The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom molecular dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) overcharge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction. To efficiently sample configurational space we explore hybrid continuum solvent models, applicable to many-protein systems, where weakly coupled ions are treated implicitly, while strongly coupled ones are treated explicitly. Good agreement is found with the primitive model of electrolytes, as well as with atomic models of protein and solvent.
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Comput Biol Chem
December 2024
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 39, Guwahati, Assam, India; Centre for Nanotechnology, Indian Institute of Technology Guwahati, 39, Guwahati, Assam, India. Electronic address:
The aberrant metabolic reprogramming endows TNBC cells with sufficient ATP and lactate required for survival and metastasis. Hence, the intervention of the metabolic network represents a promising avenue to alleviate the Warburg effect in TNBC cells to impair their invasive and metastatic potential. Multitudinous in-silico analysis identified Enolase1 (ENO1) and the surface transporter protein, GLUT4 to be the potential targets for the abrogation of the metabolic network.
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Department of Pharmacology, School of Pharmacy, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, China.
Extrachromosomal circular DNA (eccDNA), a chromosome-independent circular DNA, has garnered significant attention due to its widespread distribution and intricate biogenesis in carcinoma. Existing research findings propose that multiple eccDNAs contribute to drug resistance in cancer treatments through complex and interrelated regulatory mechanisms. The unique structure and genetic properties of eccDNA increase tumor heterogeneity.
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National Clinical Research Center for Geriatrics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China. Electronic address:
Non-structural protein 3 (Nsp3) is the largest protein encoded by the coronavirus (CoV) genome. It consists of multiple domains that perform critical functions during the viral life cycle. CoV-Y is the most C-terminal domain of Nsp3, and it exhibits evolutionary conservation across diverse CoVs; however, the exact biological function of CoV-Y remains unclear.
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June 2024
Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
Integral membrane proteins (IMPs) constitute a large fraction of organismal proteomes, playing fundamental roles in physiology and disease. Despite their importance, the mechanisms underlying dynamic features of IMPs, such as anomalous diffusion, protein-protein interactions, and protein clustering, remain largely unknown due to the high complexity of cell membrane environments. Available methods for in vitro studies are insufficient to study IMP dynamics systematically.
View Article and Find Full Text PDFJ Phys Chem Lett
April 2024
Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy.
We propose a novel approach for detecting the binding between proteins making use of the anomalous diffraction of natively present heavy elements, e.g., sulfurs, inside molecular three-dimensional structures.
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