 3.2.1.21) from Streptomyces sp. (ATCC 11238) has been predicted by computer algorithms and also estimated by Fourier-transform IR spectroscopy. From curve fitting of the deconvoluted IR spectra, the most probable distribution of the secondary-structural classes appears to be about 34% alpha-helix, 30% beta-sheet, 25% reverse turns and 11% non-ordered structures. These data showed a good agreement with data from computer prediction (35% alpha-helix, 23% beta-sheet, 31% reverse turns and 11% non-ordered structures).

scholarly journals Predicción computacional de estructura terciaria de las proteínas humanas Hsp27, αB-cristalina y HspB8

2011 ◽  
Vol 16 (1) ◽  
pp. 15 ◽  
Author(s):  
Homero Sáenz-Suárez ◽  
Leonardo René Lareo ◽  
Carlos Oribio-Quinto ◽  
Juan Martínez-Mendoza ◽  
Aura Chávez-Zobel
Keyword(s):  
Secondary Structure ◽  
Tertiary Structure ◽  
Alpha Helix ◽  
Tertiary Structures ◽  
Mutant Proteins ◽  
Native Proteins ◽  
Multiple Alignments ◽  
Human Proteins ◽  
Computational Predictions ◽  
Prediction Of Secondary Structure

<strong></strong> <p><strong></strong><strong>Objective:</strong> To make computational predictions of the structure of the human proteins Hsp27, αB-crystalline and HspB8. <strong>Materials and methods</strong>. The prediction of the secondary structure was obtained by a consensus of the programs for secondary prediction GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN and Psi-Pred. The models of tertiary structure were built from fragments homologous to proteins with tertiary known structure that were obtained by multiple alignments. Using the primary sequence we obtained the antigenicity profiles of native proteins and we analyzed the profiles of hydrophobicity, polarity, flexibility and accessibility of both native and mutant proteins. <strong>Results</strong>. Predictions of the secondary and tertiary structures of the studied proteins show that in the three cases, more than 65% are coil regions, 20-25 % are folded sheet and less than 10% are alpha helix. Analyses of the primary structure show that at least one of the studied profiles in every mutation is altered. <strong>Conclusions</strong>. The comparative analyses of structure suggest that mutations affect the solubility of the mutated proteins and hence affect their function as molecular chaperones</p> <p><strong>Key words</strong>: Hsp27, αB-cristalline, HspB8, prediction of secondary structure, computational model of tertiary structure</p><br />

Conformational changes in bovine lactoferrin induced by slow or fast temperature increases

2008 ◽  
Vol 389 (8) ◽  
Author(s):  
Waleska D. Schwarcz ◽  
Lorena Carnelocce ◽  
Jerson L. Silva ◽  
Andréa C. Oliveira ◽  
Rafael B. Gonçalves
Keyword(s):  
Secondary Structure ◽  
Conformational Changes ◽  
Tertiary Structure ◽  
Fluorescence Emission ◽  
Tryptophan Fluorescence ◽  
Heat Stability ◽  
Bovine Lactoferrin ◽  
Spectroscopic Techniques ◽  
Bioactive Component ◽  
Physiological Properties

Abstract Lactoferrin (LF) is an iron-binding protein present in several secreted substances, such as milk, and has broad antimicrobial and physiological properties. Because high temperatures may affect protein stability and its functional properties, we investigated the effect of heat on bovine LF structure and stability. The effects of temperatures used during the pasteurization process on LF and its relationship to protein functionality were studied. Conformational changes were monitored using spectroscopic techniques, such as circular dichroism (CD) and fluorescence spectroscopy. The CD data at 70°C showed that LF's secondary structure is drastically and irreversibly affected when the temperature is gradually increased. The same effect is observed when the temperature is gradually raised from 25°C to 105°C and changes are monitored by tryptophan fluorescence emission. We also verified the effects of simulating the pasteurization process; LF remained well structured during the entire process and this result was not time-dependent. Owing to preservation of the secondary structure with changes in the tertiary structure, we thus believe that pasteurization might cause LF to change into an intermediate partially folded state. A better understanding of heat stability is important for the use of LF as a bioactive component in food.

scholarly journals DNSS2: improved ab initio protein secondary structure prediction using advanced deep learning architectures

2019 ◽  
Author(s):  
Jie Hou ◽  
Zhiye Guo ◽  
Jianlin Cheng
Keyword(s):  
Deep Learning ◽  
Secondary Structure ◽  
Ab Initio ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Protein Secondary Structure Prediction ◽  
Learning Architectures

AbstractMotivationAccurate prediction of protein secondary structure (alpha-helix, beta-strand and coil) is a crucial step for protein inter-residue contact prediction and ab initio tertiary structure prediction. In a previous study, we developed a deep belief network-based protein secondary structure method (DNSS1) and successfully advanced the prediction accuracy beyond 80%. In this work, we developed multiple advanced deep learning architectures (DNSS2) to further improve secondary structure prediction.ResultsThe major improvements over the DNSS1 method include (i) designing and integrating six advanced one-dimensional deep convolutional/recurrent/residual/memory/fractal/inception networks to predict secondary structure, and (ii) using more sensitive profile features inferred from Hidden Markov model (HMM) and multiple sequence alignment (MSA). Most of the deep learning architectures are novel for protein secondary structure prediction. DNSS2 was systematically benchmarked on two independent test datasets with eight state-of-art tools and consistently ranked as one of the best methods. Particularly, DNSS2 was tested on the 82 protein targets of 2018 CASP13 experiment and achieved the best Q3 score of 83.74% and SOV score of 72.46%. DNSS2 is freely available at: https://github.com/multicom-toolbox/DNSS2.

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