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HNF1A-MODY Mutations in Nuclear Localization Signal Impair HNF1A-Import Receptor KPNA6 Interactions Protein J. (IF 1.317) Pub Date : 2021-01-18 Fareed M. A. Fareed, Sirin Korulu, Mehmet Özbil, Özlem Yalçın Çapan
Mutations in hepatocyte nuclear factor (HNF)1A gene cause the most common form of Maturity-onset diabetes of the young (MODY), a monogenic subtype of diabetes mellitus. Functional characterization of mutant proteins reveals that mutations may disrupt DNA binding capacity, transactivation ability and nuclear localization of HNF1A depending on the position of the mutation. Previously identified Arg271Trp
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QSSR Modeling of Bacillus Subtilis Lipase A Peptide Collision Cross-Sections in Ion Mobility Spectrometry: Local Descriptor Versus Global Descriptor Protein J. (IF 1.317) Pub Date : 2021-01-16 Zhong Ni, Anlin Wang, Lingyu Kang, Tiancheng Zhang
To investigate the structure-dependent peptide mobility behavior in ion mobility spectrometry (IMS), quantitative structure-spectrum relationship (QSSR) is systematically modeled and predicted for the collision cross section Ω values of totally 162 single-protonated tripeptide fragments extracted from the Bacillus subtilis lipase A. Two different types of structure characterization methods, namely
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Sequential Dihedral Angles (SDAs): A Method for Evaluating the 3D Structure of Proteins Protein J. (IF 1.317) Pub Date : 2021-01-14 Babak Esfandi, Morteza Atabati
One of the most important steps in modeling three-dimensional (3D) structures of proteins is the evaluation of the constructed models. The present study suggests that the correctness of a structure may be tested by using the characteristics of sequential dihedral angles (SDAs) between adjacent alpha-carbons (Cα) in the main chains of proteins. From our studies on protein structures in the protein data
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Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus : Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MM Protein J. (IF 1.317) Pub Date : 2021-01-09 Vikram Dalal, Poonam Dhankhar, Vishakha Singh, Vishakha Singh, Gaddy Rakhaminov, Dasantila Golemi-Kotra, Pravindra Kumar
Staphylococcus aureus is resistant to β-lactam antibiotics and causes several skin diseases to life-threatening diseases. FmtA is found to be one of the main factors involved in methicillin resistance in S. aureus. FmtA exhibits an esterase activity that removes the D-Ala from teichoic acid. Teichoic acids played a significant role in cell wall synthesis, cell division, colonization, biofilm formation
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Correction to: Aldehyde Production as a Calibrant of Ultrasonic Power Delivery During Protein Misfolding Cyclic Amplification Protein J. (IF 1.317) Pub Date : 2021-01-06 Simon C. Drew
In the original version of this article, two minor errors appear in the figure captions.
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Investigation of the Substrate‐Binding Site of a Prostaglandin E Synthase in Bombyx mori Protein J. (IF 1.317) Pub Date : 2021-01-05 Kohji Yamamoto, Aiko Hirowatari
Prostaglandin E synthase (PGES) catalyzes the conversion of prostaglandin H2 to prostaglandin E2 in the presence of glutathione (GSH) in mammals. Amid the limited knowledge on prostaglandin and its related enzymes in insects, we recently identified PGES from the silkworm Bombyx mori (bmPGES) and determined its crystal structure complexed with GSH. In the current study, we investigated the substrate-binding
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How Useful can the Voigt Profile be in Protein Folding Processes? Protein J. (IF 1.317) Pub Date : 2021-01-05 Luka Maisuradze, Gia G. Maisuradze
The analytical expression for the Voigt profile, along with its simplified forms for the Gaussian and Lorentzian dominance, is presented. The applicability of the Voigt profile in the description of anomalous diffusion phenomena, ubiquitous in different fields of science including protein folding, is discussed. It is shown that the Voigt profile is a good descriptor of the processes occurring in protein
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Targeting the Autophagy Specific Lipid Kinase VPS34 for Cancer Treatment: An Integrative Repurposing Strategy Protein J. (IF 1.317) Pub Date : 2021-01-05 Poornimaa Murali, Kanika Verma, Thanyada Rungrotmongkol, Perarasu Thangavelu, Ramanathan Karuppasamy
The impact of autophagy on cancer treatment and its corresponding responsiveness has galvanized the scientific community to develop novel inhibitors for cancer treatment. Importantly, the discovery of inhibitors that targets the early phase of autophagy was identified as a beneficial choice. Despite the number of research in recent years, screening of the DrugBank repository (9591 molecules) for the
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Update and Potential Opportunities in CBP [Cyclic Adenosine Monophosphate (cAMP) Response Element-Binding Protein (CREB)-Binding Protein] Research Using Computational Techniques Protein J. (IF 1.317) Pub Date : 2021-01-04 Oluwayimika E. Akinsiku, Opeyemi S. Soremekun, Mahmoud E. S. Soliman
CBP [cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB)-binding protein] is one of the most researched proteins for its therapeutic function. Several studies have identified its vast functions and interactions with other transcription factors to initiate cellular signals of survival. In cancer and other diseases such as Alzheimer’s, Rubinstein-taybi syndrome, and inflammatory
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Structure of Yak Lactoperoxidase at 1.55 Å Resolution Protein J. (IF 1.317) Pub Date : 2021-01-03 V. Viswanathan, Chitra Rani, Nayeem Ahmad, Prashant Kumar Singh, Pradeep Sharma, Punit Kaur, Sujata Sharma, Tej P. Singh
Lactoperoxidase (LPO) is a heme containing oxido-reductase enzyme. It is secreted from mammary, salivary, lachrymal and mucosal glands. It catalyses the conversion of thiocyanate into hypothiocyanate and halides into hypohalides. LPO belongs to the superfamily of mammalian heme peroxidases which also includes myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). The heme
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Bioactive Phytocompounds: Anti-amyloidogenic Effects Against Hen Egg-White Lysozyme Aggregation Protein J. (IF 1.317) Pub Date : 2021-01-03 Suman Chowdhury, Suresh Kumar
Amyloidosis is the process of fibril formation responsible for causing several diseases in the human being that involve protein aggregation such as Alzheimer’s, Parkinson’s, Huntington’s disease, and type II diabetes. Natural phytocompounds such as curcumin shown promising anti-amyloidogenic activity. In the present study, selective phytocompounds such as piperine, cinnamaldehyde, eugenol, and cuminaldehyde
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c.1898C>G/p.Ser633Trp Mutation in Alpha- l -Iduronidase: Clinical and Structural Implications Protein J. (IF 1.317) Pub Date : 2021-01-02 Iliana Peña-Gomar, José L. Jiménez-Mariscal, Magdalena Cerón, Jorge Rosas-Trigueros, Cesar A. Reyes-López
Mucopolysaccharidosis type I is a rare autosomal recessive genetic disease caused by deficient activity of α-l-iduronidase. As a consequence of low or absent activity of this enzyme, glycosaminoglycans accumulate in the lysosomal compartments of multiple cell types throughout the body. Mucopolysaccharidosis type I has been classified into 3 clinical subtypes, ranging from a severe Hurler form to the
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Proteomic Analysis of Extracellular Vesicles Derived from MDA-MB-231 Cells in Microgravity Protein J. (IF 1.317) Pub Date : 2021-01-02 Yundi Chen, Fei Xue, Andrea Russo, Yuan Wan
Patients with triple-negative breast cancer (TNBC) have a relatively poor prognosis and cannot benefit from endocrine and/or targeted therapy. Considerable effort has been devoted toward the elucidation of the molecular mechanisms and potential diagnostic/therapeutic targets. However, it is inefficient and often ineffective to study the biological nuances of TNBC in large-scale clinical trials. In
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Oxidative Damage? Not a Problem! The Characterization of Humanin-like Mitochondrial Peptide in Anoxia Tolerant Freshwater Turtles Protein J. (IF 1.317) Pub Date : 2021-01-02 Sanoji Wijenayake, Kenneth B. Storey
Mitochondria was long thought to be an “end function” organelle that regulated the metabolic flux and apoptosis in the cell. However, with the discovery of the mitochondrial peptide (MDP) humanin (HN/MTRNR2), the cytoprotective and pro-survival applications of MDPs have taken the forefront of therapeutic and diagnostic research. However, the regulation of humanin-like MDPs in natural model systems
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In Silico Evaluation of Prospective Anti-COVID-19 Drug Candidates as Potential SARS - CoV - 2 Main Protease Inhibitors Protein J. (IF 1.317) Pub Date : 2021-01-02 Mahmoud A. A. Ibrahim, Alaa H. M. Abdelrahman, Khaled S. Allemailem, Ahmad Almatroudi, Mahmoud F. Moustafa, Mohamed-Elamir F. Hegazy
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Exploration of Serum Marker Proteins in Mice Induced by Babesia microti Infection Using a Quantitative Proteomic Approach Protein J. (IF 1.317) Pub Date : 2021-01-02 Xiaoshuang Wang, Shuguang Ren, Xiaohong Yang, Abolfazl Masoudi, Xiaomin Xue, Mengxue Li, Hongxia Li, Xiaojing Zhang, Hui Wang, Jingze Liu
Babesia microti is a protozoan that mainly parasitizes rodent and human erythrocytes. B. microti infection can result in changes in the expression levels of various proteins in the host serum. To explore the mechanism underlying the regulation of serum proteins by the host during B. microti infection, this study used a data-independent acquisition (DIA) quantitative proteomic approach to perform comprehensive
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Basic Amino Acids Within the Juxtamembrane Domain of the Epidermal Growth Factor Receptor Regulate Receptor Dimerization and Auto-phosphorylation Protein J. (IF 1.317) Pub Date : 2020-11-19 Jordan D. Mohr, Alice Wagenknecht-Wiesner, David A. Holowka, Barbara A. Baird
Epidermal growth factor receptor (EGFR) dysregulation is observed in many human cancers and is both a cause of oncogenesis and a target for chemotherapy. We previously showed that partial charge neutralization of the juxtamembrane (JX) region of EGFR via the EGFR R1–6 mutant construct induces constitutive receptor activation and transformation of NIH 3T3 cells, both from the plasma membrane and from
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Comparison of Binding Site of Remdesivir and Its Metabolites with NSP12-NSP7-NSP8, and NSP3 of SARS CoV-2 Virus and Alternative Potential Drugs for COVID-19 Treatment Protein J. (IF 1.317) Pub Date : 2020-11-13 Lindsey S Jung, Tamara M Gund, Mahesh Narayan
Remdesivir was approved by the U.S.A. Food and Drug administration for emergency use to interfere with the replication of SARS CoV-2 virus (the agent that causes COVID-19) in adults and children hospitalized with severe disease. The crystal structure of the metabolite of remdesivir (Monophosphate of GS-441524) and NSP12-NSP8-NSP7 of SARS CoV-2 virus was recently reported. The crystal structures of
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Chemical Digestion of the -Asp-Cys- Sequence for Preparation of Post-translationally Modified Proteins Protein J. (IF 1.317) Pub Date : 2020-11-11 Shigeru Shimamoto, Natsumi Mitsuoka, Saki Takahashi, Toru Kawakami, Yuji Hidaka
Numerous studies of native proteins have been reported on protein folding in this half century. Recently, post-translationally modified proteins are also focused on protein folding. However, it is still difficult to prepare such types of proteins because it requires not only the chemical but also the recombinant techniques. Native chemical ligation (NCL) is a powerful technique for producing target
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Integrated In Silico-In Vitro Identification and Optimization of Bone Morphogenic Protein-2 Armpit Epitope as Its Antagonist Binding Site Protein J. (IF 1.317) Pub Date : 2020-11-01 Yanping Wu, Guanghong Jia, Haiyan Chi, Zhaode Jiao, Yinghua Sun
Bone morphogenic protein-2 (BMP-2) is the most documented member of BMP family and plays a crucial role in bone formation and growth. In this study, we systematically analyze and compare the complex crystal structures and interaction properties of BMP-2 with its cognate receptors BMPR-I/BMPR-II and with its natural antagonist crossveinless-2 (CV-2) using an integrated in silico-in vitro strategy. It
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About the Protein Space Vastness Protein J. (IF 1.317) Pub Date : 2020-11-01 Jorge A. Vila
An accurate estimation of the Protein Space size, in light of the factors that govern it, is a long-standing problem and of paramount importance in evolutionary biology, since it determines the nature of protein evolvability. A simple analysis will enable us to, firstly, reduce an unrealistic Protein Space size of ~ 10130 sequences, for a 100-residues polypeptide chain, to ~ 109 functional proteins
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Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography Protein J. (IF 1.317) Pub Date : 2020-10-31 Zhihong Li, Xiaoshuai Zhang, Chunran Li, Andrey Kovalevsky, Qun Wan
XynII is a family 11 glycoside hydrolase that uses the retaining mechanism for catalysis. In the active site, E177 works as the acid/base and E86 works as the nucleophile. Mutating an uncharged residue (N44) to an acidic residue (D) near E177 decreases the enzyme’s optimal pH by ~ 1.0 unit. D44 was previously suggested to be a second proton carrier for catalysis. To test this hypothesis, we abolished
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Application of a Distance-Dependent Sigmoidal Dielectric Constant to the REMC/SAAP3D Simulations of Chignolin, Trp-Cage, and the G10q Mutant Protein J. (IF 1.317) Pub Date : 2020-10-27 Michio Iwaoka, Koji Yoshida, Taku Shimosato
The replica-exchange Monte Carlo method based on the single amino acid potential (SAAP) force field, i.e., REMC/SAAP3D, was recently developed by our group for the molecular simulation of short peptides. In this study, the method has been improved by applying a distance-dependent dielectric (DDD) constant and extended to the peptides containing d-amino acid (AA) residues. For chignolin (10 AAs), a
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Bacillus sonorensis L. Asparaginase: Cloning, Expression in E. coli and Characterization Protein J. (IF 1.317) Pub Date : 2020-10-26 Nihal Aly, Amani El-Ahwany, Farid Shokry Ataya, Hesham Saeed
l-asparaginases (l-ASNases; EC 3.5.1.1) are aminohydrolases that catalyze the hydrolysis of l-asparagine (l-Asn) to l-aspartic acid and ammonia, resulting in the death of acute lymphoblastic leukemic cells and other blood cancer cells. In this study, Bacillus sonorensis (accession number MK523484) uncharacterized l-ASNase gene (accession number MN562875) was isolated by polymerase chain reaction (PCR)
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Role of Oxidative Stress on SARS-CoV (SARS) and SARS-CoV-2 (COVID-19) Infection: A Review Protein J. (IF 1.317) Pub Date : 2020-10-26 Shanzay Suhail, Jonathan Zajac, Carl Fossum, Harrison Lowater, Cailin McCracken, Nathaniel Severson, Bethany Laatsch, Alex Narkiewicz-Jodko, Benjamin Johnson, Jessica Liebau, Sudeep Bhattacharyya, Sanchita Hati
Novel coronavirus disease 2019 (COVID-19) has resulted in a global pandemic and is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several studies have suggested that a precise disulfide-thiol balance is crucial for viral entry and fusion into the host cell and that oxidative stress generated from free radicals can affect this balance. Here, we reviewed the current knowledge
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Expression, purification, and phylogenetic analysis of MDIS1-INTERACTING RECEPTOR-LIKE KINASE1 (MIK1) Protein J. (IF 1.317) Pub Date : 2020-10-26 Krittin Trihemasava, Sayan Chakraborty, Kevin Blackburn, Guozhou Xu
An abundance of protein structures has been solved in the last six decades that are paramount in defining the function of such proteins. For unsolved protein structures, however, predictions based on sequence and phylogenetic similarity can be useful for identifying key domains of interaction. Here, we describe expression and purification of a recombinant plant LRR-RLK ectodomain MIK1 using a modified
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An Overview of the Crystallized Structures of the SARS-CoV-2 Protein J. (IF 1.317) Pub Date : 2020-10-24 Mihaela Ileana Ionescu
Many research teams all over the world focus their research on the SARS-CoV-2, the new coronavirus that causes the so-called COVID-19 disease. Most of the studies identify the main protease or 3C-like protease (Mpro/3CLpro) as a valid target for large-spectrum inhibitors. Also, the interaction of the human receptor angiotensin-converting enzyme 2 (ACE2) with the viral surface glycoprotein (S) is studied
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Purification and Regulation of Pyruvate Kinase from the Foot Muscle of the Anoxia and Freeze Tolerant Marine Snail, Littorina littorea Protein J. (IF 1.317) Pub Date : 2020-10-23 Michael B. Smolinski, Anchal Varma, Stuart R. Green, Kenneth B. Storey
The intertidal marine snail, Littorina littorea, has evolved to survive bouts of anoxia and extracellular freezing brought about by changing tides and subsequent exposure to harsh environmental conditions. Survival in these anoxic conditions depends on the animals entering a state of metabolic rate depression in order to maintain an appropriate energy production-consumption balance during periods of
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RNA and DNA Binding Epitopes of the Cold Shock Protein Tm Csp from the Hyperthermophile Thermotoga maritima Protein J. (IF 1.317) Pub Date : 2020-10-22 Konstanze von König, Norman Kachel, Hans Robert Kalbitzer, Werner Kremer
Prokaryotic cold shock proteins (CSPs) are considered to play an important role in the transcriptional and translational regulation of gene expression, possibly by acting as transcription anti-terminators and “RNA chaperones”. They bind with high affinity to single-stranded nucleic acids. Here we report the binding epitope of TmCsp from Thermotoga maritima for both single-stranded DNA and RNA, using
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Influenza Hemagglutinin Head Domain Mimicry by Rational Design Protein J. (IF 1.317) Pub Date : 2020-10-17 V Vamsee Aditya Mallajosyula, Shiv Swaroop, Raghavan Varadarajan
Despite diligent vaccination efforts, influenza virus infection remains a major cause for respiratory-related illness across the globe. The less-than-optimal immunity conferred by the currently prescribed seasonal vaccines and protracted production times warrant the development of novel vaccines. Induction of an epitope-focused antibody response targeting known neutralization epitopes is a viable strategy
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ABC Exporters in Pathogenesis: Role of Synthetic Anti-Microbial Peptides Protein J. (IF 1.317) Pub Date : 2020-10-17 Ritika Kabra, Shailza Singh
ABC exporters are involved in diverse cellular processes including lipid trafficking, drug resistance, pathogenesis etc. The greatest thrust has been in the area of drug resistance that explains the underlying well-crafted canonical architecture of its structure. Interestingly, ranging from structural organisation to subsequent design and delivery aspects lays the niche of antimicrobial peptides. One
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Effect of Metal Ions on the Activity of Ten NAD-Dependent Formate Dehydrogenases Protein J. (IF 1.317) Pub Date : 2020-10-12 Huri Bulut, Jarkko Valjakka, Busra Yuksel, Berin Yilmazer, Ossi Turunen, Baris Binay
NAD-dependent formate dehydrogenase (FDH) enzymes are frequently used in industrial and scientific applications. FDH is a reversible enzyme that reduces the NAD molecule to NADH and produces CO2 by oxidation of the formate ion, whereas it causes CO2 reduction in the reverse reaction. Some transition metal elements – Fe3+, Mo6+ and W6 + – can be found in the FDH structure of anaerobic and archaeal microorganisms
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Identification of Protein Complexes Based on Core-Attachment Structure and Combination of Centrality Measures and Biological Properties in PPI Weighted Networks Protein J. (IF 1.317) Pub Date : 2020-10-11 Abdolkarim Elahi, Seyed Morteza Babamir
In protein interaction networks, a complex is a group of proteins that causes a biological process to take place. The correct identification of complexes can help to better understand function of cells used for therapeutic purposes, such as drug discoveries. This paper uses core-attachment structure, centrality measures, and biological properties of proteins to identify protein complex with the aim
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The Last Secret of Protein Folding: The Real Relationship Between Long-Range Interactions and Local Structures Protein J. (IF 1.317) Pub Date : 2020-10-10 Aoneng Cao
The protein folding problem has been extensively studied for decades, and hundreds of thousands of protein structures have been solved. Yet, how proteins fold from a linear peptide chain to their unique 3D structures is not fully understood. With key clues having emerged unexpectedly from the field of nanoscience, a “Confined Lowest Energy Fragment” (CLEF) hypothesis was proposed. The CLEF hypothesis
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Biophysical and In-Silico Studies of Phytochemicals Targeting Chorismate Synthase from Drug-Resistant Moraxella Catarrhalis Protein J. (IF 1.317) Pub Date : 2020-10-10 Neetu Neetu, Monica Sharma, Jai Krishna Mahto, Pravindra Kumar
Chorismate serves as a crucial precursor for the synthesis of many aromatic compounds essential for the survival and virulence in various bacteria and protozoans. Chorismate synthase, a vital enzyme in the shikimate pathway, is responsible for the formation of chorismate from enolpyruvylshikimate-3-phosphate (EPSP). Moraxella catarrhalis is reported to be resistant to many beta-lactam antibiotics and
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Trehalose Inhibits the Heat-Induced Formation of the Amyloid-Like Structure of Soluble Proteins Isolated from Human Cataract Lens Protein J. (IF 1.317) Pub Date : 2020-10-10 Lakshman Ram, Chandrika Mittal, Ram Swaroop Harsolia, Jay Kant Yadav
The age-dependent loss of solubility and aggregation of crystallins constitute the pathological hallmarks of cataract. Several biochemical and biophysical factors are responsible for the reduction of crystallins’ solubility and formation of irreversible protein aggregates, which display amyloid-like characteristics. The present study reports the heat-induced aggregation of soluble proteins isolated
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Perspective on the Role of Antibodies and Potential Therapeutic Drugs to Combat COVID-19 Protein J. (IF 1.317) Pub Date : 2020-10-09 Siddhi Tandon, Anchal Aggarwal, Shubhra Jain, Sanjay Shukla, Sarika Chaudhary
The sudden emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease of 2019 (COVID-19) has brought the world to a standstill. Thousands of people across the globe are biting the dust with every passing day and yet more are being tested positive for the SARS-CoV-2 infection. In order to dispense this current crisis, numerous treatment options
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Cereblon Promotes the Ubiquitination and Proteasomal Degradation of Interleukin Enhancer-Binding Factor 2 Protein J. (IF 1.317) Pub Date : 2020-10-03 Qihui Lian, Yuan Gao, Qian Li, Xian He, Xiaogang Jiang, Zhongjian Pu, Guoqiang Xu
Interleukin enhancer-binding factor 2 (ILF2) forms a heterodimer with interleukin enhancer-binding factor 3 (ILF3) via double-stranded RNA-binding motif and zinc finger associated domain and thus regulates gene expression and cancer cell growth. However, how ILF2 is degraded in cells remains elusive. In this work, using stable isotope labeling by amino acids in cell culture (SILAC) quantitative proteomics
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Aldehyde Production as a Calibrant of Ultrasonic Power Delivery During Protein Misfolding Cyclic Amplification Protein J. (IF 1.317) Pub Date : 2020-10-03 Simon C. Drew
The protein misfolding cyclic amplification (PMCA) technique employs repeated cycles of incubation and sonication to amplify minute amounts of misfolded protein conformers. Spontaneous (de novo) prion formation and ultrasonic power level represent two potentially interrelated sources of variation that frustrate attempts to replicate results from different laboratories. We previously established that
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Effect of Freezing Time on Tissue Factor Activity and Macronutrients of Human Milk Protein J. (IF 1.317) Pub Date : 2020-09-28 Begüm Gürel Gökmen, Ozan Özcan, Hava Taslak, Necla Ipar, Tuğba Tunali-Akbay
Human milk proteins are known as vital molecules for infant development and growth. Tissue factor is one of these human milk proteins that its role in human milk has not been cleared yet. Therefore, the first aim of this study was to detect the tissue factor activity of human milk and also was to investigate the effect of extended freezer storage on the milk tissue factor activity. The relationship
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Isolation and Functional Identification of an Antiplatelet RGD-Containing Disintegrin from Cerastes cerastes Venom. Protein J. (IF 1.317) Pub Date : 2020-09-22 Meriem Ameziani,Fatah Chérifi,Hamida Kiheli,Samah Saoud,Ghania Hariti,Safia Kellou-Taîri,Fatima Laraba-Djebari
The current report focuses on purification, structural and functional characterization of Cerastategrin from Cerastes cerastes venom, a novel basic disintegrin (pI 8.36) with 128 amino acid residues and a molecular weight of 13 835.25 Da measured by MALDI-MSMS. The 3D structure of Cerastategrin is organized as α-helix (13%), β-strand (15%) and disordered structure (30%) and presents homologies with
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Oligomerization of A. thaliana Heterotrimeric G Protein Subunits AGB1 and AGG2 In Vitro. Protein J. (IF 1.317) Pub Date : 2020-08-09 Burcu Kaplan-Türköz,Anıl Aktürk,Zehra Sayers
Plant heterotrimeric G proteins are a major group of signaling molecules involved in regulation of critical processes including stress adaptation, seed size, grain quality and immune responses. Despite an abundance of in situ functional studies; purification of the individual subunits of the plant heterotrimer for biophysical and structural characterization and for studies on their interactions are
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Heterologous Expression of the Barley (Hordeum vulgare L.) Xantha-f, -g and -h Genes that Encode Magnesium Chelatase Subunits. Protein J. (IF 1.317) Pub Date : 2020-07-31 Rabab Mahdi,David Stuart,Mats Hansson,Helmy M Youssef
Biosynthesis of chlorophyll involves several enzymatic reactions of which many are shared with the heme biosynthesis pathway. Magnesium chelatase is the first specific enzyme in the chlorophyll pathway. It catalyzes the formation of Mg-protoporphyrin IX from the insertion of Mg2+ into protoporphyrin IX. The enzyme consists of three subunits encoded by three genes. The three genes are named Xantha-h
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TLPdb: A Resource for Thaumatin-Like Proteins. Protein J. (IF 1.317) Pub Date : 2020-07-21 Chandana Thimme Gowda,Siva Naga Suresh Purama,Rajagopal Kammara
Antifungal proteins and peptides have drawn the attention of numerous plant biologists and Clinicians, owing to their potential value in protecting commercial crops as well as preventing fungal infections in humans. Various proteins and peptides, such as glucanases, chitinases, chitinase-like proteins, lectins, peroxidases, defensins, and lipid transfer proteins have antifungal activities. Thaumatin
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Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase. Protein J. (IF 1.317) Pub Date : 2020-07-17 Jonathan Zajac,Heidi Anderson,Lauren Adams,Dechen Wangmo,Shanzay Suhail,Aimee Almen,Lauren Berns,Breanna Coerber,Logan Dawson,Andrea Hunger,Julia Jehn,Joseph Johnson,Naomi Plack,Steven Strasser,Murphi Williams,Sudeep Bhattacharyya,Sanchita Hati
Enzymes play important roles in many biological processes. Amino acid residues in the active site pocket of an enzyme, which are in direct contact with the substrate(s), are generally believed to be critical for substrate recognition and catalysis. Identifying and understanding how these “catalytic” residues help enzymes achieve enormous rate enhancement has been the focus of many structural and biochemical
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Functional Stability and Structural Transitions of a Kunitz trypsin Inhibitor from Chickpea (CaTI2). Protein J. (IF 1.317) Pub Date : 2020-07-15 Ameya D Bendre,Ekta Shukla,Sureshkumar Ramasamy
AbstractEnzymes are important tools for various applications. We have studied structural transitions and functional stability of a Kunitz trypsin inhibitor from Chickpea (CaTI2), a potent insect gut-protease inhibitor, under different stress conditions like non-neutral pH, elevated temperature and co-solvent concentrations. CaTI2 was cloned and expressed in an eukaryotic system P. pastoris and was
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Immobilization of Cellulase onto Core-Shell Magnetic Gold Nanoparticles Functionalized by Aspartic Acid and Determination of its Activity. Protein J. (IF 1.317) Pub Date : 2020-07-15 Elahe Poorakbar,Ali Akbar Saboury,Behzad Laame Rad,Kamyar Khoshnevisan
New support was fabricated to enhance the enzyme activity of cellulase following immobilization. Functionalized core-shell magnetic gold nanoparticles were prepared and characterized by X-ray diffraction (XRD), vibrating sample magnetometer (VSM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Cellulase enzyme was immobilized on support via covalent bonding. The successful
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Lectin-Like Activity of Hemocyanin in Freshwater Prawn, Macrobrachium rosenbergii. Protein J. (IF 1.317) Pub Date : 2020-07-13 Jyotirmaya Mohanty,Sonalina Sahoo,Mohan R Badhe,Bindu R Pillai,Pramoda Kumar Sahoo,Amol R Suryawanshi,Bharat Bhusan Patnaik
Lectins are proteins that bind to the carbohydrate moieties on surface of bacteria, erythrocytes and other cells of invertebrates causing agglutination and mediate in recognition of foreign substances. In the present study, we isolated and characterized a lectin molecule present in the hemolymph of Macrobrachium rosenbergii, an important cultured freshwater prawn. Lectin in serum samples of adult prawns
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Maltose Induced Expression of Cecropin AD by SUMO Technology in Bacillus subtilis WB800N. Protein J. (IF 1.317) Pub Date : 2020-07-13 Licong Zhang,Xiaodan Li,Na Zhan,Taotao Sun,Jianping Li,Anshan Shan
Cecropin AD (CAD) is a hybrid peptide composed of 37 amino acids with the characters of strong antibacterial, antitumor properties and no hemolytic activity, which was regarded as a promising antibiotic candidate. Thus, a safe method to produce Cecropin AD is necessary to be found. In the study, Bacillus subtilis WB800N was employed as host strain. The CAD coding sequence fused with the signal peptide
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FTIR Spectroscopy Detects Intermolecular β-Sheet Formation Above the High Temperature Tm for Two Monoclonal Antibodies. Protein J. (IF 1.317) Pub Date : 2020-07-12 Garrett Baird,Chris Farrell,Jason Cheung,Andrew Semple,Jeffery Blue,Patrick L Ahl
The temperature-dependent secondary structure of two monoclonal IgG antibodies, anti-IGF1R and anti-TSLP, were examined by transmission mode Fourier Transform Infrared (FTIR) spectroscopy. Anti-IGF1R and anti-TSLP are IgG monoclonal antibodies (mAbs) directed against human Insulin-like Growth Factor 1 Receptor for anti-tumor activity and Thymic Stromal Lymphopoietin cytokine for anti-asthma activity
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Random Coils of Proteins Situated Between a Beta Strand and an Alpha Helix Demonstrate Decreased Solvent Accessibility. Protein J. (IF 1.317) Pub Date : 2020-07-05 Vladislav Victorovich Khrustalev
Surface accessibility of different types of the same elements of secondary structure has been studied in 10 non-redundant sets of proteins (total number of three-dimensional structures is 1730) with a help of DSSP (Dictionary of Secondary Structure of Proteins). Random coils (C), beta strands (B), and alpha helices (H) have been classified according to their flanking elements of secondary structure
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CxxC Zinc Finger Protein Derived Peptide, MF18 Functions Against Biofilm Formation. Protein J. (IF 1.317) Pub Date : 2020-07-03 Prabha Nagaram,Mukesh Pasupuleti,Jesu Arockiaraj
The major threat in modern medicine was biofilm forming bacterial related infections and they were highly tolerant to conventional antibiotics and a boundless demand for new drugs. In this regard, antimicrobial peptide (AMP) have been considered as potential alternative agents to conventional antibiotics. In this study, we have reported a CxxC zinc finger protein derived peptide, MF18 and its various
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Proteomic Analysis of Lipid Droplets in Sesamum indicum. Protein J. (IF 1.317) Pub Date : 2020-05-29 Satoshi Hamada,Akihiro Kishikawa,Motonobu Yoshida
We attempted to identify the total proteome in sesame lipid droplets. Results from two-dimensional electrophoresis showed 139 protein spots in lipid droplet samples. Each spot was isolated, digested with trypsin, and applied to liquid chromatography–tandem mass spectrometry (Q-Tof Premier). As a result, 103 spots were identified. Although oleosin, caleosin, and steroleosin are known major components
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Low Energy Conformations for Endogenous Mu-Receptor-Specific Peptides. Protein J. (IF 1.317) Pub Date : 2020-05-25 Bo Lin,Robert P Carty,Matthew R Pincus
We have computed the low energy minima for the two endomorphin peptides, N-acetyl-Tyr-Pro-Trp-Phe-NHCH3 (endomorphin 1) and Tyr-Pro-Phe-Phe-NHCH3 (endomorphin 2) in aqueous solution. These peptides block pain without inducing the harmful side effects of the opiates that bind to the same mu opiate receptor but have short half lives. From over 1000 starting conformations for each peptide, we find less
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The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19. Protein J. (IF 1.317) Pub Date : 2020-05-23 Francis K Yoshimoto
The devastating effects of the recent global pandemic (termed COVID-19 for “coronavirus disease 2019”) caused by the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) are paramount with new cases and deaths growing at an exponential rate. In order to provide a better understanding of SARS CoV-2, this article will review the proteins found in the SARS CoV-2 that caused this global pandemic
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2020 Letter from the Editor-in-Chief. Protein J. (IF 1.317) Pub Date : 2020-06-01 Lawrence J Berliner
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Defense Response in Chickpea Pod Wall due to Simulated Herbivory Unfolds Differential Proteome Profile. Protein J. (IF 1.317) Pub Date : 2020-04-30 Mamta Bhattacharjee,Santanu Dhar,Pratap Jyoti Handique,Sumita Acharjee,Bidyut Kumar Sarmah
The pod wall of legumes is known to protect the developing seeds from pests and pathogens. However, the mechanism of conferring defense against insects has not yet been deciphered. Here, we have utilized 2-dimensional gel electrophoresis (2D-GE) coupled with mass spectrometry (MS/MS) to identify over expressed proteins in the pod wall of two different cultivars (commercial cultivar: JG 11 and tolerant
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Molecular Characterization of Bacterial Fibrinolytic Proteins from Indonesian Traditional Fermented Foods. Protein J. (IF 1.317) Pub Date : 2020-04-28 Eni Purwaeni,Catur Riani,Debbie Soefie Retnoningrum
Previously, the crude extracts of recombinant Nattokinase (NK) variants i.e. NatTK and NatOC and one wild type Douchi Fibrinolytic Enzyme (DFE) from Indonesian traditional fermented foods has been shown to demonstrate fibrinolytic activity. Both NKs contain substitutions of D41N, V192A and 252-RLQHTLEALSTM-263 but NatOC has additional V4F. In the present study, the effects of amino acid substitutions
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Correction to: Propensities of Amino Acid Pairings in Secondary Structure of Globular Proteins. Protein J. (IF 1.317) Pub Date : 2020-04-01 Cevdet Nacar
In the original version of this article, under the Introduction section in paragraph starting "Some findings of this study..." the "Sect. 10" should be changed to "Sect. 3".
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Prokaryotic Expression of the Immunoglobulin's Domains of CRTAM to Characterize a Monoclonal Antibody. Protein J. (IF 1.317) Pub Date : 2020-04-16 Juan Carlos Barragan-Galvez,Maria Gonzalez-Orozco,Araceli Hernandez-Flores,Jose Luis Maravillas-Montero,Yedhani Chavez-Guerrero,Vianney Ortiz-Navarrete
Class-I restricted T cell-associated molecule (CRTAM) is a member of the immunoglobulin superfamily, and it is closely related to nectin-like protein. CRTAM is expressed in activated CD8 T cells, NKT cells, NK cells and in a subpopulation CD4 T cells. In this study, we produce as recombinant proteins, the Ig-domains of CRTAM (IgV–IgC), the IgV, and the IgC. These proteins were successfully purified
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