379 results match your criteria Advances in protein chemistry and structural biology[Journal]


Physicochemical determinants of antibody-protein interactions.

Adv Protein Chem Struct Biol 2020 19;121:85-114. Epub 2019 Nov 19.

Izmir Biomedicine and Genome Center, İzmir, Turkey.

Antibodies are specialized proteins generated by immune system for high specificity and affinity binding to target antigens. Because of their essential roles in immune system, antibodies have been successfully developed and engineered as biopharmaceuticals for treatment of various diseases. Analysis of antibody-protein interactions is always required to get detailed information on effectivity of such antibody-based therapeutics. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.011DOI Listing
November 2019

Role of protein-protein interactions in allosteric drug design for DNA methyltransferases.

Adv Protein Chem Struct Biol 2020 10;121:49-84. Epub 2020 Jan 10.

Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People's Republic of China.

DNA methyltransferases (DNMTs) not only play key roles in epigenetic gene regulation, but also serve as emerging targets for several diseases, especially for cancers. Due to the multi-domains of DNMT structures, targeting allosteric sites of protein-protein interactions (PPIs) is becoming an attractive strategy in epigenetic drug discovery. This chapter aims to review the major contemporary approaches utilized for the drug discovery based on PPIs in different dimensions, from the enumeration of allosteric mechanism to the identification of allosteric pockets. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.12.005DOI Listing
January 2020

Protein-protein interactions: a structural view of inhibition strategies and the IL-23/IL-17 axis.

Adv Protein Chem Struct Biol 2020 24;121:253-303. Epub 2020 Jan 24.

Lead Discovery & Profiling, Discovery Sciences, Janssen R&D LLC, Spring House, PA, United States.

Protein-protein interactions are central to biology and provide opportunities to modulate disease with small-molecule or protein therapeutics. Recent developments in the understanding of the tractability of protein-protein interactions are discussed with a focus on the ligandable nature of protein-protein interaction surfaces. General principles of inhibiting protein-protein interactions are illustrated with structural biology examples from six members of the IL-23/IL-17 signaling family (IL-1, IL-6, IL-17, IL-23 RORγT and TNFα). Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.12.006DOI Listing
January 2020

Computational approaches for identifying potential inhibitors on targeting protein interactions in drug discovery.

Adv Protein Chem Struct Biol 2020 13;121:25-47. Epub 2020 Jan 13.

Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India; Advanced Computational Drug Discovery Unit (ACDD), Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan.

In the era of big data, the interplay of artificial and human intelligence is the demanding job to address the concerns involving exchange of decisions between both sides. Drug discovery is one of the key sources of the big data, which involves synergy among various computational methods to achieve a clinical success. Rightful acquisition, mining and analysis of the data related to ligand and targets are crucial to accomplish reliable outcomes in the entire process. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.013DOI Listing
January 2020

Protein-protein complexes as targets for drug discovery against infectious diseases.

Adv Protein Chem Struct Biol 2020 18;121:237-251. Epub 2019 Dec 18.

Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.

Antibiotics are therapeutic agents against bacterial infections, however, the emergence of multiple and extremely drug-resistant microbes (Multi-Drug Resistant and Extremely Drug-Resistant) are compromising the effectiveness of the currently available treatment options. The drug resistance is not a novel crisis, the current pace of drug discovery has failed to compete with the growth of MDR and XDR pathogenic strains and therefore, it is highly central to find out novel antimicrobial drugs with unique mechanisms of action which may reduce the burden of MDR and XDR pathogenic strains. Protein-protein interactions (PPIs) are involved in a countless of the physiological and cellular phenomena and have become an attractive target to treat the diseases. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.012DOI Listing
December 2019

Tracking the functional meaning of the human oral-microbiome protein-protein interactions.

Adv Protein Chem Struct Biol 2020 16;121:199-235. Epub 2020 Jan 16.

Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal.

The interactome - the network of protein-protein interactions (PPIs) within a cell or organism - is technically difficult to assess. Bioinformatic tools can, not only, identify potential PPIs that can be later experimentally validated, but also be used to assign functional meaning to PPIs. Saliva's potential as a non-invasive diagnostic fluid is currently being explored by several research groups. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.014DOI Listing
January 2020
3.036 Impact Factor

Targeting arrestin interactions with its partners for therapeutic purposes.

Adv Protein Chem Struct Biol 2020 18;121:169-197. Epub 2019 Dec 18.

Department of Pharmacology, Vanderbilt University, Nashville, TN, United States.

Most vertebrates express four arrestin subtypes: two visual ones in photoreceptor cells and two non-visuals expressed ubiquitously. The latter two interact with hundreds of G protein-coupled receptors, certain receptors of other types, and numerous non-receptor partners. Arrestins have no enzymatic activity and work by interacting with other proteins, often assembling multi-protein signaling complexes. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.011DOI Listing
December 2019

Targeting FOXP3 complex ensemble in drug discovery.

Adv Protein Chem Struct Biol 2020 7;121:143-168. Epub 2020 Jan 7.

Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

Forkhead Box P3 (FOXP3) is a key transcriptional regulator of regulatory T cells (Tregs), especially for its function of immune suppression. The special immune suppression function of Tregs plays an important role in maintaining immune homeostasis, and is related to several diseases including cancer, and autoimmune diseases. At the same time, FOXP3 takes a place in a large transcriptional complex, whose stability and functions can be controlled by various post-translational modification. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.010DOI Listing
January 2020
3.036 Impact Factor

Cyclin-dependent kinase inhibition: an opportunity to target protein-protein interactions.

Authors:
Mark A Klein

Adv Protein Chem Struct Biol 2020 18;121:115-141. Epub 2019 Dec 18.

Hematology/Oncology Section, Primary Care Service Line, Minneapolis VA Health Care System, Minneapolis, MN, USA; Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.

Cyclin-dependent kinases (CDKs) play an integral part in cellular activities. To date, most of the activities have been evaluated in the cell cycle and transcription. Several diseases are affected by abnormalities in CDKs, related-pathways, or proteins that regulate CDK activity. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.009DOI Listing
December 2019

Latest trends in structure based drug design with protein targets.

Authors:
Angshuman Bagchi

Adv Protein Chem Struct Biol 2020 18;121:1-23. Epub 2019 Dec 18.

Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India.

Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to determine their binding efficacies with protein target. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.008DOI Listing
December 2019

Atherosclerosis: orchestrating cells and biomolecules involved in its activation and inhibition.

Adv Protein Chem Struct Biol 2020 18;120:85-122. Epub 2019 Dec 18.

Department of Genetics, Barkatullah University, Bhopal, MP, India.

The term atherosclerosis refers to the condition of deposition of lipids and other substances in and on the artery walls, called as plaque that restricts the normal blood flow. The plaque may be stable or unstable in nature. Unstable plaque can burst and trigger clot formation adding further adversities. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.002DOI Listing
December 2019

Roles of Porphyromonas gingivalis and its virulence factors in periodontitis.

Adv Protein Chem Struct Biol 2020 10;120:45-84. Epub 2020 Jan 10.

Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States.

Periodontitis is an infection-driven inflammatory disease, which is characterized by gingival inflammation and bone loss. Periodontitis is associated with various systemic diseases, including cardiovascular, respiratory, musculoskeletal, and reproductive system related abnormalities. Recent theory attributes the pathogenesis of periodontitis to oral microbial dysbiosis, in which Porphyromonas gingivalis acts as a critical agent by disrupting host immune homeostasis. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.12.001DOI Listing
January 2020

Structural sequence evolution and computational modeling approaches of the complement system in leishmaniasis.

Adv Protein Chem Struct Biol 2020 10;120:409-424. Epub 2020 Jan 10.

National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune, Maharashtra, India.

The complement system is one of the first barriers and consists of well-balanced cascades of reactions which generates anaphylatoxins such as C5a and C3a. A G-protein coupled receptor C5a anaphylatoxin chemotactic receptor 1 (C5AR1, also known as CD88) is the receptor for C5a which is present on cells of myeloid origin. Owing to difficulty in obtaining crystal structures of GPCRs in either inactive or active state, accurate structural modeling is still highly desirable for the majority of GPCRs. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.12.004DOI Listing
January 2020

Computational model to analyze and characterize the functional mutations of NOD2 protein causing inflammatory disorder - Blau syndrome.

Adv Protein Chem Struct Biol 2020 4;120:379-408. Epub 2020 Feb 4.

School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.

Blau syndrome (BS), which affects the eyes, skin, and joints, is an autosomal dominant genetic inflammatory disorder. BS is caused by mutations in the NOD2 gene. However, there are no direct treatments, and treatment with conventional anti-inflammatory drugs such as adrenal glucocorticoids, anti-metabolites, and biological agents such as anti-TNF and infliximab have all been attempted with varying degrees of success. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.005DOI Listing
February 2020

Comprehensive in silico screening and molecular dynamics studies of missense mutations in Sjogren-Larsson syndrome associated with the ALDH3A2 gene.

Adv Protein Chem Struct Biol 2020 4;120:349-377. Epub 2020 Feb 4.

Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.

Sjögren-Larsson syndrome (SLS) is an autoimmune disorder inherited in an autosomal recessive pattern. To date, 80 missense mutations have been identified in association with the Aldehyde Dehydrogenase 3 Family Member A2 (ALDH3A2) gene causing SLS. Disruption of the function of ALDH3A2 leads to excessive accumulation of fat in the cells, which interferes with the normal function of protective membranes or materials that are necessary for the body to function normally. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.004DOI Listing
February 2020

Disease modifying drugs for rheumatological diseases: a brief history of everything.

Adv Protein Chem Struct Biol 2020 7;120:313-348. Epub 2020 Jan 7.

MicroPharm Ltd, Newcastle Emlyn, Carmarthenshire, United Kingdom.

The rheumatological diseases are a group of chronic, painful, degenerative and debilitating conditions with an increasing prevalence across the globe. The pathogenesis of these disorders is complex, overlapping and not fully understood. As such, it is difficult and time consuming to achieve correct diagnosis and complete remission for an individual patient. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.007DOI Listing
January 2020

The impact of microRNAs on alterations of gene regulatory networks in allergic diseases.

Adv Protein Chem Struct Biol 2020 12;120:237-312. Epub 2020 Feb 12.

Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France.

Allergic diseases including asthma are worldwide on the rise and contribute significantly to health expenditures. Allergic diseases are prototypic diseases with a strong gene by environment interaction component and epigenetic mechanisms might mediate the effects of the environment on the disease phenotype. MicroRNAs, small non-coding RNAs (miRNAs), regulate gene expression post-transcriptionally. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.006DOI Listing
February 2020

Dietary plant flavonoids in prevention of obesity and diabetes.

Adv Protein Chem Struct Biol 2020 12;120:159-235. Epub 2019 Dec 12.

Department of Chemistry, Dasaratha Deb Memorial College, Khowai, Tripura, India.

Obesity and diabetes are the most prevailing chronic metabolic diseases worldwide from mainly lipid and glucose metabolic dysfunctions and their incidence is increasing at an alarming high rate. Obesity is characterized by excess fat accumulation in WAT and liver and is the central player of insulin resistance in the peripheral tissues from chronic inflammation, lipotoxicity and gut dysbiosis, and plays a key role for development of type 2 diabetes (T2DM) and vascular diseases. Diabetes mellitus, known as diabetes, is chiefly characterized by hyperglycaemia from impaired insulin secretion and insulin resistance. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.006DOI Listing
December 2019

Sphingolipids as mediators of inflammation and novel therapeutic target in inflammatory bowel disease.

Adv Protein Chem Struct Biol 2020 8;120:123-158. Epub 2020 Jan 8.

Lake Erie College of Osteopathic Medicine, Bradenton, FL, United States.

Morbidity of inflammatory gastrointestinal (GI) diseases continues to grow resulting in worsen quality of life and increased burden on public medical systems. Complex and heterogenous illnesses, inflammatory bowel diseases (IBDs) encompass several inflammation -associated pathologies including Crohn's disease and ulcerative colitis. IBD is often initiated by a complex interplay between host genetic and environmental factors, lifestyle and diet, and intestinal bacterial components. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.003DOI Listing
January 2020

The expanding pathways of autoinflammation: a lesson from the first 100 genes related to autoinflammatory manifestations.

Adv Protein Chem Struct Biol 2020 12;120:1-44. Epub 2019 Dec 12.

Autoinflammatory Diseases and Immunodeficiencies Centre, IRCCS Istituto Giannina Gaslini, Genova, GE, Italy.

AutoInflammatory Diseases (AIDs) are a group of innate immune system disorders characterized by sterile inflammation without evidence of pathogenic autoantibodies or auto-reactive T lymphocytes. An expanding spectrum of genes and molecular pathways are associated with AIDs. Inflammasomopathies are secondary to dysregulation of multi-protein complexes, called inflammasomes, leading to an excessive maturation and secretion of IL1β and IL18. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.11.001DOI Listing
December 2019

Pattern recognition receptors as potential drug targets in inflammatory disorders.

Adv Protein Chem Struct Biol 2020 26;119:65-109. Epub 2019 Nov 26.

Pharmacology & Therapeutics School of Medicine, Galway, Ireland.

Pattern recognition receptors (PRRs) are a key part of the innate immune system, the body's first line of defense against infection and tissue damage. This superfamily of receptors including Toll-like receptors (TLRs), NOD-like receptors (NLRs), C-type lectin-like receptors (CLRs) and RIG-like receptors (RLRs) are responsible for initiation of the inflammatory response by their recognition of molecular patterns present in invading microorganisms (such as bacteria, viruses or fungi) during infection or in molecules released following tissue damage during acute or chronic disease states (such as sepsis or arthritis). These receptors are widely expressed and located on the cell surface, in intracellular compartments or in the cytoplasm can detect a single or subset of molecules including lipoproteins, carbohydrates or nucleic acids. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.09.001DOI Listing
November 2019

Biological functions and clinical implications of interleukin-34 in inflammatory diseases.

Adv Protein Chem Struct Biol 2020 8;119:39-63. Epub 2019 Mar 8.

Trauma Research Center, Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100048, China.

Interleukin (IL)-34 is a recently discovered cytokine and ligand of the colony-stimulating factor (CSF)-1 receptor. Although CSF-1 and IL-34 share similar biological properties, their expression patterns and downstream signaling pathways are distinct. IL-34 can influence differentiation and has functions in multiple cell types (e. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.02.003DOI Listing

Sleep deprivation, oxidative stress and inflammation.

Adv Protein Chem Struct Biol 2020 24;119:309-336. Epub 2019 Apr 24.

Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, United States.

Adequate sleep is essential for normal brain function, especially during early life developmental stages as postnatal brain maturation occurs during the critical period of childhood and adolescence. Therefore, sleep disturbance and/or deficit during this period can have detrimental consequences. Many epidemiological and clinical studies have linked early life sleep disturbance with occurrence of later life behavioral and cognitive impairments. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.03.001DOI Listing

Microglial NLRP3 inflammasome activation in multiple sclerosis.

Adv Protein Chem Struct Biol 2020 26;119:247-308. Epub 2019 Nov 26.

Department of Neuroscience, Institute of Health and Science, Dokuz Eylul University Health Campus, Balcova, Izmir, Turkey.

Multiple sclerosis (MS) is a chronic, autoimmune and neuroinflammatory disease of the central nervous system (CNS) mediated by autoreactive T cells directed against myelin antigens. Although the crucial role of adaptive immunity is well established in MS, the contribution of innate immunity has only recently been appreciated. Microglia are the main innate immune cells of the CNS. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.007DOI Listing
November 2019

Interplay between inflammation and cancer.

Adv Protein Chem Struct Biol 2020 26;119:199-245. Epub 2019 Nov 26.

Department of Genetics, Barkatullah University, Bhopal, Madhya Pradesh, India.

During the 19th century, for the first time, the linkage between inflammation and cancer was established. Inflammatory microenvironment is an essential component of the tumor microenvironment. Chronic inflammation due to persistent infection due to the microbes, viruses, helminths or constant exposure to non-infectious factors like smoke, silica or asbestos eventually might result in carcinogenesis. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.09.004DOI Listing
November 2019

Inflammatory bowel disease and targeted oral anti-TNFα therapy.

Adv Protein Chem Struct Biol 2020 10;119:157-198. Epub 2020 Jan 10.

School of Health Sciences, Cardiff Metropolitan University, Cardiff, United Kingdom.

Antibodies have provided invaluable treatment options for many diseases, with immunotherapy revolutionising the treatment of several inflammatory disorders including inflammatory bowel disease (IBD). Accumulating evidence suggests that IBD results from an inappropriate response to intestinal microbes and environmental factors in genetically susceptible individuals, with overactivity of the pro-inflammatory pathways. On a pathophysiological level, IBD is a complex disease with intestinal fibrosis, stenosis and an increased incidence of cancer observed in those whose disease is inadequately controlled over time. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.009DOI Listing
January 2020

Glycosylation changes in inflammatory diseases.

Adv Protein Chem Struct Biol 2020 26;119:111-156. Epub 2019 Nov 26.

University Lille, CNRS, UMR 8576 - UGSF - Unite de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France.

Glycosylation is one of the most important modifications of proteins and lipids, and cell surface glycoconjugates are thought to play important roles in a variety of biological functions including cell-cell and cell-substrate interactions, bacterial adhesion, cell immunogenicity and cell signaling. Alterations of glycosylation are observed in a number of inflammatory diseases. Pro-inflammatory cytokines have been shown to modulate cell surface glycosylation by regulating the expression of glycosyltransferases and sulfotransferases involved in the biosynthesis of glycan chains, inducing the expression of specific carbohydrate antigens at the cell surface that can be recognized by different types of lectins or by bacterial adhesins, contributing to the development of diseases. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.008DOI Listing
November 2019

Using evasins to target the chemokine network in inflammation.

Adv Protein Chem Struct Biol 2020 26;119:1-38. Epub 2019 Nov 26.

RDM Division of Cardiovascular Medicine, University of Oxford, Oxford, United Kingdom.

Inflammation, is driven by a network comprising cytokines, chemokines, their target receptors and leukocytes, and is a major pathologic mechanism that adversely affects organ function in diverse human diseases. Despite being supported by substantial target validation, no successful anti-chemokine therapeutic to treat inflammatory disease has yet been developed. This is in part because of the robustness of the chemokine network, which emerges from a large total chemokine load in disease, promiscuous expression of receptors on leukocytes, promiscuous and synergistic interactions between chemokines and receptors, and feedforward loops created by secretion of chemokines by leukocytes themselves. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.09.003DOI Listing
November 2019

Influence of the reducing environment in the misfolding of wine proteins.

Adv Protein Chem Struct Biol 2019 19;118:413-436. Epub 2019 Oct 19.

Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro (PD), Italy; Centre for Research in Viticulture and Enology (CIRVE), Conegliano (TV), Italy.

While proteins are present in wine at low concentration, and are largely associated with undesirable haze formation in white wines, certain types or fractions make direct and indirect contributions to sensory quality and physical stability. The proteins found in wine represent a small subclass of the total pool of grape proteins that remain soluble in the non-physiological conditions of the wine matrix which is characterised by the presence of alcohol, high acidity, and relatively high levels of phenolic compounds. Although initially stable in these conditions, during storage of white and rosé wines proteins undergo changes leading to haze formation which is considered one of the most relevant non-microbiological defects, and which makes the wine commercially unacceptable. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.004DOI Listing

Misfolded proteins as a therapeutic target in Alzheimer's disease.

Adv Protein Chem Struct Biol 2019 21;118:371-411. Epub 2019 Sep 21.

Krembil Research Institute, University Health Network, Toronto, ON, Canada; Departments of Medicine (Neurology), Chemistry and Pharmaceutical Sciences, University of Toronto, Toronto, ON, Canada.

For decades, Alzheimer's Disease (AD) was defined as a disorder of protein misfolding and aggregation. In particular, the extracellular peptide fragment: amyloid-β (Aβ), and the intracellular microtubule-associated protein: tau, were thought to initiate a neurodegenerative cascade which culminated in AD's progressive loss of memory and executive function. As such, both proteins became the focus of intense scrutiny, and served as the principal pathogenic target for hundreds of clinical trials. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.003DOI Listing

Cytotoxic species in amyloid-associated diseases: Oligomers or mature fibrils.

Adv Protein Chem Struct Biol 2019 7;118:333-369. Epub 2019 Aug 7.

Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.

Amyloid diseases especially, Alzheimer's disease (AD), is characterized by an imbalance between the production and clearance of amyloid-β (Aβ) species. Amyloidogenic proteins or peptides can transform structurally from monomers into β-stranded fibrils via multiple oligomeric states. Among various amyloid species, structured oligomers are proposed to be more toxic than fibrils; however, the identification of amyloid oligomers has been challenging due to their heterogeneous and metastable nature. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.06.001DOI Listing
April 2020
3.036 Impact Factor

Combining molecular dynamics simulations and experimental analyses in protein misfolding.

Adv Protein Chem Struct Biol 2019 6;118:33-110. Epub 2020 Jan 6.

Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada.

The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.10.001DOI Listing

Liquid-liquid phase transitions and amyloid aggregation in proteins related to cancer and neurodegenerative diseases.

Adv Protein Chem Struct Biol 2019 21;118:289-331. Epub 2019 Sep 21.

Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.

Liquid-liquid phase separation (LLPS) and phase transition (LLPT) of proteins and nucleic acids have emerged as a new paradigm in cell biology. Here we will describe the recent findings about LLPS and LLPT, including the molecular and physical determinants leading to their formation, the resulting functions and their implications in cell physiology and disease. Amyloid aggregation is implicated in many neurodegenerative diseases and cancer, and LLPS of proteins involved in these diseases appear to be related to their function in different cell contexts. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.002DOI Listing

LOXL1 folding in exfoliation glaucoma.

Adv Protein Chem Struct Biol 2019 21;118:273-288. Epub 2019 Oct 21.

Eye and Vision Research Institute, Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.

Exfoliation syndrome (XFS) is an age-related disease defined by the deposition of aggregated fibrous material (XFM) in the peri-cellular space. Principal morbidity occurs in the eye, where XFM accumulates on the anterior ocular tissues. GWAS have found that certain genetic variants of lysyl oxidase-like 1 (LOXL1), a matrix cross-linking enzyme that is required for elastic fiber formation confer risk for the development of XFS, but are not a single causative factor as many genetically affected individuals do not develop XFS or subsequent glaucoma (XFG). Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.09.005DOI Listing

Misfolding of vasopressin receptors: biased agonist pharmacochaperones as potential therapeutics.

Adv Protein Chem Struct Biol 2019 26;118:249-272. Epub 2019 Nov 26.

Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France.

Biased agonists and pharmacological chaperones have demonstrated their potential to harness G protein-coupled receptor signaling and trafficking, and have collectively opened new possibilities in G protein-coupled receptor drug discovery. Combining pharmacological chaperoning and biased agonism properties into a unique given molecule would be of high therapeutic interest in many human diseases resulting from G protein-coupled receptor mutation and misfolding. This strategy perfectly fits to congenital Nephrogenic Diabetes Insipidus which is a typical conformational disease. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.07.002DOI Listing

Protein misfolding in endoplasmic reticulum stress with applications to renal diseases.

Adv Protein Chem Struct Biol 2019 23;118:217-247. Epub 2019 Sep 23.

Department of Medicine, Hamilton Centre for Kidney Research, McMaster University and St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada.

Protein misfolding may be the result of a variety of different processes that disrupt the ability of a protein to form a thermodynamically stable tertiary structure that allows it to perform its proper function. In this chapter, we explore the nature of a protein's form that allows it to have a stable tertiary structure, and examine specific mutation that are known to occur in the coding regions of DNA that disrupt a protein's ability to be folded into a thermodynamically stable tertiary structure. We examine the consequences of these protein misfoldings in terms of the endoplasmic reticulum stress response and resulting unfolded protein response. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.001DOI Listing

Functional and dysfunctional folding, association and aggregation of caseins.

Adv Protein Chem Struct Biol 2019 26;118:163-216. Epub 2019 Nov 26.

Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom.

Caseins are a group of closely related intrinsically disordered proteins (IDPs), best known for their occurrence in milk as stable, polydisperse, roughly spherical, amorphous particles, typically containing thousands of protein chains and hundreds of nanoclusters of calcium phosphate. The particles are called casein micelles though their structure bears no resemblance to detergent micelles. Caseins have an open and flexible conformation with a preponderance of poly-l-proline II secondary structure and hence cannot be described as hydrophobic proteins. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.09.002DOI Listing

The intrinsic and extrinsic factors that contribute to proteostasis decline and pathological protein misfolding.

Authors:
Elise A Kikis

Adv Protein Chem Struct Biol 2019 26;118:145-161. Epub 2019 Nov 26.

Biology Department, The University of the South, Sewanee, TN, United States.

Proteostasis refers to the ability of cells to maintain the health of the proteome. Highly conserved quality control mechanisms exist to maintain proteostasis. These include the heat shock response, the unfolded protein response, and protein clearance/degradation pathways. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.07.001DOI Listing

Mass spectrometric approaches for profiling protein folding and stability.

Adv Protein Chem Struct Biol 2019 26;118:111-144. Epub 2019 Nov 26.

Department of Chemistry, University of California, Riverside, CA, United States.

Protein stability reports on protein homeostasis, function, and binding interactions, such as to other proteins, metabolites and drugs. As such, there is a pressing need for technologies that can report on protein stability. The ideal technique could be applied in vitro or in vivo systems, proteome-wide, independently of matrix, under native conditions, with residue-level resolution, and on protein at endogenous levels. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.09.006DOI Listing

Theoretical and computational advances in protein misfolding.

Authors:
Parbati Biswas

Adv Protein Chem Struct Biol 2019 26;118:1-31. Epub 2019 Nov 26.

Department of Chemistry, University of Delhi, Delhi, India.

Misfolded proteins escape the cellular quality control mechanism and fail to fold properly or remain correctly folded leading to a loss in their functional specificity. Thus misfolding of proteins cause a large number of very different diseases ranging from errors in metabolism to various types of complex neurodegenerative diseases. A theoretical and computational perspective of protein misfolding is presented with a special emphasis on its salient features, mechanism and consequences. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.010DOI Listing

Comparison of DNA and RNA substrate effects on TET2 structure.

Adv Protein Chem Struct Biol 2019 11;117:91-112. Epub 2019 Jun 11.

Department of Chemistry, University of North Texas, Denton, TX, United States.

Ten-eleven translocation (TET) enzymes can perform the stepwise oxidation of 5-methylcytosine (5mC) to 5-carboxylcytosine on both single-stranded (ss) and double-stranded (ds) DNA and RNA. It has been established that TET2 has a preference for ds DNA substrates, but it can catalyze the oxidation reaction on both ssDNA and RNA. The reasons for this substrate preference have been investigated for only a substrate 5mC ribonucleotide in a DNA strand, but not other nucleic acid configurations (Biochemistry58 (2019) 411). Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18761623193005
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http://dx.doi.org/10.1016/bs.apcsb.2019.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036138PMC
February 2020
1 Read

Glutarate L-2-hydroxylase (CsiD/GlaH) is an archetype Fe(II)/2-oxoglutarate-dependent dioxygenase.

Adv Protein Chem Struct Biol 2019 10;117:63-90. Epub 2019 Jun 10.

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.

The Escherichia coli gene initially named ygaT is located adjacent to lhgO, encoding L-2-hydroxyglutarate oxidase/dehydrogenase, and the gabDTP gene cluster, utilized for γ-aminobutyric acid (GABA) metabolism. Because this gene is transcribed specifically during periods of carbon starvation, it was renamed csiD for carbon starvation induced. The CsiD protein was structurally characterized and shown to possess a double-stranded ß-helix fold, characteristic of a large family of non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7132994PMC
February 2020
2 Reads

Structure-function relationships in KDM7 histone demethylases.

Adv Protein Chem Struct Biol 2019 10;117:113-125. Epub 2019 Sep 10.

Department of Chemistry, Michigan Technological University, Houghton, MI, United States.

The demethylation of lysine residues of histone proteins is a key epigenetic mechanism in cells. The enzymes that catalyze these processes are called histone demethylases (KDMs). The largest family of KDMs is the Jumonji C (JmjC) domain-containing enzymes; these includes KDM2-7 subfamily of enzymes. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.08.005DOI Listing
February 2020
3 Reads
3.036 Impact Factor

Non-heme iron enzyme-catalyzed complex transformations: Endoperoxidation, cyclopropanation, orthoester, oxidative C-C and C-S bond formation reactions in natural product biosynthesis.

Adv Protein Chem Struct Biol 2019 23;117:1-61. Epub 2019 Sep 23.

Department of Chemistry, Boston University, Boston, MA, United States.

Non-heme iron enzymes catalyze a wide range of chemical transformations, serving as one of the key types of tailoring enzymes in the biosynthesis of natural products. Hydroxylation reaction is the most common type of reactions catalyzed by these enzymes and hydroxylation reactions have been extensively investigated mechanistically. However, the mechanistic details for other types of transformations remain largely unknown or unexplored. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.06.002DOI Listing
February 2020

Nucleobindins and encoded peptides: From cell signaling to physiology.

Adv Protein Chem Struct Biol 2019 17;116:91-133. Epub 2019 Apr 17.

Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, Saskatoon, SK, Canada. Electronic address:

Nucleobindins (NUCBs) are DNA and calcium binding, secreted proteins with various signaling functions. Two NUCBs, nucleobindin-1 (NUCB1) and nucleobindin-2 (NUCB2), were discovered during the 1990s. These two peptides are shown to have diverse functions, including the regulation of inflammation and bone formation, among others. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18761623193001
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http://dx.doi.org/10.1016/bs.apcsb.2019.02.001DOI Listing
February 2020
18 Reads

From traveler to homebody: Which signaling mechanisms sponge larvae use to become adult sponges?

Adv Protein Chem Struct Biol 2019 14;116:421-449. Epub 2019 Mar 14.

St. Petersburg State University, St. Petersburg, Russia; Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix Marseille University, CNRS, IRD, Avignon Université, Marseille, France.

Cell-to-cell signaling is responsible for regulation of many developmental processes such as proliferation, cell migration, survival, cell fate specification and axis patterning. In this article we discussed the role of signaling in the metamorphosis of sponges with a focus on epithelial-mesenchymal transition (EMT) accompanying this event. Sponges (Porifera) are an ancient lineage of morphologically simple animals occupying a basal position on the tree of life. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.02.002DOI Listing
February 2020
20 Reads

Recent advances in computational studies of GPCR-G protein interactions.

Adv Protein Chem Struct Biol 2019 3;116:397-419. Epub 2019 Jan 3.

Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States. Electronic address:

Protein-protein interactions are key in cellular signaling. G protein-coupled receptors (GPCRs), the largest superfamily of human membrane proteins, are able to transduce extracellular signals (e.g. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2018.11.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986689PMC
February 2020
2 Reads

Dopamine signaling in the striatum.

Adv Protein Chem Struct Biol 2019 22;116:375-396. Epub 2019 Feb 22.

Department of Cell Biology, Physiology and Immunology, Institute of Neuroscience, Autonomous University of Barcelona, Barcelona, Spain.

The striatum integrates dopamine-mediated reward signals to generate appropriate behavior in response to glutamate-mediated sensory cues. Such associative learning relies on enduring neural plasticity in striatal GABAergic spiny projection neurons which, when altered, can lead to the development of a wide variety of pathological states. Considerable progress has been made in our understanding of the intracellular signaling mechanisms in dopamine-related behaviors and pathologies. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2019.01.004DOI Listing
February 2020
5 Reads

Intracellular protein complexes involved in synapse assembly in presynaptic neurons.

Adv Protein Chem Struct Biol 2019 20;116:347-373. Epub 2018 Dec 20.

Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea. Electronic address:

The presynaptic active zone, composed of evolutionarily conserved protein complexes, is a specialized area that serves to orchestrate precise and efficient neurotransmitter release by organizing various presynaptic proteins involved in mediating docking and priming of synaptic vesicles, recruiting voltage-gated calcium channels, and modulating presynaptic nerve terminals with aligned postsynaptic structures. Among membrane proteins localized to active zone, presynaptic neurexins and LAR-RPTPs (leukocyte common antigen-related receptor tyrosine phosphatase) have emerged as hubs that orchestrate both shared and distinct extracellular synaptic adhesion pathways. In this chapter, we discuss intracellular signaling cascades involved in recruiting various intracellular proteins at both excitatory and inhibitory synaptic sites. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2018.11.008DOI Listing
February 2020
2 Reads

Aquaporin water channels: New perspectives on the potential role in inflammation.

Adv Protein Chem Struct Biol 2019 5;116:311-345. Epub 2019 Jan 5.

Department of Basic Medical Sciences, Neurosciences and Sensory Organs (SMBNOS), Section of Human Anatomy and Histology, University of Bari "Aldo Moro", Bari, Italy.

Aquaporins (AQPs) are a family of membrane water channel proteins that osmotically modulate water fluid homeostasis in several tissues; some of them also transport small solutes such as glycerol. At the cellular level, the AQPs regulate not only cell migration and transepithelial fluid transport across membranes, but also common events that are crucial for the inflammatory response. Emerging data reveal a new function of AQPs in the inflammatory process, as demonstrated by their dysregulation in a wide range of inflammatory diseases including edematous states, cancer, obesity, wound healing and several autoimmune diseases. Read More

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http://dx.doi.org/10.1016/bs.apcsb.2018.11.010DOI Listing
February 2020
2 Reads