molecular dynamics simulation


Summary: A computer simulation developed to study the motion of molecules over a period of time.

Top Publications

  1. Samatanga B, Cléry A, Barraud P, Allain F, Jelesarov I. Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs. Nucleic Acids Res. 2017;45:6037-6050 pubmed publisher
    ..Altogether, different modes employed by RRMs to bind cognate ssRNAs utilize various thermodynamics strategies during the association process. ..
  2. Yoon H, Warshel A. Simulating the fidelity and the three Mg mechanism of pol ? and clarifying the validity of transition state theory in enzyme catalysis. Proteins. 2017;85:1446-1453 pubmed publisher
    ..Proteins 2017; 85:1446-1453. © 2017 Wiley Periodicals, Inc. ..
  3. Liu B, Ã…berg C, van Eerden F, Marrink S, Poolman B, Boersma A. Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding. Biophys J. 2017;112:1929-1939 pubmed publisher
    ..The collection of new probes provides more detailed readouts on the macromolecular crowding than a single sensor. ..
  4. Risselada H. Membrane Fusion Stalks and Lipid Rafts: A Love-Hate Relationship. Biophys J. 2017;112:2475-2478 pubmed publisher
    ..These insights may explain why modeled viral fusion occurs preferentially near the lo/ld phase boundary. ..
  5. Antonietti V, Boudesocque S, Dupont L, Farvacques N, Cézard C, Da Nascimento S, et al. Synthesis, iron(III) complexation properties, molecular dynamics simulations and P. aeruginosa siderophore-like activity of two pyoverdine analogs. Eur J Med Chem. 2017;137:338-350 pubmed publisher
    ..These results showed that aPvd3 may be used to inhibit pyoverdine uptake or to promote the accumulation and release of antibiotics into the cell following a Trojan horse strategy. ..
  6. Morgan B, Zitzewitz J, Massi F. Structural Rearrangement upon Fragmentation of the Stability Core of the ALS-Linked Protein TDP-43. Biophys J. 2017;113:540-549 pubmed publisher
  7. di Palma F, Bottaro S, Bussi G. Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. BMC Bioinformatics. 2015;16 Suppl 9:S6 pubmed publisher
  8. Furmanová K, Jarešová M, Byška J, Jurčík A, Parulek J, Hauser H, et al. Interactive exploration of ligand transportation through protein tunnels. BMC Bioinformatics. 2017;18:22 pubmed publisher
    ..The tool was tested by the domain experts from protein engineering and the results confirm that it helps to navigate the user to the most interesting parts of the ligand trajectory and to understand the ligand behavior. ..
  9. Bartesaghi S, Herrera D, Martinez D, Petruk A, Demicheli V, Trujillo M, et al. Tyrosine oxidation and nitration in transmembrane peptides is connected to lipid peroxidation. Arch Biochem Biophys. 2017;622:9-25 pubmed publisher
    ..Altogether, this work underscores unique characteristics of the tyrosine oxidation and nitration process in lipid-rich milieu that is fueled via the lipid peroxidation process. ..

More Information

Publications114 found, 100 shown here

  1. Warfield B, Anderson P. Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state. PLoS ONE. 2017;12:e0176229 pubmed publisher
    ..This population change, rather than direct interactions between Mg2+ and theophylline, accounts for altered theophylline binding kinetics. ..
  2. Penkler D, Sensoy O, Atilgan C, Tastan Bishop O. Perturbation-Response Scanning Reveals Key Residues for Allosteric Control in Hsp70. J Chem Inf Model. 2017;57:1359-1374 pubmed publisher
  3. Iacovelli F, Tucci F, Macari G, Falconi M. Multiple molecular dynamics simulations of human LOX-1 and Trp150Ala mutant reveal the structural determinants causing the full deactivation of the receptor. Proteins. 2017;85:1902-1912 pubmed publisher
    ..The combined effect of these structural rearrangements generates the impairing of the receptor function. ..
  4. Xu D, Si Y, Meroueh S. A Computational Investigation of Small-Molecule Engagement of Hot Spots at Protein-Protein Interaction Interfaces. J Chem Inf Model. 2017;57:2250-2272 pubmed publisher
    ..The more effective use of hot spots in future drug design efforts may result in smaller compounds with higher ligand efficiencies that may lead to greater success in clinical trials. ..
  5. Molakarimi M, Mohseni A, Taghdir M, Pashandi Z, Gorman M, Parker M, et al. QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins. PLoS ONE. 2017;12:e0182317 pubmed publisher
    ..This work also revealed that a hydrogen bonding network formed by a D158- R41-Y204 triad could be responsible for shuttling the proton from the 2- hydroperoxy group of the substrate to bulk solvent...
  6. Marx D, Fleming K. Influence of Protein Scaffold on Side-Chain Transfer Free Energies. Biophys J. 2017;113:597-604 pubmed publisher
  7. Hiruma S, Kamasaki T, Otomo K, Nemoto T, Uehara R. Dynamics and function of ERM proteins during cytokinesis in human cells. FEBS Lett. 2017;591:3296-3309 pubmed publisher
    ..These results reveal a supportive role of ERMs in cortical activities during cytokinesis, and also provide insight into the selective mechanism that preferentially associates cytokinesis-relevant proteins with the division site. ..
  8. Muccioli L, D Avino G, Zannoni C. Simulation of vapor-phase deposition and growth of a pentacene thin film on C60 (001). Adv Mater. 2011;23:4532-6 pubmed publisher
  9. Tran To Su C, Ouyang X, Zheng J, Kwoh C. Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K. BMC Bioinformatics. 2013;14 Suppl 16:S7 pubmed publisher
    ..Combination of molecular docking and Molecular Dynamics simulation reveal that zanamivir forms more favorable and stable complex than oseltamivir and peramivir when ..
  10. McConnell M, Tal Grinspan L, Williams M, Lynn M, Schwartz B, Fass O, et al. Clinically Divergent Mutation Effects on the Structure and Function of the Human Cardiac Tropomyosin Overlap. Biochemistry. 2017;56:3403-3413 pubmed publisher
  11. Zhao Z, Xie L, Bourne P. Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome. PLoS ONE. 2017;12:e0179936 pubmed publisher
    ..studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamics simulation. Our studies provide detailed sequence, structure, interaction-fingerprint, pharmacophore and binding-..
  12. Putzu M, Kara S, Afonin S, Grage S, Bordessa A, Chaume G, et al. Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations. Biophys J. 2017;112:2602-2614 pubmed publisher
    ..The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly. ..
  13. Getman R, Bae Y, Wilmer C, Snurr R. Review and analysis of molecular simulations of methane, hydrogen, and acetylene storage in metal-organic frameworks. Chem Rev. 2012;112:703-23 pubmed publisher
  14. Choy M, Li Y, Machado L, Kunze M, Connors C, Wei X, et al. Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery. Mol Cell. 2017;65:644-658.e5 pubmed publisher
    ..This shows that both conformational rigidity and dynamics are essential for controlling protein activity. This connection between rigidity and dynamics at different timescales is likely a hallmark of all enzyme function. ..
  15. Pegoli A, She X, Wifling D, Hubner H, Bernhardt G, Gmeiner P, et al. Radiolabeled Dibenzodiazepinone-Type Antagonists Give Evidence of Dualsteric Binding at the M2 Muscarinic Acetylcholine Receptor. J Med Chem. 2017;60:3314-3334 pubmed publisher
    ..This was consistent with the results of M2R MD simulations (?2 ?s) performed with 19 and 33. ..
  16. Deganutti G, Welihinda A, Moro S. Comparison of the Human A2A Adenosine Receptor Recognition by Adenosine and Inosine: New Insight from Supervised Molecular Dynamics Simulations. ChemMedChem. 2017;12:1319-1326 pubmed publisher
    ..To better depict the differences in the mechanisms of receptor recognition between adenosine and inosine, we carried out supervised molecular dynamics (SuMD) simulations, and the results are analyzed herein. ..
  17. Zhao C, Dong L, Liu Y. A QM/MM study of the catalytic mechanism of SAM methyltransferase RlmN from Escherichia coli. Proteins. 2017;85:1967-1974 pubmed publisher
    ..These findings would deepen the understanding of the catalysis of RlmN. ..
  18. Yasui T, Yamamoto T, Sakai N, Asano K, Takai T, Yoshitomi Y, et al. Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design. Bioorg Med Chem. 2017;25:4876-4886 pubmed publisher
    ..72µM) by utilizing structure-based drug design (SBDD) based on an X-ray crystal structure of 1a bound to BCL6. Compound 8c also showed a good pharmacokinetic profile, which was acceptable for both in vitro and in vivo studies. ..
  19. Rekand I, Brenk R. Ligand design for riboswitches, an emerging target class for novel antibiotics. Future Med Chem. 2017;9:1649-1663 pubmed publisher
    ..In this review, we highlight the most advanced drug design work of riboswitch ligands and discuss the challenges in the field with respect to the development of antibiotics with a new mechanism of action. ..
  20. Dholakia D, Goyal S, Jamal S, Singh A, Das A, Grover A. Molecular modeling and lead design of substituted zanamivir derivatives as potent anti-influenza drugs. BMC Bioinformatics. 2016;17:512 pubmed publisher
    ..Ligand-bound complexes of both H1N1 and H3N2 were observed to be stable for 11 ns and 7 ns respectively. ADME descriptors were also calculated to study the pharmacokinetic properties of AMA which revealed its drug-like properties. ..
  21. Lee X, Verma C, Sim A. Designing dual inhibitors of Mdm2/MdmX: Unexpected coupling of water with gatekeeper Y100/99. Proteins. 2017;85:1493-1506 pubmed publisher
    ..The recently developed potent dual inhibitory stapled peptide Atsp7041 appears to be agnostic to the conformation of the gatekeeper residue. Proteins 2017; 85:1493-1506. © 2017 Wiley Periodicals, Inc. ..
  22. Garakani K, Shams H, Mofrad M. Mechanosensitive Conformation of Vinculin Regulates Its Binding to MAPK1. Biophys J. 2017;112:1885-1893 pubmed publisher
    ..Finally, we demonstrate that changes in the size of the D3-D4 cleft provide a structural basis for the conformational selectivity of the interaction. ..
  23. Feng W, Lei H, Si J, Zhang T. Study of structural stability and damaging effect on membrane for four A?42 dimers. PLoS ONE. 2017;12:e0179147 pubmed publisher
    ..Based on the results, the 2NCb is considered as a stable dimeric unit for aggregating the larger A?42 oligomer, and has a potent ability to disrupt the membrane. ..
  24. Novinec M. Computational investigation of conformational variability and allostery in cathepsin K and other related peptidases. PLoS ONE. 2017;12:e0182387 pubmed publisher
    ..Comparison with other related enzymes shows that similar conformational variability and, by implication, allostery also exist in other papain-like endopeptidases. ..
  25. Weber I, Harrison R. Decoding HIV resistance: from genotype to therapy. Future Med Chem. 2017;9:1529-1538 pubmed publisher
    ..Adding classifiers such as information on the atomic structure of the protein can further enhance the predictions...
  26. Vu C, Rotkrua P, Tantirungrotechai Y, Soontornworajit B. Oligonucleotide Hybridization Combined with Competitive Antibody Binding for the Truncation of a High-Affinity Aptamer. ACS Comb Sci. 2017;19:609-617 pubmed publisher
    ..The effect of the truncated aptamer on PDGF-BB-stimulated fibroblasts was found to be equivalent to that of the full-length aptamer. ..
  27. Joshi H, Seniya S, Suryanarayanan V, Patidar N, Singh S, Jain V. Dissecting the structure-function relationship in lysozyme domain of mycobacteriophage D29-encoded peptidoglycan hydrolase. FEBS Lett. 2017;591:3276-3287 pubmed publisher
    ..We further complement our in vitro experiments with detailed in silico investigations. We present LD as a potent candidate for developing phage-based broad-spectrum therapeutics. ..
  28. Kaufmann T, Grishkovskaya I, Polyansky A, Kostrhon S, Kukolj E, Olek K, et al. A novel non-canonical PIP-box mediates PARG interaction with PCNA. Nucleic Acids Res. 2017;45:9741-9759 pubmed publisher
    ..Our data explain the mechanism of PARG-PCNA interaction through a new PARG PIP-box that exhibits non-canonical sequence properties but a canonical mode of PCNA binding. ..
  29. Kaczmarski J, Corry B. Investigating the size and dynamics of voltage-gated sodium channel fenestrations. Channels (Austin). 2014;8:264-77 pubmed
    ..Together, the results suggest that fenestrations provide viable pathways for small, flexible, hydrophobic drugs. ..
  30. Zhao Y, She N, Zhang X, Wang C, Mo Y. Product release mechanism and the complete enzyme catalysis cycle in yeast cytosine deaminase (yCD): A computational study. Biochim Biophys Acta Proteins Proteom. 2017;1865:1020-1029 pubmed publisher
    ..Finally, the full cycle of the enzymatic catalysis has been determined, making the whole process computationally more precise. ..
  31. Hannaoui S, Amidian S, Cheng Y, Duque Velasquez C, Dorosh L, Law S, et al. Destabilizing polymorphism in cervid prion protein hydrophobic core determines prion conformation and conversion efficiency. PLoS Pathog. 2017;13:e1006553 pubmed publisher
    ..Therefore, a thorough analysis of CWD isolates and re-assessment of species-barriers is important in order to fully exclude a zoonotic potential of CWD. ..
  32. Wang Y, Lu C, Hour T, Cheng T. Inhibitor and substrate binding by New Delhi metallo-beta-lactamase-1: a molecular dynamics studies. Curr Comput Aided Drug Des. 2014;10:197-204 pubmed
    ..From our simulations, we found that the 5 residues Asp223, His120, His122, His162 and His189 are responsible for the selectivity of NDM-1 associated drugs. ..
  33. Molt R, Georgiadis M, Richards N. Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 ?s molecular dynamics simulations. Nucleic Acids Res. 2017;45:3643-3653 pubmed publisher
    ..Second, differences are seen in the base stacking of pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in with ?-electrons of the adjacent base. ..
  34. Tanwar H, Sneha P, Thirumal Kumar D, Siva R, Walter C, George Priya Doss C. A Computational Approach to Identify the Biophysical and Structural Aspects of Methylenetetrahydrofolate Reductase (MTHFR) Mutations (A222V, E429A, and R594Q) Leading to Schizophrenia. Adv Protein Chem Struct Biol. 2017;108:105-125 pubmed publisher
    ..we proposed a computational pipeline using in silico prediction tools, molecular docking, and molecular dynamics simulation analysis...
  35. Nagy G, Oostenbrink C, Hritz J. Exploring the binding pathways of the 14-3-3? protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints. PLoS ONE. 2017;12:e0180633 pubmed publisher
    ..Binding affinities calculated from the potential of mean force along the binding pathway are in line with the available experimental estimates for two of the studied systems. ..
  36. Tamura K, Hayashi S. Atomistic modeling of alternating access of a mitochondrial ADP/ATP membrane transporter with molecular simulations. PLoS ONE. 2017;12:e0181489 pubmed publisher
  37. Karain W. Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method. BMC Bioinformatics. 2017;18:525 pubmed publisher
    ..We apply this technique to a 132 ns long molecular dynamics simulation of the β-Lactamase Inhibitory Protein BLIP...
  38. Goyal S, Jamal S, Shanker A, Grover A. Structural investigations of T854A mutation in EGFR and identification of novel inhibitors using structure activity relationships. BMC Genomics. 2015;16 Suppl 5:S8 pubmed publisher
    ..We report two novel compounds having high predicted inhibitory activity to EGFR TK domain with both wild-type and mutant structure. ..
  39. Noinaj N, GUMBART J, Buchanan S. The ?-barrel assembly machinery in motion. Nat Rev Microbiol. 2017;15:197-204 pubmed publisher
    ..We also detail the mechanistic insights that have been gained from structural data, mutagenesis studies and molecular dynamics simulations, and explore two emerging models for the BAM-mediated biogenesis of OMPs in bacteria. ..
  40. Das J, Aleksandrov A, Cui L, He L, Riordan J, Dokholyan N. Transmembrane helical interactions in the CFTR channel pore. PLoS Comput Biol. 2017;13:e1005594 pubmed publisher an outward (OWF) and develop an inward (IWF) facing model employing an integrated experimental-molecular dynamics simulation (200 ns) approach...
  41. Strasser A, Wittmann H, Seifert R. Binding Kinetics and Pathways of Ligands to GPCRs. Trends Pharmacol Sci. 2017;38:717-732 pubmed publisher
    ..The kinetics of drug binding to GPCRs are complex and depend on several factors, including charge distribution on the receptor surface, ligand-receptor interactions in the binding channel and the binding site, or solvation. ..
  42. Sayama M, Inoue A, Nakamura S, Jung S, Ikubo M, Otani Y, et al. Probing the Hydrophobic Binding Pocket of G-Protein-Coupled Lysophosphatidylserine Receptor GPR34/LPS1 by Docking-Aided Structure-Activity Analysis. J Med Chem. 2017;60:6384-6399 pubmed publisher
    ..A tetrabenzene-based lipid analogue bearing a bulky tert-butyl group at the 4-position of the terminal benzene ring exhibited potent GPR34 agonistic activity, validating the present hydrophobic binding pocket model. ..
  43. Zhao Q, Heyda J, Dzubiella J, Täuber K, Dunlop J, Yuan J. Sensing Solvents with Ultrasensitive Porous Poly(ionic liquid) Actuators. Adv Mater. 2015;27:2913-7 pubmed publisher
  44. Shindou H, Koso H, Sasaki J, Nakanishi H, Sagara H, Nakagawa K, et al. Docosahexaenoic acid preserves visual function by maintaining correct disc morphology in retinal photoreceptor cells. J Biol Chem. 2017;292:12054-12064 pubmed publisher
    ..This study thus provides the reason why DHA is required for visual acuity and may help inform approaches for overcoming retinal disorders associated with DHA deficiency or dysfunction. ..
  45. Mishra P, Dixit A, Ray M, Sabat S. Mechanistic study of CuZn-SOD from Ipomoea carnea mutated at dimer interface: enhancement of peroxidase activity upon monomerization. Biochimie. 2014;97:181-93 pubmed
    ..Increased peroxidative activity of the enzyme, upon monomerization may have physiological implication essentially in presence of high concentration of H2O2, as in case of plant cells specifically under stress conditions...
  46. Chadha N, Silakari O. Identification of low micromolar dual inhibitors for aldose reductase (ALR2) and poly (ADP-ribose) polymerase (PARP-1) using structure based design approach. Bioorg Med Chem Lett. 2017;27:2324-2330 pubmed publisher
    ..The positive results of the biochemical assay suggest that these compounds may be further optimized and utilized for the treatment of diabetic retinopathy. ..
  47. Kamble A, Fandilolu P, Sambhare S, Sonawane K. Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, ?m5U present at 'wobble' position in anticodon loop of tRNALeu: A molecular modeling approach. PLoS ONE. 2017;12:e0176756 pubmed publisher
    ..Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with ?m5U34 to recognize UUG and UUA codons. ..
  48. Ruiz Rodríguez M, Vedani A, Flores Mireles A, Cháirez Ramírez M, Gallegos Infante J, González Laredo R. In Silico Prediction of the Toxic Potential of Lupeol. Chem Res Toxicol. 2017;30:1562-1571 pubmed publisher
    ..Our results indicate that there is a moderate toxic potential for lupeol and some of its analogues, by targeting and binding to nuclear receptors involved in fertility, which could trigger undesired adverse effects. ..
  49. Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F, et al. Dynamics of the protein structure of T169S pyranose 2-oxidase in solution: Molecular dynamics simulation. Proteins. 2017;85:1913-1924 pubmed publisher
    ..structure of a mutated P2O, T169S (Thr169 is replaced by Ser), in solution was studied by means of molecular dynamics simulation and analyses of photoinduced electron transfer (ET) from Trp168 to excited isoalloxazine (Iso*), and ..
  50. Vunnam N, Campbell Bezat C, Lewis A, Sachs J. Death Receptor 5 Activation Is Energetically Coupled to Opening of the Transmembrane Domain Dimer. Biophys J. 2017;113:381-392 pubmed publisher
    ..The single mutants had a small effect on TM domain separation and cell death, whereas the double mutant significantly increased the TM domain separation and more than doubled the sensitivity of cells to ligand stimulation. ..
  51. Basher M, Rahman K, Jackson P, Thurston D, Fox K. Sequence-selective binding of C8-conjugated pyrrolobenzodiazepines (PBDs) to DNA. Biophys Chem. 2017;230:53-61 pubmed publisher
    ..Melting studies with 14-mer oligonucleotide duplexes confirm covalent attachment of the conjugates, which show a different selectivity to anthramycin and reveal that more than one ligand molecule can bind to each duplex. ..
  52. Li Z, He Y, Liu Q, Zhao L, Wong L, Kwoh C, et al. Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. BMC Bioinformatics. 2013;14 Suppl 16:S11 pubmed publisher
    ..Our study reveals that a large cluster of water buried in protein interfaces is fragile and high-maintenance, closely related to the structure, function and evolution of the whole protein. ..
  53. Aaldering L, Poongavanam V, Langkjaer N, Murugan N, Jørgensen P, Wengel J, et al. Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule. Chembiochem. 2017;18:755-763 pubmed publisher
    ..The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties. ..
  54. Healy E. A prion-like mechanism for the propagated misfolding of SOD1 from in silico modeling of solvated near-native conformers. PLoS ONE. 2017;12:e0177284 pubmed publisher
    ..This enervation is caused in turn by the formation of transient, non-obligate oligomers between pathogenic SOD1 mutants and wt SOD1. ..
  55. Pan K, Bricker W, Ratanalert S, Bathe M. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Res. 2017;45:6284-6298 pubmed publisher
  56. Esaki S, Evich M, Erlitzki N, Germann M, Poon G. Multiple DNA-binding modes for the ETS family transcription factor PU.1. J Biol Chem. 2017;292:16044-16054 pubmed publisher
    ..As sequential dimerization did not occur with the ETS domain of Ets-1, a close structural homolog of PU.1, 2:1 complex formation may represent an alternative autoinhibitory mechanism in the ETS family at the protein-DNA level. ..
  57. Skutkova H, Vítek M, Babula P, Kizek R, Provaznik I. Classification of genomic signals using dynamic time warping. BMC Bioinformatics. 2013;14 Suppl 10:S1 pubmed publisher
    ..Classification of genomic signals using dynamic time warping is an adequate variant to phylogenetic analysis using the symbolic DNA sequences alignment; in addition, it is robust, quick and more precise technique. ..
  58. Mukherjee S, Karolak A, Debant M, Buscaglia P, Renaudineau Y, Mignen O, et al. Molecular Dynamics Simulations of Membrane-Bound STIM1 to Investigate Conformational Changes during STIM1 Activation upon Calcium Release. J Chem Inf Model. 2017;57:335-344 pubmed publisher
    ..Altogether, understanding conformational changes in STIM1 can help in drug discovery when targeting this key protein in intracellular calcium functions. ..
  59. Wiechert M, Beitz E. Mechanism of formate-nitrite transporters by dielectric shift of substrate acidity. EMBO J. 2017;36:949-958 pubmed publisher
    ..We define substrate neutralization by proton transfer for transport via a hydrophobic transport path as a general theme of the Amt/Mep/Rh ammonium and formate-nitrite transporters. ..
  60. Tang Y, Lu L, Li H, Evangelinos C, Grinberg L, Sachdeva V, et al. OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution. Biophys J. 2017;112:2030-2037 pubmed publisher
    ..It outperforms a legacy simulator by almost an order of magnitude in time-to-solution and >40 times in problem size, thus providing, to our knowledge, a new platform for probing the biomechanics of red blood cells. ..
  61. Narzi D, Coccia E, Manzoli M, Guidoni L. Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II. Biophys Chem. 2017;229:93-98 pubmed publisher
    ..Many peripheral chromophores undergo fluctuations larger then 10kJ/mol around the average values. Possible physiological roles of such fluctuations are discussed. ..
  62. Gulay S, Bista S, Varshney A, Kirmizialtin S, Sanbonmatsu K, Dinman J. Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. Nucleic Acids Res. 2017;45:4958-4971 pubmed publisher
    ..set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex...
  63. Shaik M, Bhattacharjee N, Feliks M, Ng K, Field M. Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences. Proteins. 2017;85:1435-1445 pubmed publisher
    ..The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435-1445. © 2017 Wiley Periodicals, Inc. ..
  64. Pan L, Song L, Miao Y, Yang Y, Merz K. Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?. Biochemistry. 2017;56:2995-3007 pubmed publisher
  65. Zolghadr A, Heydari Dokoohaki M. How Does the P7C3-Series of Neuroprotective Small Molecules Prevent Membrane Disruption?. J Chem Inf Model. 2017;57:2009-2019 pubmed publisher
  66. Chiodo L, Malliavin T, Maragliano L, Cottone G. A possible desensitized state conformation of the human ?7 nicotinic receptor: A molecular dynamics study. Biophys Chem. 2017;229:99-109 pubmed publisher
    ..The obtained structure is assessed against experimental data for other ligand gated ion channels that have been putatively associated to active, inactive and desensitized conditions. ..
  67. Álvarez Almazán S, Bello M, Tamay Cach F, Martínez Archundia M, Alemán González Duhart D, Correa Basurto J, et al. Study of new interactions of glitazone's stereoisomers and the endogenous ligand 15d-PGJ2 on six different PPAR gamma proteins. Biochem Pharmacol. 2017;142:168-193 pubmed publisher
    ..An energetic analysis revealed binding free energy trends that supported known experimental findings of other authors describing better binding properties for PIO, ROSI and (S,S)-TRO than for 15d-PGJ2 and the TZD ring. ..
  68. Shibuta Y, Sakane S, Miyoshi E, Okita S, Takaki T, Ohno M. Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal. Nat Commun. 2017;8:10 pubmed publisher
    ..Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains ..
  69. Piotto S, Sessa L, Iannelli P, Concilio S. Computational study on human sphingomyelin synthase 1 (hSMS1). Biochim Biophys Acta Biomembr. 2017;1859:1517-1525 pubmed publisher
    ..This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá. ..
  70. Niewieczerzal S, Sulkowska J. Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume. PLoS ONE. 2017;12:e0176744 pubmed publisher
    ..In addition, we find that as the size of the cage decreases, folding times increase almost exponentially in a certain range of cage sizes, in accordance with confinement theory and experimental data for unknotted proteins. ..
  71. Hu W, Mao A, Wong P, Larsen A, Yazaki P, Wong J, et al. Characterization of 1,2-Distearoyl-sn-glycero-3-phosphoethanolamine-N-[Methoxy(polyethylene glycerol)-2000] and Its Complex with Doxorubicin Using Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics. Bioconjug Chem. 2017;28:1777-1790 pubmed publisher
    ..This study provides an advanced basic approach that can be used to study a wide range of drug-LNP interactions...
  72. Nandy A, Saenz Méndez P, Gorman A, Samali A, Eriksson L. Homology model of the human tRNA splicing ligase RtcB. Proteins. 2017;85:1983-1993 pubmed publisher
    ..Our results furthermore clearly show that the GTP binding site of the enzyme is a well-defined pocket that can be utilized as target site for in silico drug discovery. ..
  73. Mas Moruno C, Beck J, Doedens L, Frank A, Marinelli L, Cosconati S, et al. Increasing ?v?3 selectivity of the anti-angiogenic drug cilengitide by N-methylation. Angew Chem Int Ed Engl. 2011;50:9496-500 pubmed publisher
  74. Howes S, Geyer E, LaFrance B, Zhang R, Kellogg E, Westermann S, et al. Structural differences between yeast and mammalian microtubules revealed by cryo-EM. J Cell Biol. 2017;216:2669-2677 pubmed publisher
    ..These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures. ..
  75. Nelson D, Applegate G, Beio M, Graham D, Berkowitz D. Human serine racemase structure/activity relationship studies provide mechanistic insight and point to position 84 as a hot spot for ?-elimination function. J Biol Chem. 2017;292:13986-14002 pubmed publisher
  76. Anthony N, Baiget J, Berretta G, Boyd M, Breen D, Edwards J, et al. Inhibitory Kappa B Kinase ? (IKK?) Inhibitors That Recapitulate Their Selectivity in Cells against Isoform-Related Biomarkers. J Med Chem. 2017;60:7043-7066 pubmed publisher
    ..These compounds represent the first chemical tools that can be used to further characterize the role of IKK? in cellular signaling, to dissect this from IKK? and to validate it in its own right as a target in inflammatory diseases. ..
  77. Tubiana T, Boulard Y, Bressanelli S. Dynamics and asymmetry in the dimer of the norovirus major capsid protein. PLoS ONE. 2017;12:e0182056 pubmed publisher
    ..Our work brings new lights on the surprising conformational range encoded in the norovirus major capsid protein. ..
  78. Huang Y, Gao M, Yang F, Zhang L, Su Z. Deciphering the promiscuous interactions between intrinsically disordered transactivation domains and the KIX domain. Proteins. 2017;85:2088-2095 pubmed publisher
    ..This study highlights the importance of long-range electrostatic interactions in molecular recognition process involving multi-motif intrinsically disordered proteins and promiscuous interactions. ..
  79. Chandra B, Bhowmik D, Maity B, Mote K, Dhara D, Venkatramani R, et al. Major Reaction Coordinates Linking Transient Amyloid-? Oligomers to Fibrils Measured at Atomic Level. Biophys J. 2017;113:805-816 pubmed publisher
    ..Overall, we propose interstrand separation and salt-bridge formation as key reaction coordinates describing the structural transition of the small A?40 oligomers to fibrils. ..
  80. Silva I, Fernandes V, Souza C, Treptow W, Santos G. Biophysical studies of cholesterol effects on chromatin. J Lipid Res. 2017;58:934-940 pubmed publisher
    ..Our findings support that cholesterol assists 10 and 30 nm chromatin formation and induces folding of long chromatin fibers as a result of direct interaction of the cholesterol to six nucleosomal binding sites. ..
  81. Paparin J, Amador A, Badaroux E, Bot S, Caillet C, Convard T, et al. Discovery of benzophosphadiazine drug candidate IDX375: A novel hepatitis C allosteric NS5B RdRp inhibitor. Bioorg Med Chem Lett. 2017;27:2634-2640 pubmed publisher
    ..The structure and binding domain of IDX375 were confirmed by X-ray co-crystalisation study. ..
  82. Tangprasertchai N, Di Felice R, Zhang X, Slaymaker I, Vazquez Reyes C, Jiang W, et al. CRISPR-Cas9 Mediated DNA Unwinding Detected Using Site-Directed Spin Labeling. ACS Chem Biol. 2017;12:1489-1493 pubmed publisher
  83. Pilipczuk J, Zalewska Piatek B, Bruzdziak P, Czub J, Wieczór M, Olszewski M, et al. Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli. J Biol Chem. 2017;292:16136-16149 pubmed publisher
    ..We also show that the disulfide bond in DraE is recognized by the DraB chaperone, indicating a mechanism that precludes the incorporation of less stable, non-oxidized DraE forms into the fimbriae. ..
  84. Pang Y. How fast fast-folding proteins fold in silico. Biochem Biophys Res Commun. 2017;492:135-139 pubmed publisher
    ..Then the genetic information that encodes proteins can be better read in the context of intricate biological functions. ..
  85. Sala D, Ciambellotti S, Giachetti A, Turano P, Rosato A. Investigation of the Iron(II) Release Mechanism of Human H-Ferritin as a Function of pH. J Chem Inf Model. 2017;57:2112-2118 pubmed publisher
    ..Double protonation of His residues at pH 4 facilitates the removal of the iron ligands within the C3 channel through the formation of salt bridges, resulting in a significantly lower release energy barrier than pH 9. ..
  86. Yang H, Ouyang Y, Ma H, Cong H, Zhuang C, Lok W, et al. Design and synthesis of novel PRMT1 inhibitors and investigation of their binding preferences using molecular modelling. Bioorg Med Chem Lett. 2017;27:4635-4642 pubmed publisher
    ..Our results show for the first time that PRMT1 inhibitors can target the Asp84 binding site, which will be helpful for future drug discovery studies. ..
  87. Narayanan C, Bafna K, Roux L, Agarwal P, Doucet N. Applications of NMR and computational methodologies to study protein dynamics. Arch Biochem Biophys. 2017;628:71-80 pubmed publisher
  88. Blasco P, Patel D, Engström O, Im W, Widmalm G. Conformational Dynamics of the Lipopolysaccharide from Escherichia coli O91 Revealed by Nuclear Magnetic Resonance Spectroscopy and Molecular Simulations. Biochemistry. 2017;56:3826-3839 pubmed publisher
  89. Cang Z, Wei G. TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions. PLoS Comput Biol. 2017;13:e1005690 pubmed publisher ..
  90. van Dijk M, ter Laak A, Wichard J, Capoferri L, Vermeulen N, Geerke D. Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors. J Chem Inf Model. 2017;57:2294-2308 pubmed publisher
    ..5 kJ mol-1), with good cross-validation statistics. ..
  91. Yao C, Tu Y, Ding L, Li C, Wang J, Fang H, et al. Tumor Cell-Specific Nuclear Targeting of Functionalized Graphene Quantum Dots In Vivo. Bioconjug Chem. 2017;28:2608-2619 pubmed publisher
    ..Our study showed that IFP is a previously unrecognized mechanism for specific targeting of tumor cell nuclei and suggested that sulfonic-GQDs may be developed into novel tools for tumor-specific imaging and therapeutics...
  92. Kong R, Xu L, Piao L, Zhang D, Hou T, Chang S. Exploring the RNA-bound and RNA-free human Argonaute-2 by molecular dynamics simulation method. Chem Biol Drug Des. 2017;90:753-763 pubmed publisher
    ..It is speculated that PAZ domain could be a key regulator in hAgo2-mediated miRNA-induced gene regulation. ..