Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny
Summary: This article investigates the structure and function of Connexins and pannexins proteins. Through comparative analysis, it is found that their hydrophobicity distribution and external force field characteristics are different, thus affecting their activity in different environments.
Article
Biochemistry & Molecular Biology
Elena T. Aliper, Nikolay A. Krylov, Dmitry E. Nolde, Anton A. Polyansky, Roman G. Efremov
Summary: This study proposes a comprehensive computational framework to model the spike transmembrane domain (TMD) of SARS-CoV-2 spike protein based on its primary structure. The stability of the model was tested through molecular dynamics simulations and was found to conform to basic principles of TM helix packing. The framework shows promise and can potentially be applied to construct 3D models of transmembrane trimers for other membrane proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Young-Ki Paik, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, Susan Weintraub, Michael H. A. Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yu-Ju Chen, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: The 2021 Metrics of the HUPO Human Proteome Project (HPP) reveal significant progress in detecting protein expression in the human genome. The number of missing proteins has decreased, and the utilization of proteomics in biological and clinical research continues to expand and integrate effectively with other omics platforms. This represents a promising advancement in understanding the human proteome and its potential applications in healthcare.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny
Summary: Beta-barrel membrane proteins exhibit distinct distribution patterns of residues using 3D Gauss functions, impacting their biological activity and substrate specificity. Compared to soluble proteins, beta-barrel membrane proteins show differences in interaction with antibiotics.
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: According to the 2022 metrics of the HUPO Human Proteome Project (HPP), protein expression has been detected for 93.2% of the predicted proteins in the human genome. The number of missing proteins has been reduced, indicating experimental progress and reclassification. Proteomics continues to yield significant findings in biological and clinical studies and integrates with other omics platforms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Snehal Dilip Karpe, Vikas Tiwari, Sowdhamini Ramanathan
Summary: The webserver "InsectOR" accurately predicts and validates insect olfactory receptor genes using multiple gene prediction algorithms, outperforming popular genome annotation pipelines in terms of sensitivity and precision. It has a low percentage of missed gene loci and can be freely accessed online.
Article
Multidisciplinary Sciences
Alejandra Boronat-Garcia, James Iben, Eunice Dominguez-Martin, Mark Stopfer
Summary: This study identified 179 putative odorant receptors (ORs) in the transcriptomes of the main olfactory organs, antenna and palp, of the locust Schistocerca americana. Most ORs were found to be expressed in the antennae, while only a few were expressed in the palps. Additionally, the study revealed the existence of one OR specifically detected in the palps and seven ORs that are differentially expressed based on sex. The organization of ORs within the antennal sensilla was found to be non-random. Comparisons with other Acrididae species showed homologous relationships among predicted OR protein sequences.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Leszek Konieczny
Summary: This analysis focuses on the stability and local flexibility of transmembrane proteins, particularly those related to their biological activity. Different anchoring systems were found to stabilize protein molecules, while allowing for local fluctuations.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Seong Beom Ahn, Karthik S. Kamath, Abidali Mohamedali, Zainab Noor, Jemma X. Wu, Dana Pascovici, Subash Adhikari, Harish R. Cheruku, Gilles J. Guillemin, Matthew J. McKay, Edouard C. Nice, Mark S. Baker
Summary: The study successfully identified cancer-associated low abundance plasma proteins using a mixture of selected recombinant proteins and SWATH/DIA identification method, addressing the challenge of detecting low abundance proteins in precision medicine biomarker discovery with mass spectrometry.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Ophthalmology
Samridhi Sharma, Nitin Chitranshi, Roshana Vander Wall, Devaraj Basavarajappa, Vivek Gupta, Mehdi Mirzaei, Stuart L. Graham, Alexander Klistorner, Yuyi You
Summary: There is a strong interrelationship between eye and brain diseases, as neurodegenerative changes can spread bidirectionally in the visual pathway. This process, known as trans-synaptic degeneration, contributes to the progression of various neurodegenerative disorders.
SURVEY OF OPHTHALMOLOGY
(2022)
Article
Engineering, Electrical & Electronic
Benjamin Heng, Seong Beom Ahn, Anna Guller
Summary: Transcranial magnetic stimulation (TMS) is a widely available technology used for diagnostics and treatment of brain disorders. This study explored the effects of TMS-like magnetic stimulation on colorectal and liver cancer cells. The results showed specific effects of TMS on different tumor types and stimulation protocols, suggesting potential applications in cancer treatment.
IEEE TRANSACTIONS ON MAGNETICS
(2022)
Article
Biochemistry & Molecular Biology
Soumalya Sarkar, Vivek K. Gupta, Samridhi Sharma, Ting Shen, Veer Gupta, Mehdi Mirzaei, Stuart L. Graham, Nitin Chitranshi
Summary: Alterations in RXR signalling are associated with neurodegenerative disorders. This study identified deleterious SNPs that affect the structure and function of RXR isoforms. Seven missense mutations were found in RXR isoforms, including two novel mutations. In silico prediction tools were used to assess the pathogenicity and stability of RXR mutations. The analysis showed a mix of conclusive and inconclusive genotype-phenotype correlations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Neurosciences
Samridhi Sharma, Ting Shen, Nitin Chitranshi, Veer Gupta, Devaraj Basavarajappa, Mehdi Mirzaei, Yuyi You, Wojciech Krezel, Stuart L. Graham, Vivek Gupta
Summary: Retinoid X receptors (RXRs) play critical roles in various neurological disorders by regulating gene expression and influencing neurodevelopment, metabolism, and biochemical processes. Abnormal RXR signaling affects neuronal stress and neuroinflammatory networks. Targeting RXRs through pharmacological ligands has shown protective effects in neuronal injury models. This review summarizes the roles of RXR, its interacting partners, and ligands in CNS disorders, providing insights for further research.
MOLECULAR NEUROBIOLOGY
(2022)
Editorial Material
Neurosciences
Samridhi Sharma, Yuyi You
FRONTIERS IN NEUROSCIENCE
(2022)
Review
Oncology
Shivani Krishnamurthy, David Gilot, Seong Beom Ahn, Vincent Lam, Joo-Shik Shin, Gilles Jackie Guillemin, Benjamin Heng
Summary: The kynurenine pathway is significantly activated in cancer, leading to immune tolerance towards tumors. Liver cancer remains a major concern as the second and third leading cancer-related deaths in men and worldwide, respectively. Early detection and novel treatment options are urgently needed.
Review
Biochemistry & Molecular Biology
Angela Godinez, Rashi Rajput, Nitin Chitranshi, Veer Gupta, Devaraj Basavarajappa, Samridhi Sharma, Yuyi You, Kanishka Pushpitha, Kunal Dhiman, Mehdi Mirzaei, Stuart Graham, Vivek Gupta
Summary: Neuroserpin is a crucial protein involved in neuronal development and various diseases, with mutations affecting its function and leading to pathological conditions. Understanding the alterations of neuroserpin and its cellular signaling networks is essential for studying its detrimental consequences and potential therapeutic targeting.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Umut Rende, Seong Beom Ahn, Subash Adhikari, Edward S. X. Moh, Carol A. A. Pollock, Sonia Saad, Anna Guller
Summary: Precise characterization of a tissue's extracellular matrix protein composition is crucial for biomedicine. However, extracting the extracellular matrix proteins from specific organs remains a challenge for matrisome studies. In this study, we comprehensively characterized the matrisome of kidneys in healthy mice and identified a total of 113 matrisome proteins, including 22 novel proteins. We also compared the kidney matrisome composition between humans and mice. These findings provide a valuable reference database for studying the renal matrisome in mice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Hemaasri-Neya Girithar, Ananda Staats Pires, Seong Beom Ahn, Gilles J. Guillemin, Laurence Gluch, Benjamin Heng
Summary: Breast cancer is the leading cause of cancer incidence and mortality in women worldwide. Metastasis is the main cause of death in breast cancer patients, as current treatment strategies are not effective in treating metastatic tumors. Immunotherapy and the kynurenine pathway (KP) have emerged as potential new approaches for breast cancer metastasis. This review discusses the mechanisms of immune suppression and cancer growth mediated by the KP, and provides an overview of studies and clinical trials targeting KP enzymes in breast cancer.
BRITISH JOURNAL OF CANCER
(2023)
Article
Biotechnology & Applied Microbiology
Nitin Chitranshi, Rashi Rajput, Angela Godinez, Kanishka Pushpitha, Mehdi Mirzaei, Devaraj Basavarajappa, Veer Gupta, Samridhi Sharma, Yuyi You, Giovanna Galliciotti, Ghasem H. Salekdeh, Mark S. Baker, Stuart L. Graham, Vivek K. Gupta
Summary: Our research shows that oxidation deactivation impairs the inhibitory activity of the serine protease inhibitor neuroserpin (NS) in glaucoma. The loss of NS is detrimental to retinal structure and function, and perturbations in autophagy and microglial and synaptic markers are associated with NS ablation. On the other hand, upregulation of NS promotes retinal ganglion cell (RGC) survival and protects against glaucoma-induced degeneration.
Meeting Abstract
Oncology
Shivani Krishnamurthy, Charlie Ahn, Vincent Lam, Joo-Shik Shin, Gilles Guillemin, Benjamin Heng
ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY
(2021)
Review
Biochemical Research Methods
Zainab Noor, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali
Summary: Accurate protein identification is crucial in proteomics, with mass spectrometry being the primary technique used. Understanding data generation and parameters used in computational tools is essential for proper protein identification. Bioinformatics and computational methodologies are also important for validating protein identification in proteomics.
BRIEFINGS IN BIOINFORMATICS
(2021)