Biomolecules

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Open AccessArticle

Self-Assembly of Human Serum Albumin: A Simplex Phenomenon

by Garima Thakur, Kovur Prashanthi, Keren Jiang and Thomas Thundat

Biomolecules 2017, 7(3), 69; https://doi.org/10.3390/biom7030069 - 20 Sep 2017

Cited by 2 | Viewed by 5748

Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display [...] Read more.

Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display a behavior which is geometrically related to a n-simplex model and is explained through thermodynamics and chemical kinetics. Full article

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Graphical abstract

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Open AccessArticle

Structure-Dependent Interfacial Properties of Chaplin F from Streptomyces coelicolor

by Mina Dokouhaki, Emma L. Prime, Andrew Hung, Greg G. Qiao, Li Day and Sally L. Gras

Biomolecules 2017, 7(3), 68; https://doi.org/10.3390/biom7030068 - 19 Sep 2017

Cited by 2 | Viewed by 4454

Abstract

Chaplin F (Chp F) is a secreted surface-active peptide involved in the aerial growth of Streptomyces. While Chp E demonstrates a pH-responsive surface activity, the relationship between Chp F structure, function and the effect of solution pH is unknown. Chp F peptides [...] Read more.

Chaplin F (Chp F) is a secreted surface-active peptide involved in the aerial growth of Streptomyces. While Chp E demonstrates a pH-responsive surface activity, the relationship between Chp F structure, function and the effect of solution pH is unknown. Chp F peptides were found to self-assemble into amyloid fibrils at acidic pH (3.0 or the isoelectric point (pI) of 4.2), with ~99% of peptides converted into insoluble fibrils. In contrast, Chp F formed short assemblies containing a mixture of random coil and β-sheet structure at a basic pH of 10.0, where only 40% of the peptides converted to fibrils. The cysteine residues in Chp F did not appear to play a role in fibril assembly. The interfacial properties of Chp F at the air/water interface were altered by the structures adopted at different pH, with Chp F molecules forming a higher surface-active film at pH 10.0 with a lower area per molecule compared to Chp F fibrils at pH 3.0. These data show that the pH responsiveness of Chp F surface activity is the reverse of that observed for Chp E, which could prove useful in potential applications where surface activity is desired over a wide range of solution pH. Full article

(This article belongs to the Special Issue Functional Amyloids)

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Graphical abstract

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Open AccessArticle

Functional Amyloid Protection in the Eye Lens: Retention of α-Crystallin Molecular Chaperone Activity after Modification into Amyloid Fibrils

by Megan Garvey, Heath Ecroyd, Nicholas J. Ray, Juliet A. Gerrard and John A. Carver

Biomolecules 2017, 7(3), 67; https://doi.org/10.3390/biom7030067 - 12 Sep 2017

Cited by 22 | Viewed by 5905

Abstract

Amyloid fibril formation occurs from a wide range of peptides and proteins and is typically associated with a loss of protein function and/or a gain of toxic function, as the native structure of the protein undergoes major alteration to form a cross β-sheet [...] Read more.

Amyloid fibril formation occurs from a wide range of peptides and proteins and is typically associated with a loss of protein function and/or a gain of toxic function, as the native structure of the protein undergoes major alteration to form a cross β-sheet array. It is now well recognised that some amyloid fibrils have a biological function, which has led to increased interest in the potential that these so-called functional amyloids may either retain the function of the native protein, or gain function upon adopting a fibrillar structure. Herein, we investigate the molecular chaperone ability of α-crystallin, the predominant eye lens protein which is composed of two related subunits αA- and αB-crystallin, and its capacity to retain and even enhance its chaperone activity after forming aggregate structures under conditions of thermal and chemical stress. We demonstrate that both eye lens α-crystallin and αB-crystallin (which is also found extensively outside the lens) retain, to a significant degree, their molecular chaperone activity under conditions of structural change, including after formation into amyloid fibrils and amorphous aggregates. The results can be related directly to the effects of aging on the structure and chaperone function of α-crystallin in the eye lens, particularly its ability to prevent crystallin protein aggregation and hence lens opacification associated with cataract formation. Full article

(This article belongs to the Special Issue Functional Amyloids)

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Open AccessReview

The TORC2‐Dependent Signaling Network in the Yeast Saccharomyces cerevisiae

by Françoise M. Roelants, Kristin L. Leskoske, Maria Nieves Martinez Marshall, Melissa N. Locke and Jeremy Thorner

Biomolecules 2017, 7(3), 66; https://doi.org/10.3390/biom7030066 - 5 Sep 2017

Cited by 59 | Viewed by 10042

Abstract

To grow, eukaryotic cells must expand by inserting glycerolipids, sphingolipids, sterols, and proteins into their plasma membrane, and maintain the proper levels and bilayer distribution. A fungal cell must coordinate growth with enlargement of its cell wall. In Saccharomyces cerevisiae, a plasma [...] Read more.

To grow, eukaryotic cells must expand by inserting glycerolipids, sphingolipids, sterols, and proteins into their plasma membrane, and maintain the proper levels and bilayer distribution. A fungal cell must coordinate growth with enlargement of its cell wall. In Saccharomyces cerevisiae, a plasma membrane‐localized protein kinase complex, Target of Rapamicin (TOR) complex‐2 (TORC2) (mammalian ortholog is mTORC2), serves as a sensor and masterregulator of these plasma membrane‐ and cell wall‐associated events by directly phosphorylating and thereby stimulating the activity of two types of effector protein kinases: Ypk1 (mammalian ortholog is SGK1), along with a paralog (Ypk2); and, Pkc1 (mammalian ortholog is PKN2/PRK2). Ypk1 is a central regulator of pathways and processes required for plasma membrane lipid and protein homeostasis, and requires phosphorylation on its T‐loop by eisosome‐associated protein kinase Pkh1 (mammalian ortholog is PDK1) and a paralog (Pkh2). For cell survival under various stresses, Ypk1 function requires TORC2‐mediated phosphorylation at multiple sites near its C terminus. Pkc1 controls diverse processes, especially cell wall synthesis and integrity. Pkc1 is also regulated by Pkh1‐ and TORC2‐dependent phosphorylation, but, in addition, by interaction with Rho1‐GTP and lipids phosphatidylserine (PtdSer) and diacylglycerol (DAG). We also describe here what is currently known about the downstream substrates modulated by Ypk1‐mediated and Pkc1‐mediated phosphorylation. Full article

(This article belongs to the Special Issue TOR Signaling Pathway)

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Open AccessArticle

tRNA Modification Detection Using Graphene Nanopores: A Simulation Study

by Khadijah Onanuga, Thomas J. Begley, Alan A. Chen and Srivathsan V. Ranganathan

Biomolecules 2017, 7(3), 65; https://doi.org/10.3390/biom7030065 - 25 Aug 2017

Cited by 1 | Viewed by 5749

Abstract

There are over 100 enzyme-catalyzed modifications on transfer RNA (tRNA) molecules. The levels and identity of wobble uridine (U) modifications are affected by environmental conditions and diseased states, making wobble U detection a potential biomarker for exposures and pathological conditions. The current detection [...] Read more.

There are over 100 enzyme-catalyzed modifications on transfer RNA (tRNA) molecules. The levels and identity of wobble uridine (U) modifications are affected by environmental conditions and diseased states, making wobble U detection a potential biomarker for exposures and pathological conditions. The current detection of RNA modifications requires working with nucleosides in bulk samples. Nanopore detection technology uses a single-molecule approach that has the potential to detect tRNA modifications. To evaluate the feasibility of this approach, we have performed all-atom molecular dynamics (MD) simulation studies of a five-layered graphene nanopore by localizing canonical and modified uridine nucleosides. We found that in a 1 M KCl solution with applied positive and negative biases not exceeding 2 V, nanopores can distinguish U from 5-carbonylmethyluridine (cm⁵U), 5-methoxycarbonylmethyluridine (mcm⁵U), 5-methoxycarbonylmethyl-2-thiouridine (mcm⁵s²U), and 5-methoxycarbonylmethyl-2′-O-methyluridine (mcm⁵Um) based on changes in the resistance of the nanopore. Specifically, we observed that in nanopores with dimensions less than 3 nm diameter, a localized mcm⁵Um and mcm⁵U modifications could be clearly distinguished from the canonical uridine, while the other modifications showed a modest yet detectable decrease in their respective nanopore conductance. We have compared the results between nanopores of various sizes to aid in the design, optimization, and fabrication of graphene nanopores devices for tRNA modification detection. Full article

(This article belongs to the Collection RNA Modifications)

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Open AccessArticle

Comparative Degradation of a Thiazole Pollutant by an Advanced Oxidation Process and an Enzymatic Approach

by Khadega A. Al-Maqdi, Soleiman M. Hisaindee, Muhammad A. Rauf and Syed Salman Ashraf

Biomolecules 2017, 7(3), 64; https://doi.org/10.3390/biom7030064 - 24 Aug 2017

Cited by 24 | Viewed by 5365

Abstract

Organic pollutants, especially those found in water bodies, pose a direct threat to various aquatic organisms as well as humans. A variety of different remediation approaches, including chemical and biological methods, have been developed for the degradation of various organic pollutants. However, comparative [...] Read more.

Organic pollutants, especially those found in water bodies, pose a direct threat to various aquatic organisms as well as humans. A variety of different remediation approaches, including chemical and biological methods, have been developed for the degradation of various organic pollutants. However, comparative mechanistic studies of pollutant degradation by these different systems are almost non-existent. In this study, the degradation of a model thiazole pollutant, thioflavin T (ThT), was carried out in the presence of either an advanced oxidation process (ultraviolet (UV) + H₂O₂) or a chloroperoxidase enzyme system (CPO + H₂O₂). The degradation was followed both spectrophotometrically and using liquid chromatography-mass spectroscopy (LC-MS), and the products formed were identified using tandem liquid chromatography-mass spectrometry-mass spectrometry (LC-MS-MS). The results show that the two remediation approaches produced different sets of intermediates, with only one common species (a demethylated form of ThT). This suggests that different degradation schemes were operating in the two systems. Interestingly, one of the major intermediates produced by the CPO + H₂O₂ system was a chlorinated form of thioflavin. Phytotoxicity studies showed that the CPO + H₂O₂-treated ThT solution was significantly (p <0.05) less toxic than the UV + H₂O₂-treated ThT solution. This is the first time that a comparative mechanistic study showing in detail the intermediates generated in chemical and biological remediation methods has been presented. Furthermore, the results show that different remediation systems have very different degradation schemes and result in products having different toxicities. Full article

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Open AccessReview

In Quest for Improved Drugs against Diabetes: The Added Value of X-ray Powder Diffraction Methods

by Fotini Karavassili, Alexandros Valmas, Stavroula Fili, Christos D. Georgiou and Irene Margiolaki

Biomolecules 2017, 7(3), 63; https://doi.org/10.3390/biom7030063 - 22 Aug 2017

Cited by 17 | Viewed by 5973

Abstract

Human insulin (HI) is a well-characterized natural hormone which regulates glycose levels into the blood-stream and is widely used for diabetes treatment. Numerous studies have manifested that despite significant efforts devoted to structural characterization of this molecule and its complexes with organic compounds [...] Read more.

Human insulin (HI) is a well-characterized natural hormone which regulates glycose levels into the blood-stream and is widely used for diabetes treatment. Numerous studies have manifested that despite significant efforts devoted to structural characterization of this molecule and its complexes with organic compounds (ligands), there is still a rich diagram of phase transitions and novel crystalline forms to be discovered. Towards the improvement of drug delivery, identification of new insulin polymorphs from polycrystalline samples, simulating the commercially available drugs, is feasible today via macromolecular X-ray powder diffraction (XRPD). This approach has been developed, and is considered as a respectable method, which can be employed in biosciences for various purposes, such as observing phase transitions and characterizing bulk pharmaceuticals. An overview of the structural studies on human insulin complexes performed over the past decade employing both synchrotron and laboratory sources for XRPD measurements, is reported herein. This review aims to assemble all of the recent advances in the diabetes treatment field in terms of drug formulation, verifying in parallel the efficiency and applicability of protein XRPD for quick and accurate preliminary structural characterization in the large scale. Full article

(This article belongs to the Special Issue Protein Crystallography 2016)

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Open AccessReview

Organ–Organ Crosstalk and Alcoholic Liver Disease

by Lauren G. Poole, Christine E. Dolin and Gavin E. Arteel

Biomolecules 2017, 7(3), 62; https://doi.org/10.3390/biom7030062 - 16 Aug 2017

Cited by 34 | Viewed by 11275

Abstract

Alcohol consumption is a common custom worldwide, and the toxic effects of alcohol on several target organs are well-understood. Given the poor prognosis of treating clinically-relevant alcoholic liver disease (ALD) (i.e., alcoholic hepatitis (AH) and cirrhosis), additional research is required to develop more [...] Read more.

Alcohol consumption is a common custom worldwide, and the toxic effects of alcohol on several target organs are well-understood. Given the poor prognosis of treating clinically-relevant alcoholic liver disease (ALD) (i.e., alcoholic hepatitis (AH) and cirrhosis), additional research is required to develop more effective therapies. While the stages of ALD have been well-characterized, targeted therapies to prevent or reverse this process in humans are still needed. Better understanding of risk factors and mechanisms underlying disease progression can lead to the development of rational therapies to prevent or reverse ALD in the clinic. A potential area of targeted therapy for ALD may be organ–organ communication in the early stages of the disease. In contrast to AH and end-stage liver diseases, the involvement of multiple organs in the development of ALD is less understood. The impact of these changes on pathology to the liver and other organs may not only influence disease progression during the development of the disease, but also outcomes of end stages diseases. The purpose of this review is to summarize the established and proposed communication between the liver and other organ systems that may contribute to the development and progression of liver disease, as well as to other organs. Potential mechanisms of this organ–organ communication are also discussed. Full article

(This article belongs to the Special Issue Multi-Organ Alcohol-Related Damage: Mechanisms and Treatment)

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Open AccessReview

Alcohol and Cancer: Mechanisms and Therapies

by Anuradha Ratna and Pranoti Mandrekar

Biomolecules 2017, 7(3), 61; https://doi.org/10.3390/biom7030061 - 14 Aug 2017

Cited by 94 | Viewed by 15512

Abstract

Several scientific and clinical studies have shown an association between chronic alcohol consumption and the occurrence of cancer in humans. The mechanism for alcohol-induced carcinogenesis has not been fully understood, although plausible events include genotoxic effects of acetaldehyde, cytochrome P450 2E1 (CYP2E1)-mediated generation [...] Read more.

Several scientific and clinical studies have shown an association between chronic alcohol consumption and the occurrence of cancer in humans. The mechanism for alcohol-induced carcinogenesis has not been fully understood, although plausible events include genotoxic effects of acetaldehyde, cytochrome P450 2E1 (CYP2E1)-mediated generation of reactive oxygen species, aberrant metabolism of folate and retinoids, increased estrogen, and genetic polymorphisms. Here, we summarize the impact of alcohol drinking on the risk of cancer development and potential underlying molecular mechanisms. The interactions between alcohol abuse, anti-tumor immune response, tumor growth, and metastasis are complex. However, multiple studies have linked the immunosuppressive effects of alcohol with tumor progression and metastasis. The influence of alcohol on the host immune system and the development of possible effective immunotherapy for cancer in alcoholics are also discussed here. The conclusive biological effects of alcohol on tumor progression and malignancy have not been investigated extensively using an animal model that mimics the human disease. This review provides insights into cancer pathogenesis in alcoholics, alcohol and immune interactions in different cancers, and scope and future of targeted immunotherapeutic modalities in patients with alcohol abuse. Full article

(This article belongs to the Special Issue Multi-Organ Alcohol-Related Damage: Mechanisms and Treatment)

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Open AccessReview

The Role of Functional Amyloids in Multicellular Growth and Development of Gram-Positive Bacteria

by Anna Dragoš, Ákos T. Kovács and Dennis Claessen

Biomolecules 2017, 7(3), 60; https://doi.org/10.3390/biom7030060 - 7 Aug 2017

Cited by 27 | Viewed by 7446

Abstract

Amyloid fibrils play pivotal roles in all domains of life. In bacteria, these fibrillar structures are often part of an extracellular matrix that surrounds the producing organism and thereby provides protection to harsh environmental conditions. Here, we discuss the role of amyloid fibrils [...] Read more.

Amyloid fibrils play pivotal roles in all domains of life. In bacteria, these fibrillar structures are often part of an extracellular matrix that surrounds the producing organism and thereby provides protection to harsh environmental conditions. Here, we discuss the role of amyloid fibrils in the two distant Gram-positive bacteria, Streptomyces coelicolor and Bacillus subtilis. We describe how amyloid fibrils contribute to a multitude of developmental processes in each of these systems, including multicellular growth and community development. Despite this variety of tasks, we know surprisingly little about how their assembly is organized to fulfill all these roles. Full article

(This article belongs to the Special Issue Functional Amyloids)

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Open AccessReview

Coupling TOR to the Cell Cycle by the Greatwall–Endosulfine–PP2A-B55 Pathway

by Livia Pérez-Hidalgo and Sergio Moreno

Biomolecules 2017, 7(3), 59; https://doi.org/10.3390/biom7030059 - 4 Aug 2017

Cited by 22 | Viewed by 7438

Abstract

Cell growth and division are two processes tightly coupled in proliferating cells. While Target of Rapamycin (TOR) is the master regulator of growth, the cell cycle is dictated by the activity of the cyclin-dependent kinases (CDKs). A long-standing question in cell biology is [...] Read more.

Cell growth and division are two processes tightly coupled in proliferating cells. While Target of Rapamycin (TOR) is the master regulator of growth, the cell cycle is dictated by the activity of the cyclin-dependent kinases (CDKs). A long-standing question in cell biology is how these processes may be connected. Recent work has highlighted that regulating the phosphatases that revert CDK phosphorylations is as important as regulating the CDKs for cell cycle progression. At mitosis, maintaining a low level of protein phosphatase 2A (PP2A)-B55 activity is essential for CDK substrates to achieve the correct level of phosphorylation. The conserved Greatwall–Endosulfine pathway has been shown to be required for PP2A-B55 inhibition at mitosis in yeasts and multicellular organisms. Interestingly, in yeasts, the Greatwall–Endosulfine pathway is negatively regulated by TOR Complex 1 (TORC1). Moreover, Greatwall–Endosulfine activation upon TORC1 inhibition has been shown to regulate the progression of the cell cycle at different points: the G1 phase in budding yeast, the G2/M transition and the differentiation response in fission yeast, and the entry into quiescence in both budding and fission yeasts. In this review, we discuss the recent findings on how the Greatwall–Endosulfine pathway may provide a connection between cell growth and the cell cycle machinery. Full article

(This article belongs to the Special Issue TOR Signaling Pathway)

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Open AccessArticle

Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry

by Heidi N. Danielsen, Susan H. Hansen, Florian-Alexander Herbst, Henrik Kjeldal, Allan Stensballe, Per H. Nielsen and Morten S. Dueholm

Biomolecules 2017, 7(3), 58; https://doi.org/10.3390/biom7030058 - 4 Aug 2017

Cited by 12 | Viewed by 6777

Abstract

Functional amyloids are important structural and functional components of many biofilms, yet our knowledge of these fascinating polymers is limited to a few examples for which the native amyloids have been isolated in pure form. Isolation of the functional amyloids from other cell [...] Read more.

Functional amyloids are important structural and functional components of many biofilms, yet our knowledge of these fascinating polymers is limited to a few examples for which the native amyloids have been isolated in pure form. Isolation of the functional amyloids from other cell components represents a major bottleneck in the search for new functional amyloid systems. Here we present a label-free quantitative mass spectrometry method that allows identification of amyloid proteins directly in cell lysates. The method takes advantage of the extreme structural stability and polymeric nature of functional amyloids and the ability of concentrated formic acid to depolymerize the amyloids. An automated data processing pipeline that provides a short list of amyloid protein candidates was developed based on an amyloid-specific sigmoidal abundance signature in samples treated with increasing concentrations of formic acid. The method was evaluated using the Escherichia coli curli and the Pseudomonas Fap system. It confidently identified the major amyloid subunit for both systems, as well as the minor subunit for the curli system. A few non-amyloid proteins also displayed the sigmoidal abundance signature. However, only one of these contained a sec-dependent signal peptide, which characterizes most of all secreted proteins, including all currently known functional bacterial amyloids. Full article

(This article belongs to the Special Issue Functional Amyloids)

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Open AccessArticle

Metal Binding Properties of the N-Terminus of the Functional Amyloid Orb2

by Thalia H. Bajakian, Silvia A. Cervantes, Maria A. Soria, Maïwenn Beaugrand, Ji Yun Kim, Rachel J. Service and Ansgar B. Siemer

Biomolecules 2017, 7(3), 57; https://doi.org/10.3390/biom7030057 - 1 Aug 2017

Cited by 4 | Viewed by 4786

Abstract

The cytoplasmic polyadenylation element binding protein (CPEB) homologue Orb2 is a functional amyloid that plays a key regulatory role for long-term memory in Drosophila. Orb2 has a glutamine, histidine-rich (Q/H-rich) domain that resembles the Q/H-rich, metal binding domain of the Hpn-like protein [...] Read more.

The cytoplasmic polyadenylation element binding protein (CPEB) homologue Orb2 is a functional amyloid that plays a key regulatory role for long-term memory in Drosophila. Orb2 has a glutamine, histidine-rich (Q/H-rich) domain that resembles the Q/H-rich, metal binding domain of the Hpn-like protein (Hpnl) found in Helicobacter pylori. In the present study, we used chromatography and isothermal titration calorimetry (ITC) to show that the Q/H-rich domain of Orb2 binds Ni²⁺ and other transition metals ions with μM affinity. Using site directed mutagenesis, we show that several histidine residues are important for binding. In particular, the H61Y mutation, which was previously shown to affect the aggregation of Orb2 in cell culture, completely inhibited metal binding of Orb2. Finally, we used thioflavin T fluorescence and electron microscopy images to show that Ni²⁺ binding induces the aggregating of Orb2 into structures that are distinct from the amyloid fibrils formed in the absence of Ni²⁺. These data suggest that transition metal binding might be important for the function of Orb2 and potentially long-term memory in Drosophila. Full article

(This article belongs to the Special Issue Functional Amyloids)

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Open AccessBrief Report

Suppression of mRNA Nanoparticle Transfection in Human Fibroblasts by Selected Interferon Inhibiting Small Molecule Compounds

by Yang Liu, Manoj N. Krishnan and Kyle K.L. Phua

Biomolecules 2017, 7(3), 56; https://doi.org/10.3390/biom7030056 - 31 Jul 2017

Cited by 9 | Viewed by 4244

Abstract

In vitro transcribed (IVT) mRNA is increasingly applied in lieu of DNA to deliver reprogramming genes to fibroblasts for stem cell derivation. However, IVT mRNA induces interferon (IFN) responses from mammalian cells that reduces transfection efficiency. It has been previously suggested that small [...] Read more.

In vitro transcribed (IVT) mRNA is increasingly applied in lieu of DNA to deliver reprogramming genes to fibroblasts for stem cell derivation. However, IVT mRNA induces interferon (IFN) responses from mammalian cells that reduces transfection efficiency. It has been previously suggested that small molecule inhibitors of IFN are a viable strategy to enhance mRNA transfection efficiency. Herein, we screen a list of commercially available small molecules, including published IFN inhibitors, for their potential to enhance mRNA transfection in BJ fibroblasts. Transfection enhancement is quantified by relative mean fluorescence intensity of translated green fluorescent protein (GFP) in treated cells compared to dimethyl sulfoxide treated controls. Within toxicological constrains, all tested small molecules did not enhance mRNA transfection in BJ fibroblasts while a third of the tested compounds unexpectedly inhibited GFP expression even though IFN-β production is inhibited. Based on the results of our study, we conclude that small molecule inhibitors, including IFN inhibitors, tested in this study do not enhance in vitro mRNA transfection efficiency in human fibroblasts. Full article

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Open AccessArticle

Altered Protein Interactions of the Endogenous Interactome of PTPIP51 towards MAPK Signaling

by Alexander Brobeil, Rajaa Chehab, Eric Dietel, Stefan Gattenlöhner and Monika Wimmer

Biomolecules 2017, 7(3), 55; https://doi.org/10.3390/biom7030055 - 21 Jul 2017

Cited by 6 | Viewed by 5370

Abstract

Protein–protein interactions play a pivotal role in normal cellular functions as well as in carcinogenesis. The protein–protein interactions form functional clusters during signal transduction. To elucidate the fine calibration of the protein–protein interactions of protein tyrosine phosphatase interacting protein 51 (PTPIP51) a small [...] Read more.

Protein–protein interactions play a pivotal role in normal cellular functions as well as in carcinogenesis. The protein–protein interactions form functional clusters during signal transduction. To elucidate the fine calibration of the protein–protein interactions of protein tyrosine phosphatase interacting protein 51 (PTPIP51) a small molecule drug, namely LDC-3, directly targeting PTPIP51 is now available. Therefore, LDC-3 allows for the studying of the regulation of the endogenous interactome by modulating PTPIP51 binding capacity. Small interfering ribonucleic acid (siRNA) experiments show that the modification in PTPIP51 binding capacity is induced by LDC-3. Application of LDC-3 annuls the known regulatory phosphorylation mechanisms for PTPIP51 and consequently, significantly alters the assembly of the PTPIP51 associated protein complexes. The treatment of human keratinocytes (HaCaT cells) with LDC-3 induces an altered protein–protein interaction profile of the endogenous interactome of PTPIP51. In addition, LDC-3 stabilizes PTPIP51 within a mitogen activated protein kinase (MAPK) complex composed of Raf-1 and the scaffold protein 14-3-3, independent of the phosphorylation status of PTPIP51. Of note, under LDC-3 treatment the regulatory function of the PTP1B on PTPIP51 fails to impact the PTPIP51 interaction characteristics, as reported for the HaCaT cell line. In summary, LDC-3 gives the unique opportunity to directly modulate PTPIP51 in malignant cells, thus targeting potential dysregulated signal transduction pathways such as the MAPK cascade. The provided data give critical insights in the therapeutic potential of PTPIP51 protein interactions and thus are basic for possible targeted therapy regimens. Full article

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Open AccessReview

The TOR Signaling Network in the Model Unicellular Green Alga Chlamydomonas reinhardtii

by María Esther Pérez-Pérez, Inmaculada Couso and José L. Crespo

Biomolecules 2017, 7(3), 54; https://doi.org/10.3390/biom7030054 - 12 Jul 2017

Cited by 52 | Viewed by 10010

Abstract

Cell growth is tightly coupled to nutrient availability. The target of rapamycin (TOR) kinase transmits nutritional and environmental cues to the cellular growth machinery. TOR functions in two distinct multiprotein complexes, termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2). While the [...] Read more.

Cell growth is tightly coupled to nutrient availability. The target of rapamycin (TOR) kinase transmits nutritional and environmental cues to the cellular growth machinery. TOR functions in two distinct multiprotein complexes, termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2). While the structure and functions of TORC1 are highly conserved in all eukaryotes, including algae and plants, TORC2 core proteins seem to be missing in photosynthetic organisms. TORC1 controls cell growth by promoting anabolic processes, including protein synthesis and ribosome biogenesis, and inhibiting catabolic processes such as autophagy. Recent studies identified rapamycin-sensitive TORC1 signaling regulating cell growth, autophagy, lipid metabolism, and central metabolic pathways in the model unicellular green alga Chlamydomonas reinhardtii. The central role that microalgae play in global biomass production, together with the high biotechnological potential of these organisms in biofuel production, has drawn attention to the study of proteins that regulate cell growth such as the TOR kinase. In this review we discuss the recent progress on TOR signaling in algae. Full article

(This article belongs to the Special Issue TOR Signaling Pathway)

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Open AccessReview

MYC-Driven Pathways in Breast Cancer Subtypes

by Yassi Fallah, Janetta Brundage, Paul Allegakoen and Ayesha N. Shajahan-Haq

Biomolecules 2017, 7(3), 53; https://doi.org/10.3390/biom7030053 - 11 Jul 2017

Cited by 143 | Viewed by 9743

Abstract

The transcription factor MYC (MYC proto-oncogene, bHLH transcription factor) is an essential signaling hub in multiple cellular processes that sustain growth of many types of cancers. MYC regulates expression of RNA, both protein and non-coding, that control central metabolic pathways, cell death, proliferation, [...] Read more.

The transcription factor MYC (MYC proto-oncogene, bHLH transcription factor) is an essential signaling hub in multiple cellular processes that sustain growth of many types of cancers. MYC regulates expression of RNA, both protein and non-coding, that control central metabolic pathways, cell death, proliferation, differentiation, stress pathways, and mechanisms of drug resistance. Activation of MYC has been widely reported in breast cancer progression. Breast cancer is a complex heterogeneous disease and treatment options are primarily guided by histological and biochemical evaluations of the tumors. Based on biochemical markers, three main breast cancer categories are ER+ (estrogen receptor alpha positive), HER2+ (human epidermal growth factor receptor 2 positive), and TNBC (triple-negative breast cancer; estrogen receptor negative, progesterone receptor negative, HER2 negative). MYC is elevated in TNBC compared with other cancer subtypes. Interestingly, MYC-driven pathways are further elevated in aggressive breast cancer cells and tumors that display drug resistant phenotype. Identification of MYC target genes is essential in isolating signaling pathways that drive tumor development. In this review, we address the role of MYC in the three major breast cancer subtypes and highlight the most promising leads to target MYC functions. Full article

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Open AccessReview

Regulation of Autophagy through TORC1 and mTORC1

by Takeshi Noda

Biomolecules 2017, 7(3), 52; https://doi.org/10.3390/biom7030052 - 7 Jul 2017

Cited by 112 | Viewed by 11092

Abstract

Autophagy is an intracellular protein-degradation process that is conserved across eukaryotes including yeast and humans. Under nutrient starvation conditions, intracellular proteins are transported to lysosomes and vacuoles via membranous structures known as autophagosomes, and are degraded. The various steps of autophagy are regulated [...] Read more.

Autophagy is an intracellular protein-degradation process that is conserved across eukaryotes including yeast and humans. Under nutrient starvation conditions, intracellular proteins are transported to lysosomes and vacuoles via membranous structures known as autophagosomes, and are degraded. The various steps of autophagy are regulated by the target of rapamycin complex 1 (TORC1/mTORC1). In this review, a history of this regulation and recent advances in such regulation both in yeast and mammals will be discussed. Recently, the mechanism of autophagy initiation in yeast has been deduced. The autophagy-related gene 13 (Atg13) and the unc-51 like autophagy activating kinase 1 (Ulk1) are the most crucial substrates of TORC1 in autophagy, and by its dephosphorylation, autophagosome formation is initiated. Phosphorylation/dephosphorylation of Atg13 is regulated spatially inside the cell. Another TORC1-dependent regulation lies in the expression of autophagy genes and vacuolar/lysosomal hydrolases. Several transcriptional and post-transcriptional regulations are controlled by TORC1, which affects autophagy activity in yeast and mammals. Full article

(This article belongs to the Special Issue TOR Signaling Pathway)

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Open AccessReview

Lysosomal Regulation of mTORC1 by Amino Acids in Mammalian Cells

by Yao Yao, Edith Jones and Ken Inoki

Biomolecules 2017, 7(3), 51; https://doi.org/10.3390/biom7030051 - 7 Jul 2017

Cited by 52 | Viewed by 13549

Abstract

The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth in eukaryotic cells. The active mTORC1 promotes cellular anabolic processes including protein, pyrimidine, and lipid biosynthesis, and inhibits catabolic processes such as autophagy. Consistent with its growth-promoting functions, [...] Read more.

The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth in eukaryotic cells. The active mTORC1 promotes cellular anabolic processes including protein, pyrimidine, and lipid biosynthesis, and inhibits catabolic processes such as autophagy. Consistent with its growth-promoting functions, hyper-activation of mTORC1 signaling is one of the important pathomechanisms underlying major human health problems including diabetes, neurodegenerative disorders, and cancer. The mTORC1 receives multiple upstream signals such as an abundance of amino acids and growth factors, thus it regulates a wide range of downstream events relevant to cell growth and proliferation control. The regulation of mTORC1 by amino acids is a fast-evolving field with its detailed mechanisms currently being revealed as the precise picture emerges. In this review, we summarize recent progress with respect to biochemical and biological findings in the regulation of mTORC1 signaling on the lysosomal membrane by amino acids. Full article

(This article belongs to the Special Issue TOR Signaling Pathway)

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Open AccessReview

TORC1-Dependent Phosphorylation Targets in Fission Yeast

by Yoko Otsubo, Akio Nakashima, Masayuki Yamamoto and Akira Yamashita

Biomolecules 2017, 7(3), 50; https://doi.org/10.3390/biom7030050 - 3 Jul 2017

Cited by 43 | Viewed by 9736

Abstract

Target of rapamycin (TOR) kinase controls cell metabolism and growth in response to environmental cues such as nutrients, growth factors, and stress. TOR kinase is widely conserved across eukaryotes. As in other organisms, the fission yeast Schizosaccharomyces pombe has two types of TOR [...] Read more.

Target of rapamycin (TOR) kinase controls cell metabolism and growth in response to environmental cues such as nutrients, growth factors, and stress. TOR kinase is widely conserved across eukaryotes. As in other organisms, the fission yeast Schizosaccharomyces pombe has two types of TOR complex, namely TOR complex 1 (TORC1) and TORC2. It is interesting that the two TOR complexes in S. pombe have opposite roles in sexual differentiation, which is induced by nutrient starvation. TORC1, which contains Tor2 as a catalytic subunit, promotes vegetative growth and represses sexual differentiation in nutrient-rich conditions, while TORC2 is required for the initiation of sexual differentiation. Multiple targets of TORC1 have been identified. Some of these, such as S6 kinase and an autophagy regulator Atg13, are known targets in other organisms. In addition, there is a novel group of TORC1 targets involved in the regulation of sexual differentiation. Here, we review recent findings on phosphorylation targets of TORC1 in S. pombe. Furthermore, we briefly report a novel S. pombe target of TORC1. Full article

(This article belongs to the Special Issue TOR Signaling Pathway)

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Open AccessArticle

Mutations in Cancer Cause Gain of Cysteine, Histidine, and Tryptophan at the Expense of a Net Loss of Arginine on the Proteome Level

by Viktoriia Tsuber, Yunus Kadamov, Lars Brautigam, Ulrika Warpman Berglund and Thomas Helleday

Biomolecules 2017, 7(3), 49; https://doi.org/10.3390/biom7030049 - 3 Jul 2017

Cited by 21 | Viewed by 7573

Abstract

Accumulation of somatic mutations is critical for the transition of a normal cell to become cancerous. Mutations cause amino acid substitutions that change properties of proteins. However, it has not been studied as to what extent the composition and accordingly chemical properties of [...] Read more.

Accumulation of somatic mutations is critical for the transition of a normal cell to become cancerous. Mutations cause amino acid substitutions that change properties of proteins. However, it has not been studied as to what extent the composition and accordingly chemical properties of the cell proteome is altered as a result of the increased mutation load in cancer. Here, we analyzed data on amino acid substitutions caused by mutations in about 2000 protein coding genes from the Cancer Cell Line Encyclopedia that contains information on nucleotide and amino acid alterations in 782 cancer cell lines, and validated the analysis with information on amino acid substitutions for the same set of proteins in the Catalogue of Somatic Mutations in Cancer (COSMIC; v78) in circa 18,000 tumor samples. We found that nonsynonymous single nucleotide substitutions in the analyzed proteome subset ultimately result in a net gain of cysteine, histidine, and tryptophan at the expense of a net loss of arginine. The extraordinary loss of arginine may be attributed to some extent to composition of its codons as well as to the importance of arginine in the functioning of prominent tumor suppressor proteins like p53. Full article

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Open AccessArticle

Preparation of Self-Assembled Chitin Nanofiber-Natural Rubber Composite Sheets and Porous Materials

by Akito Kawano, Kazuya Yamamoto and Jun-ichi Kadokawa

Biomolecules 2017, 7(3), 47; https://doi.org/10.3390/biom7030047 - 1 Jul 2017

Cited by 26 | Viewed by 5299

Abstract

We previously reported the preparation of a self-assembled chitin nanofiber (CNF) film via regeneration from an ion gel with an ionic liquid, followed by sonication and filtration. Based on the finding that CNFs were redispersed in a mixture of the film with ammonia [...] Read more.

We previously reported the preparation of a self-assembled chitin nanofiber (CNF) film via regeneration from an ion gel with an ionic liquid, followed by sonication and filtration. Based on the finding that CNFs were redispersed in a mixture of the film with ammonia aqueous solution (aq.), in this study, CNF-natural rubber (NR) composite sheets were fabricated by mixing redispersed CNF with NR latex stabilized by ammonia, followed by drying under reduced pressure. Tensile testing of the sheets indicated the reinforcing effect of CNFs. Further, CNF-NR composite porous materials were fabricated by evaporating ammonia from the CNF-NR dispersion, followed by lyophilization. The mechanism for the formation of porous structures was evaluated. Full article

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Open AccessReview

The Architecture of the Rag GTPase Signaling Network

by Raffaele Nicastro, Alessandro Sardu, Nicolas Panchaud and Claudio De Virgilio

Biomolecules 2017, 7(3), 48; https://doi.org/10.3390/biom7030048 - 30 Jun 2017

Cited by 54 | Viewed by 9892

Abstract

The evolutionarily conserved target of rapamycin complex 1 (TORC1) couples an array of intra- and extracellular stimuli to cell growth, proliferation and metabolism, and its deregulation is associated with various human pathologies such as immunodeficiency, epilepsy, and cancer. Among the diverse stimuli impinging [...] Read more.

The evolutionarily conserved target of rapamycin complex 1 (TORC1) couples an array of intra- and extracellular stimuli to cell growth, proliferation and metabolism, and its deregulation is associated with various human pathologies such as immunodeficiency, epilepsy, and cancer. Among the diverse stimuli impinging on TORC1, amino acids represent essential input signals, but how they control TORC1 has long remained a mystery. The recent discovery of the Rag GTPases, which assemble as heterodimeric complexes on vacuolar/lysosomal membranes, as central elements of an amino acid signaling network upstream of TORC1 in yeast, flies, and mammalian cells represented a breakthrough in this field. Here, we review the architecture of the Rag GTPase signaling network with a special focus on structural aspects of the Rag GTPases and their regulators in yeast and highlight both the evolutionary conservation and divergence of the mechanisms that control Rag GTPases. Full article

(This article belongs to the Special Issue TOR Signaling Pathway)

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Functional Amyloids in Reproduction

by Aveline Hewetson, Hoa Quynh Do, Caitlyn Myers, Archana Muthusubramanian, Roger Bryan Sutton, Benjamin J. Wylie and Gail A. Cornwall

Biomolecules 2017, 7(3), 46; https://doi.org/10.3390/biom7030046 - 29 Jun 2017

Cited by 43 | Viewed by 6437

Abstract

Amyloids are traditionally considered pathological protein aggregates that play causative roles in neurodegenerative disease, diabetes and prionopathies. However, increasing evidence indicates that in many biological systems nonpathological amyloids are formed for functional purposes. In this review, we will specifically describe amyloids that carry [...] Read more.

Amyloids are traditionally considered pathological protein aggregates that play causative roles in neurodegenerative disease, diabetes and prionopathies. However, increasing evidence indicates that in many biological systems nonpathological amyloids are formed for functional purposes. In this review, we will specifically describe amyloids that carry out biological roles in sexual reproduction including the processes of gametogenesis, germline specification, sperm maturation and fertilization. Several of these functional amyloids are evolutionarily conserved across several taxa, including human, emphasizing the critical role amyloids perform in reproduction. Evidence will also be presented suggesting that, if altered, some functional amyloids may become pathological. Full article

(This article belongs to the Special Issue Functional Amyloids)

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Applications of Functional Amyloids from Fungi: Surface Modification by Class I Hydrophobins

by Alessandra Piscitelli, Paola Cicatiello, Alfredo Maria Gravagnuolo, Ilaria Sorrentino, Cinzia Pezzella and Paola Giardina

Biomolecules 2017, 7(3), 45; https://doi.org/10.3390/biom7030045 - 26 Jun 2017

Cited by 33 | Viewed by 5641

Abstract

Class I hydrophobins produced from fungi are amongst the first proteins recognized as functional amyloids. They are amphiphilic proteins involved in the formation of aerial structures such as spores or fruiting bodies. They form chemically robust layers which can only be dissolved in [...] Read more.

Class I hydrophobins produced from fungi are amongst the first proteins recognized as functional amyloids. They are amphiphilic proteins involved in the formation of aerial structures such as spores or fruiting bodies. They form chemically robust layers which can only be dissolved in strong acids. These layers adhere to different surfaces, changing their wettability, and allow the binding of other proteins. Herein, the modification of diverse types of surfaces with Class I hydrophobins is reported, highlighting the applications of the coated surfaces. Indeed, these coatings can be exploited in several fields, spanning from biomedical to industrial applications, which include biosensing and textile manufacturing. Full article

(This article belongs to the Special Issue Functional Amyloids)

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Biomolecules, Volume 7, Issue 3 (September 2017) – 25 articles

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