The influence of sterols on the conformation of recombinant mitochondrial porin in detergent

Denice C. Bay; Joe D. O’Neil; Deborah A. Court

doi:10.1139/o08-132

The influence of sterols on the conformation of recombinant mitochondrial porin in detergent

Biochemistry and Cell Biology ◽

10.1139/o08-132 ◽

2008 ◽

Vol 86 (6) ◽

pp. 539-545 ◽

Cited By ~ 6

Author(s):

Denice C. Bay ◽

Joe D. O’Neil ◽

Deborah A. Court

Keyword(s):

Amino Acids ◽

High Resolution ◽

Secondary Structure ◽

Sodium Dodecylsulfate ◽

Aromatic Amino Acids ◽

Structural Studies ◽

High Concentration ◽

Mitochondrial Porin ◽

Voltage Dependent ◽

Artificial Bilayers

Mitochondrial porins (voltage-dependent anion-selective channels, VDAC) are key contributors to cellular metabolism. When isolated from mitochondria porins copurify with sterols, and some isolated forms of the protein require sterol for insertion into artificial membranes. Nonetheless, the contributions of sterols to the folded state of mitochondrial porin are not understood. Recently, with the goal of high-resolution structural studies, several laboratories have developed methods for folding recombinant porins at high concentration in detergent. In the present study, recombinant Neurospora crassa porin solubilized in detergent–sterol mixtures was examined. Sterols do not significantly alter the secondary structure of porin in lauryl dimethylamine oxide, nor in a mixture of sodium dodecylsulfate and dodecylmaltopyranoside. However, as detected by near-UV circular dichroism spectropolarimetry and fluorescence spectroscopy, the environments surrounding the aromatic amino acids in the detergent–sterol solubilized protein are measurably different from those in detergent alone. Furthermore, the effects are different in the presence of ergosterol, the native sterol in fungal mitochondria, and cholesterol. While these influences on the tertiary arrangement of detergent-solubilized porin are subtle, they may contribute to the generation of a form of the protein competent for insertion into the artificial bilayers used for electrophysiological analyses, and should be considered in future structural studies of porin.

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Conformational properties of streptokinase—secondary structure and localization of aromatic amino acids

International Journal of Biological Macromolecules ◽

10.1016/s0141-8130(05)80013-3 ◽

1992 ◽

Vol 14 (1) ◽

pp. 9-18 ◽

Cited By ~ 16

Author(s):

H. Welfle ◽

R. Misselwitz ◽

H. Fabian ◽

W. Damerau ◽

W. Hoelzer ◽

...

Keyword(s):

Amino Acids ◽

Secondary Structure ◽

Aromatic Amino Acids ◽

Conformational Properties

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In Silico Analysis of β-Galactosidases Primary and Secondary Structure in relation to Temperature Adaptation

Journal of Amino Acids ◽

10.1155/2014/475839 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 10

Author(s):

Vijay Kumar ◽

Nikhil Sharma ◽

Tek Chand Bhalla

Keyword(s):

Amino Acids ◽

Secondary Structure ◽

Aromatic Amino Acids ◽

In Silico Analysis ◽

Catalytic Efficiency ◽

Life Forms ◽

Temperature Tolerance ◽

Temperature Adaptation ◽

Thermal Habitat ◽

Cold Active

β-D-Galactosidases (EC 3.2.1.23) hydrolyze the terminal nonreducing β-D-galactose residues in β-D-galactosides and are ubiquitously present in all life forms including extremophiles. Eighteen microbial β-galactosidase protein sequences, six each from psychrophilic, mesophilic, and thermophilic microbes, were analyzed. Primary structure reveals alanine, glycine, serine, and arginine to be higher in psychrophilic β-galactosidases whereas valine, glutamine, glutamic acid, phenylalanine, threonine, and tyrosine are found to be statistically preferred by thermophilic β-galactosidases. Cold active β-galactosidase has a strong preference towards tiny and small amino acids, whereas high temperature inhabitants had higher content of basic and aromatic amino acids. Thermophilic β-galactosidases have higher percentage of α-helix region responsible for temperature tolerance while cold loving β-galactosidases had higher percentage of sheet and coil region. Secondary structure analysis revealed that charged and aromatic amino acids were significant for sheet region of thermophiles. Alanine was found to be significant and high in the helix region of psychrophiles and valine counters in thermophilic β-galactosidase. Coil region of cold active β-galactosidase has higher content of tiny amino acids which explains their high catalytic efficiency over their counterparts from thermal habitat. The present study has revealed the preference or prevalence of certain amino acids in primary and secondary structure of psychrophilic, mesophilic, and thermophilic β-galactosidase.

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Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur

Australian Journal of Chemistry ◽

10.1071/ch14598 ◽

2015 ◽

Vol 68 (3) ◽

pp. 385 ◽

Cited By ~ 13

Author(s):

Hanzala B. Hussain ◽

Katie A. Wilson ◽

Stacey D. Wetmore

Keyword(s):

Amino Acids ◽

High Resolution ◽

Protein Stability ◽

Crystal Structures ◽

Protein Complexes ◽

Aromatic Amino Acids ◽

Biological Macromolecules ◽

Great Stability ◽

Π Interactions ◽

And Function

Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.

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Combination of high resolution mass spectrometry and a halogen extraction code to identify chlorinated disinfection byproducts formed from aromatic amino acids

Water Research ◽

10.1016/j.watres.2020.116710 ◽

2021 ◽

Vol 190 ◽

pp. 116710

Author(s):

Yao Lu ◽

Zhi-Min Song ◽

Chao Wang ◽

Jun-Kun Liang ◽

Nan Xu ◽

...

Keyword(s):

Mass Spectrometry ◽

Amino Acids ◽

High Resolution ◽

High Resolution Mass Spectrometry ◽

Aromatic Amino Acids ◽

Disinfection Byproducts ◽

High Resolution Mass ◽

Resolution Mass

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Changes in the Structure and Digestibility of Myoglobin Treated With Sodium Chloride

Current Developments in Nutrition ◽

10.1093/cdn/nzab045_043 ◽

2021 ◽

Vol 5 (Supplement_2) ◽

pp. 661-661

Author(s):

Hui Liu ◽

Qian Li ◽

Chunbao Li

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Sodium Chloride ◽

Secondary Structure ◽

Digestive Enzymes ◽

Structural Changes ◽

Tertiary Structure ◽

Dynamics Simulation ◽

High Concentration ◽

Salt Ions

Abstract Objectives Changes in the structure of myoglobin affect its digestibility and myoglobin can't be completely broken down of pepsin. The exact mechanism of this breakdown is not clear. It can be inferred that myoglobin is broken down into polypeptides whose structures do not fully conform to the spatial characteristics of digestive enzymes. Myoglobin dissolution in different salt concentrations and changes in secondary structure were examined by spectroscopic examination. The molecular dynamics simulation was used to study the stability of these structural changes and their combination with digestive enzymes. Finally, since the products of digestion are determined by the catalytic centers of digestive enzymes, the substrate channel is extended to study the relationship between digestive enzymes and substrates. Methods In this study, different concentrations of sodium chloride were added for a certain period of time in advance to detect changes in the secondary structure of myoglobin, leading to changes in digestibility. Myoglobin and digestive enzymes were docked for molecular dynamics simulations to analyze the energy and structural changes in the interactions between substrates and proteins. Results Salt-treated protein can affect the secondary structure changes of protein. High concentration of salt-treated protein will lead to protein aggregation and denaturation, affecting digestibility. Low concentration of salt-treated protein may lead to exposure of sleeping areas, reducing digestibility. In terms of structure, salt ions lead to changes in the bonding of amino acids in the protein and affect the substrate's entry into the enzyme activity center. Conclusions Treatment of myoglobin with different salt concentrations did not change its tertiary structure but low salt concentrations lowered its digestibility, probably due to salt ions altering a number of key amino acid bonds, making the structure more stable and less susceptible to digest. Some low molecular weight peptides remain after pepsin digestion. This may be due to the distance between the key amino acids in the active catalytic center of pepsin being insufficient to form stable conformations with small peptides. Funding Sources This work was supported by the grants from NSFC (32072211).

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The Interaction of Fast Electrons with Aromatic Amino Acids

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100096709 ◽

1972 ◽

Vol 30 ◽

pp. 690-691

Author(s):

Paul Shau-Da Lin

Keyword(s):

Amino Acids ◽

High Resolution ◽

Energy Loss ◽

Field Emission ◽

Aromatic Amino Acids ◽

Close Correlation ◽

Biological Molecules ◽

Scanning Microscope ◽

Fast Electrons ◽

Radiation Spectra

As part of a program in investigating the interaction of electrons with biological molecules in a field emission scanning microscope, we have studied the energy loss spectra of aromatic amino acids: Tryptophan, Tyrosine and Phenylalanine.The instrument used is the simple multipurpose scanning microscope previously constructed. The high resolution magnetic spectrometer installed in this microscope enables a resolution of ∽.2 ev as limited by the energy spread in field emission only.The energy loss spectra of Tyrosine and Tryptophan are shown in Figs. 1 and 2. In general, they consist of several peaks below ∼l0 ev, a broad one around 25 ev, and some shoulders on the broad peak. The structure below ∽10 ev bears close correlation with UV, far UV or synchrotron radiation spectra, and can be deduced from each other by Kramers-Kronig transformation. For biological specimens, this has more recently been demonstrated for Nuclei-Acid Bases.

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Rerouting Citrate Metabolism in Lactococcus lactis to Citrate-Driven Transamination

Applied and Environmental Microbiology ◽

10.1128/aem.01811-12 ◽

2012 ◽

Vol 78 (18) ◽

pp. 6665-6673 ◽

Cited By ~ 14

Author(s):

Agata M. Pudlik ◽

Juke S. Lolkema

Keyword(s):

Amino Acids ◽

Lactococcus Lactis ◽

Aromatic Amino Acids ◽

High Concentration ◽

Content Type ◽

Citrate Transporter ◽

Keto Acids ◽

Citrate Fermentation ◽

Branched Chain

ABSTRACTOxaloacetate is an intermediate of the citrate fermentation pathway that accumulates in the cytoplasm ofLactococcus lactisILCitM(pFL3) at a high concentration due to the inactivation of oxaloacetate decarboxylase. An excess of toxic oxaloacetate is excreted into the medium in exchange for citrate by the citrate transporter CitP (A. M. Pudlik and J. S. Lolkema, J. Bacteriol. 193:4049–4056, 2011). In this study, transamination of amino acids with oxaloacetate as the keto donor is described as an additional mechanism to relieve toxic stress. Redirection of the citrate metabolic pathway into the transamination route in the presence of the branched-chain amino acids Ile, Leu, and Val; the aromatic amino acids Phe, Trp, and Tyr; and Met resulted in the formation of aspartate and the corresponding α-keto acids. Cells grown in the presence of citrate showed 3.5 to 7 times higher transaminase activity in the cytoplasm than cells grown in the absence of citrate. The study demonstrates that transaminases ofL. lactisaccept oxaloacetate as a keto donor. A significant fraction of 2-keto-4-methylthiobutyrate formed from methionine by citrate-driven transaminationin vivowas further metabolized, yielding the cheese aroma compounds 2-hydroxy-4-methylthiobutyrate and methyl-3-methylthiopropionate. Reducing equivalents required for the former compound were produced in the citrate fermentation pathway as NADH. Similarly, phenylpyruvate, the transamination product of phenylalanine, was reduced to phenyllactate, while the dehydrogenase activity was not observed for the branched-chain keto acids. Both α-keto acids and α-hydroxy acids are known substrates of CitP and may be excreted from the cell in exchange for citrate or oxaloacetate.

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The Fine Structure of Phloem Cells

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100119867 ◽

1985 ◽

Vol 43 ◽

pp. 632-635

Author(s):

James Cronshaw

Keyword(s):

Structural Studies ◽

High Concentration ◽

Long Distance ◽

Phloem Tissue ◽

Sieve Elements ◽

Long Distance Transport ◽

P Protein ◽

Companion Cells ◽

Electron Microscopical ◽

Distance Transport

Long distance transport in plants takes place in phloem tissue which has characteristic cells, the sieve elements. At maturity these cells have sieve areas in their end walls with specialized perforations. They are associated with companion cells, parenchyma cells, and in some species, with transfer cells. The protoplast of the functioning sieve element contains a high concentration of sugar, and consequently a high hydrostatic pressure, which makes it extremely difficult to fix mature sieve elements for electron microscopical observation without the formation of surge artifacts. Despite many structural studies which have attempted to prevent surge artifacts, several features of mature sieve elements, such as the distribution of P-protein and the nature of the contents of the sieve area pores, remain controversial.

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