Article
Multidisciplinary Sciences
Lick Pui Lai, Nicole Fer, William Burgan, Vanessa E. Wall, Bingfang Xu, Daniel Soppet, Dominic Esposito, Dwight Nissley, Frank McCormick
Summary: RAF inhibitors unexpectedly activate ERK signaling in both normal and tumor cells with elevated RAS activity. This study demonstrates that RAF inhibitors can cause paradoxical ERK activation in KRAS(G12C)-dependent lung cancer cell lines. It also reveals that classical RAS proteins are not essential for this process, and the MRAS/SHOC2 complex plays a vital role.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Mary C. Clay, Tamjeed Saleh, Samuel Kamatham, Paolo Rossi, Charalampos G. Kalodimos
Summary: Methyl-TROSY spectroscopy has expanded the application of solution-state NMR to study supra-molecular machineries. Accurate methyl chemical shift assignment remains a challenge. This work presents the current technology for methyl labeling, data collection, data analysis, and automated methyl assignment approaches, along with Python extensions and a standalone network analysis program for the task.
Article
Multidisciplinary Sciences
Xuehua Xu, Xi Wen, Amer Moosa, Smit Bhimani, Tian Jin
Summary: The study demonstrates the important role of CAPRI in mediating GPCR activation-induced Ras adaptation in human neutrophils. By reducing cell sensitivity, CAPRI enables neutrophils to chemotax through higher concentration gradients of chemoattractants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biophysics
Chunhua Yuan, Alexandar L. Hansen, Lei Bruschweiler-Li, Rafael Bruschweiler
Summary: This study reports the sequence-specific resonance assignments of wild-type and oncogenic G12C and G12D mutants of K-Ras protein in the GTP-complexed active forms, providing a basis for comprehensive functional dynamics study.
BIOMOLECULAR NMR ASSIGNMENTS
(2023)
Article
Biology
Lara A. Patel, Timothy J. Waybright, Andrew G. Stephen, Chris Neale
Summary: Functional interaction between Ras signaling proteins and negative regulatory GTPase activating proteins (GAPs) is crucial for cellular decision making. The catalytic transition state for Ras deactivation involves an arginine residue from the GAP, a glutamine residue from Ras, and a water molecule for nucleophilic attack on GTP. In the presence of Ras mutations inhibiting arginine finger penetration, drug-based chemical rescue of GTP hydrolysis may have more challenging requirements compared to other enzymes with arginine-to-alanine mutations.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Hao Zhang, Duan Ni, Jigang Fan, Minyu Li, Jian Zhang, Chen Hua, Ruth Nussinov, Shaoyong Lu
Summary: This study reveals the transition pathway of the C-terminal hypervariable region (HVR) of K-Ras4B, identifies key conformational substates, and uncovers important interactions between the HVR and the catalytic domain. These findings are essential for a deeper understanding of the HVR transition mechanism and the regulation of K-Ras4B activity.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Multidisciplinary
Fa-An Chao, Srisathiyanarayanan Dharmaiah, Troy Taylor, Simon Messing, William Gillette, Dominic Esposito, Dwight Nissley, Frank McCormick, R. Andrew Byrd, Dhirendra K. Simanshu, Gabriel Cornilescu
Summary: This article investigates the influence of conformational dynamics of RAS proteins on their interactions with downstream effectors and explains and predicts the altered binding affinities of different mutants.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Manil Kanade, Ningthoujam Birjeet Singh, Sonal Lagad, Jyoti Baranwal, Pananghat Gayathri
Summary: Two small Ras-like GTPases, MglA and SofG, work together to drive cell polarity and motility in Myxococcus xanthus. MglA regulates cell motility and polarity reversals, while SofG regulates social motility enabled by the type IV pili machinery. The biochemical studies showed that MglB acts as a GAP for both GTPases, potentially contributing to concerted regulation of their activities in motility.
Review
Chemistry, Medicinal
Huan Xiao, Guan Wang, Min Zhao, Wen Shuai, Liang Ouyang, Qiu Sun
Summary: This review mainly summarizes the important role of GAPs in human tumors by introducing their classification, function, and regulatory mechanism. The relationship between dysregulated GAPs and a certain type of tumor is comprehensively described. In addition, the current status, research progress, and clinical value of GAPs as therapeutic targets, as well as the challenges and future direction in cancer therapy, are discussed.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Sharon L. Campbell, Mark R. Philips
Summary: Mutations in RAS genes are the most common driving force behind cancer development. RAS proteins, acting as binary molecular switches, control cellular growth through a complex signaling pathway. In addition to nucleotide-binding properties, RAS proteins are also regulated by numerous post-translational modifications, which are currently a high priority for drug discovery research in the field of RAS biology.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Anthony C. Bishop, Glorise Torres-Montalvo, Sravya Kotaru, Kyle Mimun, A. Joshua Wand
Summary: The authors propose BARASA, an approach for assigning backbone triple resonance spectra of proteins. The algorithm uses Bayesian statistical analysis and inter-spin connectivities from triple resonance spectroscopy to identify the optimal resonance assignments. BARASA outperforms current algorithms, especially in cases of sparse data, and can be evaluated in real-time during data acquisition.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Chih-Cheng Chen, Chia-Chen Hsu, Sung-Lin Chen, Po-Han Lin, Ju-Pei Chen, Yi-Ru Pan, Cih-En Huang, Ying-Ju Chen, Yi-Yang Chen, Yu-Ying Wu, Muh-Hwa Yang
Summary: The BET inhibitor JQ1 abrogates amoeboid movement of DLBCL cells through restrained RAS signaling and MYC-mediated suppression of GTP-RhoA activity, while also increasing IQGAP3 expression, impacting the prognosis of specific DLBCL patients. Inhibitors targeting both BET and RAS activities effectively suppress DLBCL dissemination in vivo, suggesting their potential synergistic therapeutic effect for specific DLBCL subtypes.
Article
Oncology
Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H-F Zhang, Ossama W. Tawfik, Fariba Behbod, Eric C. Chang
Summary: The study suggests that elevated NRAS levels in DCIS can control the emergence of basal-like features, leading to more aggressive tumor activity. Targeting NRAS and/or downstream pathways may block disease progression for a subset of DCIS patients with high NRAS.
BREAST CANCER RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Jun-ichi Takino, Shouhei Miyazaki, Kentaro Nagamine, Takamitsu Hori
Summary: RAS guanyl nucleotide-releasing proteins (RASGRPs) are important in activating small GTPases for intracellular signaling, with RASGRP2 showing unique characteristics among the family in targeting small GTPases. Research links RASGRP2 to diseases like Huntington's, tumors, and rheumatoid arthritis, while recent studies reveal its expression in vascular endothelial cells and its involvement in vasculogenesis and signaling pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Gyula Palfy, Dora K. Menyhard, Hanna Akontz-Kiss, Istvan Vida, Gyula Batta, Orsolya Toke, Andras Perczel
Summary: NMR relaxation techniques and molecular dynamics simulations were used to investigate the slow dynamics in K-Ras. A two-state conformational exchange on the ms timescale was observed in both GDP- and GTP-bound K-Ras. Furthermore, a low-populated higher energy state in GDP-loaded K-Ras was identified, which is involved in the interaction with nucleotide exchange factors and subsequent reactivation.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Medicinal
Hristo L. Svilenov, Alina Kulakova, Matja Zalar, Alexander P. Golovanov, Pernille Harris, Gerhard Winter
JOURNAL OF PHARMACEUTICAL SCIENCES
(2020)
Article
Pharmacology & Pharmacy
Matja Zalar, Hristo L. Svilenov, Alexander P. Golovanov
EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS
(2020)
Article
Biochemistry & Molecular Biology
Hugh Smith, Nicolas Guthertz, Emma E. Cawood, Roberto Maya-Martinez, Alexander L. Breeze, Sheena E. Radford
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Medicine, Research & Experimental
Christin Pohl, Matja Zalar, Inas El Bialy, Sowmya Indrakumar, Gunther H. J. Peters, Wolfgang Friess, Alexander P. Golovanov, Werner W. Streicher, Allan Noergaard, Pernille Harris
MOLECULAR PHARMACEUTICS
(2020)
Article
Pharmacology & Pharmacy
Sowmya Indrakumar, Matja Zalar, Nuska Tschammer, Christin Pohl, Allan Norgaard, Werner Streicher, Pernille Harris, Alexander P. Golovanov, Gunther H. J. Peters
Summary: The study developed a fast screening method using the therapeutic peptide plectasin, combining microscale thermophoresis titration assays and molecular dynamics simulations, with validation through H-1-C-13-HSQC NMR titration experiments. The results demonstrate the reliability of this approach in relatively ranking excipients and predicting possible binding sites for other peptides and proteins.
EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS
(2021)
Article
Multidisciplinary Sciences
Jack E. Bramham, Alexander P. Golovanov
Summary: This study demonstrates the use of a probe molecule and NMR spectroscopy to characterize the kinetics of protein liquid-liquid phase separation. The chemical shift and linewidth of the probe molecule provide information on the formation and evolution of the two phases.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Yong Xu, Roberto Maya-Martinez, Nicolas Guthertz, George R. Heath, Iain W. Manfield, Alexander L. Breeze, Frank Sobott, Richard Foster, Sheena E. Radford
Summary: This study applied chemical kinetics to investigate the assembly mechanism of hIAPP and discovered two small-molecule modulators that can regulate hIAPP assembly, which can serve as promising starting-points for research on hIAPP aggregation and the development of therapeutics for T2D.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Jack E. Bramham, Alexander P. Golovanov
Summary: This study demonstrates a new sample illumination device that allows users to perform in situ photo-NMR experiments easily. By placing an LED array directly at the top of a special sample tube, the device solves the challenge of illuminating NMR samples deep within the bore of a spectrometer magnet. The setup shows potential for studying a wide range of light-dependent chemical and biological phenomena.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Pharmacology & Pharmacy
Amy Gorman, Alexander P. Golovanov
Summary: Lipopolysaccharide (LPS), a component of Gram-negative bacteria, is released into the bloodstream during cell division or bacterial cell death, causing pro-inflammatory immune responses. Detecting LPS is crucial in the pharmaceutical and food industries. The Limulus Amebocyte Lysate (LAL) assay is commonly used; however, recent research has highlighted the phenomenon of Low Endotoxin Recovery (LER), where LAL assays fail to detect LPS due to a masking effect caused by formulation excipients. This article provides a comprehensive review of LER research, discussing the relationship between LPS structure and toxicity, conditions that alter LPS supramolecular arrangement, hypothesized mechanisms of LER, and the potential risk of masked LPS remaining biologically toxic.
EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS
(2022)
Article
Chemistry, Medicinal
Hristo L. Svilenov, Katharina T. Kopp, Alexander P. Golovanov, Gerhard Winter, Matja Zalar
Summary: This study demonstrates the application of saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy in detecting protein-surfactant interactions. It was found that polysorbate 20 binds with interferon alpha, with stronger binding at pH closer to the protein's iso-electric point. In contrast, no interactions were detected between poloxamer 407 and interferon alpha. This research highlights the potential of STD-NMR for quickly assessing surfactant-protein interactions and aiding in surfactant selection for protein formulation.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Marshall J. Smith, Jack E. Bramham, Mathias Nilsson, Gareth A. Morris, Laura Castanar, Alexander P. Golovanov
Summary: Fluorine is widely used in medicinal chemistry, both in drug molecules and molecular probes, due to its convenient monitoring capabilities by NMR spectroscopy in complex environments. However, NMR sensitivity is limited, especially at low concentrations of molecules.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Jack E. Bramham, Matja Zalar, Alexander P. Golovanov
Summary: Photocaging is an attractive strategy to control molecular behavior, and this study demonstrates the effective and controlled release of photocages using the in situ illumination by the LED NMRtorch approach. The subsequent reactions were simultaneously monitored by solution NMR spectroscopy.
CHEMICAL COMMUNICATIONS
(2022)
Article
Medicine, Research & Experimental
Jack E. Bramham, Stephanie A. Davies, Adrian Podmore, Alexander P. Golovanov
Summary: Concentrating proteins by conventional techniques can be time-consuming and challenging, but using the dense fraction produced by macroscopic liquid-liquid phase separation (LLPS) can effectively produce high-concentration protein formulations with demonstrated stability. Concentrating mAb solutions by LLPS results in a stable high-concentration protein formulation, providing a simple and effective technique for bioprocessing or administration.
Article
Chemistry, Medicinal
Jack E. Bramham, Adrian Podmore, Stephanie A. Davies, Alexander P. Golovanov
Summary: In this study, H-1 nuclear magnetic resonance (NMR) spectroscopy was utilized to study the protein and small molecule content and stability in high-concentration antibody formulations. Protein degradation and fragmentation can be detected through changes in 1D H-1 NMR signal intensity, while relaxation rates are sensitive to antibody fragmentation. Additionally, relaxation-filtered spectra can reveal the presence and degradation of small molecule components and changes in solution properties such as pH.
ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE
(2021)
Article
Chemistry, Analytical
Paul I. C. Richardson, Howbeer Muhamadali, Yang Lei, Alexander P. Golovanov, David I. Ellis, Royston Goodacre
