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Items: 1 to 50 of 103

1.

Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions.

Frenkel-Pinter M, Haynes JW, C M, Petrov AS, Burcar BT, Krishnamurthy R, Hud NV, Leman LJ, Williams LD.

Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16338-16346. doi: 10.1073/pnas.1904849116. Epub 2019 Jul 29.

2.

G-Quadruplexes in Human Ribosomal RNA.

Mestre-Fos S, Penev PI, Suttapitugsakul S, Hu M, Ito C, Petrov AS, Wartell RM, Wu R, Williams LD.

J Mol Biol. 2019 May 3;431(10):1940-1955. doi: 10.1016/j.jmb.2019.03.010. Epub 2019 Mar 15.

PMID:
30885721
3.

Structural Patching Fosters Divergence of Mitochondrial Ribosomes.

Petrov AS, Wood EC, Bernier CR, Norris AM, Brown A, Amunts A.

Mol Biol Evol. 2019 Feb 1;36(2):207-219. doi: 10.1093/molbev/msy221.

4.

Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.

Runnels CM, Lanier KA, Williams JK, Bowman JC, Petrov AS, Hud NV, Williams LD.

J Mol Evol. 2018 Dec;86(9):598-610. doi: 10.1007/s00239-018-9876-2. Epub 2018 Nov 19.

5.

Multiple prebiotic metals mediate translation.

Bray MS, Lenz TK, Haynes JW, Bowman JC, Petrov AS, Reddi AR, Hud NV, Williams LD, Glass JB.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12164-12169. doi: 10.1073/pnas.1803636115. Epub 2018 Nov 9.

6.

Circular Permutation Obscures Universality of a Ribosomal Protein.

Kovacs NA, Penev PI, Venapally A, Petrov AS, Williams LD.

J Mol Evol. 2018 Oct;86(8):581-592. doi: 10.1007/s00239-018-9869-1. Epub 2018 Oct 10.

PMID:
30306205
7.

[Influence of anastomotic leakage on the long-term outcomes in patients with colorectal cancer].

Karachun AM, Petrov AS, Panayotti LL, Ol'kina AY.

Khirurgiia (Mosk). 2018;(8. Vyp. 2):42-46. doi: 10.17116/hirurgia201808242. Review. Russian.

PMID:
30199050
8.

Translation: The Universal Structural Core of Life.

Bernier CR, Petrov AS, Kovacs NA, Penev PI, Williams LD.

Mol Biol Evol. 2018 Aug 1;35(8):2065-2076. doi: 10.1093/molbev/msy101.

9.

Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets.

Gómez Ramos LM, Degtyareva NN, Kovacs NA, Holguin SY, Jiang L, Petrov AS, Biesiada M, Hu MY, Purzycka KJ, Arya DP, Williams LD.

Biochemistry. 2017 Oct 10;56(40):5288-5299. doi: 10.1021/acs.biochem.7b00703. Epub 2017 Sep 26.

PMID:
28895721
10.

Surveying the sequence diversity of model prebiotic peptides by mass spectrometry.

Forsythe JG, Petrov AS, Millar WC, Yu SS, Krishnamurthy R, Grover MA, Hud NV, Fernández FM.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7652-E7659. doi: 10.1073/pnas.1711631114. Epub 2017 Aug 28.

11.

The Central Symbiosis of Molecular Biology: Molecules in Mutualism.

Lanier KA, Petrov AS, Williams LD.

J Mol Evol. 2017 Aug;85(1-2):8-13. doi: 10.1007/s00239-017-9804-x. Epub 2017 Aug 7. Review.

12.

Collision cross section predictions using 2-dimensional molecular descriptors.

Soper-Hopper MT, Petrov AS, Howard JN, Yu SS, Forsythe JG, Grover MA, Fernández FM.

Chem Commun (Camb). 2017 Jul 4;53(54):7624-7627. doi: 10.1039/c7cc04257d.

PMID:
28640293
13.

Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event.

Okafor CD, Lanier KA, Petrov AS, Athavale SS, Bowman JC, Hud NV, Williams LD.

Nucleic Acids Res. 2017 Apr 20;45(7):3634-3642. doi: 10.1093/nar/gkx171.

14.

Frozen in Time: The History of Proteins.

Kovacs NA, Petrov AS, Lanier KA, Williams LD.

Mol Biol Evol. 2017 May 1;34(5):1252-1260. doi: 10.1093/molbev/msx086.

15.

Imprint of Ancient Evolution on rRNA Folding.

Lanier KA, Athavale SS, Petrov AS, Wartell R, Williams LD.

Biochemistry. 2016 Aug 23;55(33):4603-13. doi: 10.1021/acs.biochem.6b00168. Epub 2016 Aug 10.

PMID:
27428664
16.

Ribosomal small subunit domains radiate from a central core.

Gulen B, Petrov AS, Okafor CD, Vander Wood D, O'Neill EB, Hud NV, Williams LD.

Sci Rep. 2016 Feb 15;6:20885. doi: 10.1038/srep20885.

17.

[Modern trends in surgery of gastrointestinal tract tumors].

Belyaev AM, Karachun AM, Petrov AS, Samsonov DV.

Vopr Onkol. 2016;62(2):187-95. Review. Russian.

PMID:
30452193
19.

History of the ribosome and the origin of translation.

Petrov AS, Gulen B, Norris AM, Kovacs NA, Bernier CR, Lanier KA, Fox GE, Harvey SC, Wartell RM, Hud NV, Williams LD.

Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):15396-401. doi: 10.1073/pnas.1509761112. Epub 2015 Nov 30.

20.

Collision cross section calibrants for negative ion mode traveling wave ion mobility-mass spectrometry.

Forsythe JG, Petrov AS, Walker CA, Allen SJ, Pellissier JS, Bush MF, Hud NV, Fernández FM.

Analyst. 2015 Oct 21;140(20):6853-61. doi: 10.1039/c5an00946d.

PMID:
26148962
21.

The ancient heart of the ribosomal large subunit: a response to Caetano-Anolles.

Petrov AS, Williams LD.

J Mol Evol. 2015 Apr;80(3-4):166-70. doi: 10.1007/s00239-015-9678-8. Epub 2015 Apr 16.

PMID:
25877522
22.

[Laparoscopic surgery for rectal cancer: a literature review and own experience].

Karachun AM, Petrova EA, Pelipas YV, Samsonov DV, Petrov AS, Kozlov OA, Sapronov PA.

Vopr Onkol. 2015;61(6):861-6. Review. Russian.

PMID:
26995972
23.

RiboVision suite for visualization and analysis of ribosomes.

Bernier CR, Petrov AS, Waterbury CC, Jett J, Li F, Freil LE, Xiong X, Wang L, Migliozzi BL, Hershkovits E, Xue Y, Hsiao C, Bowman JC, Harvey SC, Grover MA, Wartell ZJ, Williams LD.

Faraday Discuss. 2014;169:195-207. doi: 10.1039/c3fd00126a. Epub 2014 May 28.

PMID:
25340471
24.

[Thoracic endometriosis--the rare pathology in thoracic surgery].

Pichurov AA, Orzheshkovskiĭ OV, Dvorakovskaia IV, Romanova LA, Ivanishchak BE, Karel'skaia EA, Petrun'kin AM, Petrov AS, Atiukov MA, Iablonskiĭ PK.

Vestn Khir Im I I Grek. 2014;173(1):26-9. Russian.

PMID:
25055505
25.

Evolution of the ribosome at atomic resolution.

Petrov AS, Bernier CR, Hsiao C, Norris AM, Kovacs NA, Waterbury CC, Stepanov VG, Harvey SC, Fox GE, Wartell RM, Hud NV, Williams LD.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10251-6. doi: 10.1073/pnas.1407205111. Epub 2014 Jun 30.

26.

Secondary structures of rRNAs from all three domains of life.

Petrov AS, Bernier CR, Gulen B, Waterbury CC, Hershkovits E, Hsiao C, Harvey SC, Hud NV, Fox GE, Wartell RM, Williams LD.

PLoS One. 2014 Feb 5;9(2):e88222. doi: 10.1371/journal.pone.0088222. eCollection 2014.

27.

Secondary structure and domain architecture of the 23S and 5S rRNAs.

Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD.

Nucleic Acids Res. 2013 Aug;41(15):7522-35. doi: 10.1093/nar/gkt513. Epub 2013 Jun 14.

28.

RNA with iron(II) as a cofactor catalyses electron transfer.

Hsiao C, Chou IC, Okafor CD, Bowman JC, O'Neill EB, Athavale SS, Petrov AS, Hud NV, Wartell RM, Harvey SC, Williams LD.

Nat Chem. 2013 Jun;5(6):525-8. doi: 10.1038/nchem.1649. Epub 2013 May 19.

PMID:
23695635
29.

Effects of pulling forces, osmotic pressure, condensing agents and viscosity on the thermodynamics and kinetics of DNA ejection from bacteriophages to bacterial cells: a computational study.

Petrov AS, Douglas SS, Harvey SC.

J Phys Condens Matter. 2013 Mar 20;25(11):115101. doi: 10.1088/0953-8984/25/11/115101. Epub 2013 Feb 12.

30.

Molecular paleontology: a biochemical model of the ancestral ribosome.

Hsiao C, Lenz TK, Peters JK, Fang PY, Schneider DM, Anderson EJ, Preeprem T, Bowman JC, O'Neill EB, Lie L, Athavale SS, Gossett JJ, Trippe C, Murray J, Petrov AS, Wartell RM, Harvey SC, Hud NV, Williams LD.

Nucleic Acids Res. 2013 Mar 1;41(5):3373-85. doi: 10.1093/nar/gkt023. Epub 2013 Jan 25.

31.
32.

RNA-magnesium-protein interactions in large ribosomal subunit.

Petrov AS, Bernier CR, Hsiao C, Okafor CD, Tannenbaum E, Stern J, Gaucher E, Schneider D, Hud NV, Harvey SC, Williams LD.

J Phys Chem B. 2012 Jul 19;116(28):8113-20. doi: 10.1021/jp304723w. Epub 2012 Jul 11.

PMID:
22712611
33.

RNA folding and catalysis mediated by iron (II).

Athavale SS, Petrov AS, Hsiao C, Watkins D, Prickett CD, Gossett JJ, Lie L, Bowman JC, O'Neill E, Bernier CR, Hud NV, Wartell RM, Harvey SC, Williams LD.

PLoS One. 2012;7(5):e38024. doi: 10.1371/journal.pone.0038024. Epub 2012 May 31.

34.

Effect of the observed climate changes and extreme weather phenomena on the emission component of the carbon cycle in different ecosystems of the southern taiga zone.

Kurganova IN, Lopes de Gerenyu VO, Petrov AS, Myakshina TN, Sapronov DV, Ableeva VA, Kudeyarov VN.

Dokl Biol Sci. 2011 Nov-Dec;441:412-6. doi: 10.1134/S0012496611060214. Epub 2012 Jan 7. No abstract available.

PMID:
22227694
35.

Computational approaches to modeling viral structure and assembly.

Harvey SC, Petrov AS, Devkota B, Boz MB.

Methods Enzymol. 2011;487:513-43. doi: 10.1016/B978-0-12-381270-4.00018-4.

PMID:
21187237
36.

Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding.

Petrov AS, Bowman JC, Harvey SC, Williams LD.

RNA. 2011 Feb;17(2):291-7. doi: 10.1261/rna.2390311. Epub 2010 Dec 20.

37.

Role of DNA-DNA interactions on the structure and thermodynamics of bacteriophages Lambda and P4.

Petrov AS, Harvey SC.

J Struct Biol. 2011 Apr;174(1):137-46. doi: 10.1016/j.jsb.2010.11.007. Epub 2010 Nov 11.

38.

Viral assembly: a molecular modeling perspective.

Harvey SC, Petrov AS, Devkota B, Boz MB.

Phys Chem Chem Phys. 2009 Dec 7;11(45):10553-64. doi: 10.1039/b912884k. Epub 2009 Oct 19. Review.

PMID:
20145801
39.

Characterization of DNA conformation inside bacterial viruses.

Petrov AS, Locker CR, Harvey SC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Aug;80(2 Pt 1):021914. Epub 2009 Aug 14.

PMID:
19792158
40.

Structural and electrostatic characterization of pariacoto virus: implications for viral assembly.

Devkota B, Petrov AS, Lemieux S, Boz MB, Tang L, Schneemann A, Johnson JE, Harvey SC.

Biopolymers. 2009 Jul;91(7):530-8. doi: 10.1002/bip.21168.

41.

Integration host factor (IHF) dictates the structure of polyamine-DNA condensates: implications for the role of IHF in the compaction of bacterial chromatin.

Sarkar T, Petrov AS, Vitko JR, Santai CT, Harvey SC, Mukerji I, Hud NV.

Biochemistry. 2009 Feb 3;48(4):667-75. doi: 10.1021/bi8019965.

PMID:
19132923
42.

Packaging double-helical DNA into viral capsids: structures, forces, and energetics.

Petrov AS, Harvey SC.

Biophys J. 2008 Jul;95(2):497-502. doi: 10.1529/biophysj.108.131797. Epub 2008 May 16. Review.

43.

The role of DNA twist in the packaging of viral genomes.

Rollins GC, Petrov AS, Harvey SC.

Biophys J. 2008 Mar 1;94(5):L38-40. doi: 10.1529/biophysj.107.126698. Epub 2008 Jan 11.

44.

The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape.

Petrov AS, Boz MB, Harvey SC.

J Struct Biol. 2007 Nov;160(2):241-8. Epub 2007 Aug 29.

45.

Packaging of DNA by bacteriophage epsilon15: structure, forces, and thermodynamics.

Petrov AS, Lim-Hing K, Harvey SC.

Structure. 2007 Jul;15(7):807-12.

46.

Structural and thermodynamic principles of viral packaging.

Petrov AS, Harvey SC.

Structure. 2007 Jan;15(1):21-7.

47.

[Anticarcinogenic action of dietary supplement pheocarpin and its active component].

Bespalov VG, Aleksandrov VA, Petrov AS.

Vopr Onkol. 2006;52(2):169-74. Russian.

PMID:
17195642
48.

[Experience with continuous epidural anesthesia used in the complex of combined anesthesia at gastropancreatoduodenal surgery].

Obukhov VA, Petrova MM, Obukhova TV, Petrov AS, Nikolaev SV, Fedankov IN.

Anesteziol Reanimatol. 2006 Jul-Aug;(4):27-30. Russian.

PMID:
17061578
49.

[A comparative study of the thermal stability of formate dehydrogenases from microorganisms and plants].

Sadykhov EG, Serov AE, Voĭnova NS, Uglanova SV, Petrov AS, Alekseeva AA, Kleĭmenov SIu, Popov VI, Tishkov VI.

Prikl Biokhim Mikrobiol. 2006 May-Jun;42(3):269-73. Russian.

PMID:
16878540
50.

YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.

Tan RK, Petrov AS, Harvey SC.

J Chem Theory Comput. 2006 May 1;2(3):529-540. Epub 2006 Mar 18.

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