Review
Biochemistry & Molecular Biology
H. Jane Dyson
Summary: Viruses infect all kingdoms of life and employ disordered proteins to accomplish various functions. Disordered proteins have been discovered in almost all viruses studied, regardless of the viral genome composition or the viral capsid configuration. This review presents a collection of stories illustrating the diverse functions of disordered proteins in viruses, providing a survey of the field's expansion.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Rakesh Trivedi, Hampapathalu Adimurthy Nagarajaram
Summary: This review discusses different aspects of disordered proteins and protein regions, as well as the experimental and computational methods used to characterize them. Additionally, the role of disordered proteins in diseases and their potential as drug targets are explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Aakriti Upadhyay, Chinwe Ekenna
Summary: Understanding the binding behavior and conformational dynamics of intrinsically disordered proteins (IDPs) is crucial. We proposed an algorithm that explores IDP binding behavior with protein complexes by extracting topological and geometric features from the protein surface model. Our method outperformed the compared methods in computation performance and binding affinity in experimental conformations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ellen Rieloff, Marie Skepo
Summary: Phosphorylation is a common post-translational modification in intrinsically disordered proteins, and computer simulations are useful tools to study its effects. In this study, CHARMM36m consistently produced more compact conformations with a higher content of bends in phosphorylated peptides compared to Amber ff99SB-ILDN+TIP4P-D. Despite a reduction in salt-bridging probability, changes in ionic strength had negligible effects on the conformational ensembles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ellen Rieloff, Marie Skepo
Summary: Phosphorylation plays a crucial role in regulating the function of intrinsically disordered proteins, with the distribution of phosphorylated and positively charged residues throughout the sequence impacting the formation of salt bridges. Understanding the structural implications of phosphorylation remains a challenge, as factors beyond net charge, such as specific residue interactions, can influence the global dimensions of disordered proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Fan Jin, Frauke Grater
Summary: The study found that multi-site phosphorylation causes V-shaped changes in collapse propensity of all proteins based on their initial net charge, expanding neutral or overall negatively charged IDPs and shrinking positively charged IDPs. In two of the IDPs, only two biologically relevant phosphorylation sites are enough to significantly expose the adjacent negatively charged active site, increasing the likelihood of interaction with other binding partners.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Rebecca B. Berlow, H. Jane Dyson, Peter E. Wright
Summary: Intrinsically disordered proteins compete for binding to common regulatory targets to carry out their biological functions. The activation domains of HIF-1 alpha and CITED2 function as a unidirectional, allosteric molecular switch to control transcription of adaptive genes. The mechanistic details of this molecular switch were characterized through NMR spectroscopy and biophysical methods, revealing the contributions of individual binding motifs in CITED2. These findings provide insight into the complexity of molecular interactions involving disordered proteins and how they compete for occupancy of common targets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Vladimir D. Manyilov, Nikolay S. Ilyinsky, Semen V. Nesterov, Baraa M. G. A. Saqr, Guy W. Dayhoff, Egor V. Zinovev, Simon S. Matrenok, Alexander V. Fonin, Irina M. Kuznetsova, Konstantin K. Turoverov, Valentin Ivanovich, Vladimir N. Uversky
Summary: This article examines the impact of intrinsically disordered proteins and regions on aging-related processes. The findings indicate that these disordered components play significant roles in aging, particularly in genome regulation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Rachel Evans, Sravani Ramisetty, Prakash Kulkarni, Keith Weninger
Summary: Intense study of intrinsically disordered proteins (IDPs) began in the late 1990s and revealed their important functions. Over the past two decades, it has become clear that IDPs play critical roles in various biological phenomena. The application of integrative structural biology has emerged as an essential approach to understanding IDP phenomena.
Article
Biochemistry & Molecular Biology
Jaime Santos, Irantzu Pallares, Valentin Iglesias, Salvador Ventura
Summary: The prevalence of cryptic amyloidogenic regions (CARs) of polar nature in intrinsically disordered regions (IDRs) has been explored. CARs are associated with protein function and interactions, but also carry a risk of malfunction. The existence of ancestral CARs may have evolved into functional interacting regions, playing a significant role in protein evolution at the origins of life.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Prakash Kulkarni, Amita Behal, Atish Mohanty, Ravi Salgia, Aurora M. Nedelcu, Vladimir N. Uversky
Summary: Intrinsically disordered proteins (IDPs) play crucial roles in the early evolution of complex multicellularity by rewiring cellular protein interaction networks and facilitating the co-option of ancestral pathways for specialized multicellular functions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Biochemistry & Molecular Biology
Tanuj Handa, Debanjan Kundu, Vikash Kumar Dubey
Summary: The importance of protein structure in performing biological functions optimally is being challenged by the emergence of intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs). Understanding the evolutionary and functional significance of these proteins is crucial in studying various organisms. This review highlights the importance of IDPs in the physiology of specific organisms and establishes a positive correlation between IDPs and their relevance in human health and future medicine. Extensive research on IDPs and IDPRs will greatly contribute to expanding the field of structural biology, aiding in the comprehension of protein folding, misfolding, associated diseases, and drug design.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Tobias Gruber, Marc Lewitzky, Lisa Machner, Ulrich Weininger, Stephan M. Feller, Jochen Balbach
Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure elements and play important roles in cellular processes. This study focuses on the C-terminal region of Gab1, an IDP, and investigates its induced structure and binding properties under both non-crowding and crowding conditions. The results show that under crowding conditions, pre-structured motifs are formed in certain regions of Gab1, which are also the binding regions for the protein SHP2. Phosphorylation has no impact on the dynamics and disordered nature of Gab1. Therefore, biological crowders can enhance the binding capacity of SHP2 to Gab1, even in the absence of phosphorylation.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Chandan Thapa, Pekka Roivas, Tatu Haataja, Perttu Permi, Ulla Pentikainen
Summary: PP2A activity is crucial for cellular functions, but can be inhibited in pathological conditions. ARPP-19 protein is connected to various cancer types, and understanding its interaction with PP2A is important for disease development and treatment. The structural characterization and interaction mechanism of ARPP-19 with PP2A provide insights for future therapeutic development.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Karen E. Lee, Rebecca Procopio, Jose S. Pulido, Kammi B. Gunton
Summary: Intrinsically disordered regions (IDRs) are protein regions that lack stable tertiary structures and play important roles in signaling and regulation through dynamic interactions. Understanding IDRs and their association with biological function may shed light on the development of inherited retinal diseases (IRDs). This study aims to investigate the level of disorder in 14 proteins related to IRDs and its correlation with the number of pathogenic missense variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Kenneth Lundstrom, Altijana Hromic-Jahjefendic, Esma Bilajac, Alaa A. A. Aljabali, Katarina Baralic, Nagwa A. Sabri, Eslam M. Shehata, Mohamed Raslan, Ana Claudia B. H. Ferreira, Lidiane Orlandi, Angel Serrano-Aroca, Murtaza M. Tambuwala, Vladimir N. Uversky, Vasco Azevedo, Khalid J. Alzahrani, Khalaf F. Alsharifm, Ibrahim F. Halawani, Fuad M. Alzahrani, Elrashdy M. Redwan, Debmalya Barhl
Summary: This review summarizes major events of SARS-CoV-2 infection route, immune response following host-cell infection as an important factor for disease outcome, as well as comorbidity issues of various tissues and organs arising due to COVID-19. Investigations on alterations of host-cell machinery and viral interactions with multiple intracellular signaling pathways could represent a major factor in more effective disease management.
CELLULAR SIGNALLING
(2023)
Article
Cell Biology
Debmalya Barh, Sandeep Tiwari, Lucas Gabriel Rodrigues Gomes, Cecilia Horta Ramalho Pinto, Bruno Silva Andrade, Shaban Ahmad, Alaa A. A. Aljabali, Khalid J. Alzahrani, Hamsa Jameel Banjer, Sk Sarif Hassan, Elrashdy M. Redwan, Khalid Raza, Aristoteles Goes-Neto, Robinson Sabino-Silva, Kenneth Lundstrom, Vladimir N. Uversky, Vasco Azevedo, Murtaza M. Tambuwala
Summary: The Omicron variant of SARS-CoV-2 is highly transmissible with decreased disease severity. It has lower pathogenicity but higher antigenicity compared to other variants. These findings contribute to our understanding of variant dynamics and can help in managing emerging variants.
Article
Agriculture, Dairy & Animal Science
Hossein Hosseini, Noah Esmaeili, Aref Sepehr, Mahyar Zare, Artur Rombenso, Raied Badierah, Elrashdy M. Redwan
Summary: This study investigated the effects of extruded flaxseed with and without herbs mixture on egg performance, yolk fatty acids, lipid components, blood biochemistry, serological enzymes, antioxidants, and immune system of Hy-Line W-36 hens. The results showed that hens fed herbs mixture had better egg performance and improved antioxidant and immune parameters compared to those fed diets without herbs. High levels of extruded flaxseed without herbs appeared to impair the antioxidant system, immunohematological parameters, and serological enzymes, but the supplementation of herbs mixture corrected these effects.
Article
Cell Biology
Kenneth Lundstrom, Altijana Hromic-Jahjefendic, Esma Bilajac, Alaa A. A. Aljabali, Katarina Baralic, Nagwa A. Sabri, Eslam M. Shehata, Mohamed Raslan, Sara A. Raslan, Ana Claudia B. H. Ferreira, Lidiane Orlandi, Angel Serrano-Aroca, Vladimir N. Uversky, Sk. Sarif Hassan, Elrashdy M. Redwan, Vasco Azevedo, Khalid J. Alzahrani, Khalaf F. Alsharif, Ibrahim F. Halawani, Fuad M. Alzahrani, Murtaza M. Tambuwala, Debmalya Barh
Summary: The COVID-19 pandemic has led to extensive research and development of drugs and vaccines for SARS-CoV-2. Vaccines based on viral vectors, nucleic acids, and whole viral particles have been particularly successful and have received emergency authorization for global mass vaccination. However, emerging variants have raised concerns about vaccine efficacy.
CELLULAR SIGNALLING
(2023)
Review
Biochemistry & Molecular Biology
Yousra A. El-Maradny, Alberto Rubio-Casillas, Vladimir N. Uversky, Elrashdy M. Redwan
Summary: The severity of COVID-19 has reduced due to widespread vaccination campaigns and mutations in the virus. However, the long-term side effects of the infection and vaccines, known as long-COVID, are spreading rapidly. The reasons behind this phenomenon are still unclear.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Nutrition & Dietetics
Hosam M. Habib, Hamada El-Gendi, Esmail M. El-Fakharany, Mohamed G. El-Ziney, Ahmed F. El-Yazbi, Fatima T. Al Meqbaali, Wissam H. Ibrahim
Summary: The polyphenolic profile of pomegranate juice concentrate was investigated for the first time, revealing its potential health benefits and antioxidant activity. The concentrate exhibited inhibitory effects on oxidative damage and enzyme activities. It also demonstrated antibacterial effects and dose-dependent apoptosis on cancer cells.
Article
Nutrition & Dietetics
Hosam M. Habib, Esmail M. El-Fakharany, Hamada El-Gendi, Mohamed G. El-Ziney, Ahmed F. El-Yazbi, Wissam H. Ibrahim
Summary: The study aimed to examine the properties of palm fruit pollen extract (PFPE), including antioxidant, antimicrobial, anticancer, enzyme inhibition, bovine serum albumin (BSA), and DNA-protective activities. The results demonstrated that PFPE exhibited strong antioxidant activity and antimicrobial effects. It also displayed inhibitory effects on enzymes and showed anticancer properties. These findings suggest that PFPE could be utilized in the pharmaceutical, nutraceutical, and functional food industries.
Editorial Material
Geriatrics & Gerontology
Arif Tasleem Jan, Safikur Rahman, Diana K. Sarko, Elrashdy M. Redwan
FRONTIERS IN AGING NEUROSCIENCE
(2023)
Review
Immunology
Vivek P. Chavda, Nidhi Raval, Soham Sheta, Lalitkumar K. Vora, Fatma Elrashdy, Elrashdy M. Redwan, Vladimir N. Uversky, Yavuz Nuri Ertas
Summary: The newly emerged SARS-CoV-2 is highly infectious and rapidly mutating, causing severe effects on various body organs. Multiple approaches, including medications and supportive devices, have been successfully used for the intervention of COVID-19. Hemadsorption devices are discussed in this report as part of supportive treatment for the cytokine storm associated with COVID-19.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Oncology
Shaghayegh Khanmohammadi, Sahar Saeedi Moghaddam, Sina Azadnajafabad, Negar Rezaei, Zahra Esfahani, Nazila Rezaei, Mohsen Naghavi, Bagher Larijani, Farshad Farzadfar
Summary: The study aimed to estimate the burden of tracheal, bronchus, and lung cancer and its risk factors in the North Africa and Middle East region from 1990 to 2019. The results showed that TBL cancer caused significant deaths and had increasing incidence rates, especially in women. Tobacco use remained the leading risk factor. Controlling risk factors, particularly tobacco use, could significantly reduce the burden of the disease.
FRONTIERS IN ONCOLOGY
(2023)
Article
Pharmacology & Pharmacy
Kholoud H. Hamza, Ahmed A. El-Shanshory, Mona M. Agwa, Mohamed I. Abo-Alkasem, Esmail M. El-Fakharany, Abdallah S. Abdelsattar, Ali A. El-Bardan, Taher S. Kassem, Xiumei Mo, Hesham M. A. Soliman
Summary: A multifunctional antibacterial biopolymer-based tri-layered hierarchically nanofibrous scaffold was constructed with hydrophilic silk fibroin (SF), fish skin collagen (COL), and hydrophobic poly-3-hydroxybutyrate (PHB) containing amoxicillin (AMX) for wound healing. The scaffold exhibited excellent biocompatibility, significant antimicrobial activity, and accelerated full-thickness wound healing in a rat model. The results suggest its potential as an effective wound dressing scaffold.
Article
Immunology
Rasha Ashmawy, Ehab Kamal, Wagdy Amin, Sandy Sharaf, Samar Kabeel, Raed Albiheyri, Yousra A. El-Maradny, Ebtisam Hassanin, Noura Elsaka, Ola Fahmy, Ahmed Awd, Heba Aboeldahab, Mai Nayle, Magda Afifi, Marwa Ibrahim, Raghda Rafaat, Shahinda Aly, Elrashdy M. Redwan
Summary: The study evaluated the safety and efficacy of Egypt's first approved Sinopharm vaccine (BBIBP-CorV) and found it to be effective in protecting healthcare workers from COVID-19. Vaccination was associated with a significant reduction in hospitalization rate and work absenteeism, with mild adverse events reported.
Review
Immunology
Nawal Abd El-Baky, Amro A. Amara, Elrashdy M. Redwan
Summary: The adaptive immune response plays a crucial role in determining the clinical outcome and vaccine efficacy after SARS-CoV-2 infection. T cells recognize viral-derived peptides bound to major histocompatibility complexes (MHCs) to initiate cell-mediated immunity or support high-affinity antibody response. Immunopeptidomics techniques can identify potential vaccine targets or therapeutic approaches and reveal heterogeneity in clinical outcomes by characterizing SARS-CoV-2-derived peptides bound to MHCs.
Review
Immunology
Vladimir N. Uversky, Elrashdy M. Redwan, William Makis, Alberto Rubio-Casillas
Summary: The effectiveness of the COVID-19 vaccines in preventing severe disease and hospitalization in individuals with comorbidities is being questioned. Recent investigations have found abnormally high levels of IgG4 in individuals who received mRNA vaccines, which may suppress natural antiviral responses and promote SARS-CoV2 infection and replication.