studies of drug resistance and the dynamic behavior of hiv 1 protease through molecular dynamics simulations
Báo cáo khoa học: Molecular basis for substrate recognition and drug ˚ resistance from 1.1 to 1.6 A resolution crystal structures of HIV-1 protease mutants with substrate analogs pptx
... CA-p2 P 212 12 p2-NC P 212 12 p2-NC P 212 12 p2-NC P 212 12 p6pol-PR P 212 12 p6pol-PR P 212 12 p1-p6 P 212 12 p1-p6 P 212 12 57.89 85.96 46 .19 50 1. 54 34 544 6.5 (37 .1) 13 .4 (5.8) 10 1. 54 0 .12 0 .19 19 4 58.00 ... 50 1. 40 44 2 91 10 .1 (45.6) 8.9 (2 .1) 10 1. 40 0 .15 0 .19 18 8 58.02 85.89 46. 61 50 1. 10 95 318 10 .2 (37.7) 10 .4 (2 .1) 10 1. 10 0 .13 0 .17 206 57.80 85.59 46.46 50 1. 30 55 009 7.9 (33.0) 14 .4 (3.2) 10 1. 30 ... 99.2 (93 .1) 90.3 (10 0) 89.2 (96.2) 99.9 (10 0) 0. 010 0.029 0. 011 0.029 0. 015 0.033 0. 013 0.030 0.009 0.029 0. 011 0.0 31 0. 010 0.030 0. 012 0.034 15 .9 21. 9 27.5 31. 5 8.0 12 .2 14 .0 23.7 9.0 13 .7 10 .6...
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Báo cáo y học: " Kinetic studies of HIV-1 and HIV-2 envelope glycoprotein-mediated fusion" potx
... 80 10 0 12 0 14 0 16 0 Time (Min) Figure of Kinetics HIV- 1 and HIV- 2 Env-mediated fusion Kinetics of HIV- 1 and HIV- 2 Env-mediated fusion HIV- 1IIIB (squares), HIV- 2SBL (triangles), and HIV- 2ROD (circles) ... http://www.retrovirology.com/content/3 /1/ 90 Figure Sequence comparison of HIV- 1 and HIV- 2 Envs Sequence comparison of HIV- 1 and HIV- 2 Envs The HIV- 1 subtype B infectious molecular clone HXB2 Env gp 41 sequence (Database ... cells using the following vaccinia recombinants;vPE16, for the IIIB strain of HIV- 1 [39], vvROD, for the ROD strain of HIV- 2 [40], and vSC50 for the SBL/ISY strain of HIV- 2 [ 41] These recombinants...
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Tài liệu Báo cáo khoa học: Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV-1 protease inhibitors docx
... Inhibitor N1-CA1-C1-C2 CA1-C1-C2-N2 C1-C2-N2–CA2 C2-N2–CA2-C3 N1-CA1-C1 CA2-C3-N2 OE RE SE 11 2 56 60 -89 -17 5 -17 3 16 5 -14 8 -14 2 - 21 77 67 14 1 14 8 14 8 Fig 10 Stereoview of the position of inhibitor ... However, the Glu Oe1 and Oe2 in OE and RE overlap and make the same network of hydrogen bonds to the Asp29 S3¢ OE I50 A128 D129 D130 V132 I147 G148 RE SE – 14 – – 2 11 – – 31 18 23 OE R8 D129 G148 G149 ... S1 17 17 OE G27 G48 G49 I50 L123 P1 81 V182 RE SE – 1 5 – – – 17 16 12 S2¢ OE L23 D25 T80 P 81 V82 I84 G127 G149 I150 RE SE – 1 7 26 – 1 – 31 – – 19 from the catalytic aspartates at the bottom of...
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Báo cáo khoa học: Adaptability and flexibility of HIV-1 protease potx
... Fig 2B 1LV1 1LV1 1HWR 1DMP 1QBS 1HVR 1QBR 1QBT 1HWR 1DMP 1QBS 1HVR 1QBR 1QBT 0.00 0.39 0.00 0.37 0.38 0.00 0.34 0.39 0.32 0.00 0.32 0. 41 0.36 0. 31 0.00 0.35 0. 41 0.33 0.33 0.37 0.00 0.35 0. 41 0.34 ... 1HVR, 1QBS, 1DMP, 1QBR and 1QBT) are of complexes between different types of inhibitor molecules and HIV- 1 protease containing the C95A mutation In two of these structures (1DAZ and 1A94), the protein ... plot (A) 1LV1 vs 1G6L (A) 1LV1 vs 1QBS identification of the changes, if any, brought about by inhibitor binding The unliganded and all six of the urea inhibitor complex structures belong to the same...
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Báo cáo y học: " The L76V mutation in HIV-1 protease is potentially associated with hypersusceptibility to protease inhibitors Atazanavir and Saquinavir: is there a clinical advantage" potx
... 219 Q 41L 67N 69E 75I 10 3N 10 8I 11 8I 17 8M 210 W 215 Y 41L 67N 74V 10 1Q 18 4V 215 Y 41L 44D 67N 10 1E 10 3N 11 8I 18 4V 210 W 215 Y 219 E n.d 41L 67ss 69S 10 1Q 18 1C 19 0S 215 Y 65R 70R 10 3N 10 8I 11 5F 15 1M 17 9E ... mutations 41L 44D 67N 98G 10 3N 11 8I 210 F 215 Y 219 R 41L 67ss 69S 18 8L 215 Y 41L 11 8I 18 4V 215 Y 41L 44A 67N 75I 10 3N 10 8I 11 8I 210 W 215 Y 41L 67N 69D 70R 74V 10 3N 18 1C 210 W 215 F 219 Q 67N 70R 10 3NS 19 0A 18 4V ... 17 9E 18 4V 219 E 67N 18 4V 210 W 215 Y 219 Q 41L 44D 67N 75L 11 8I 18 1C 18 4V 19 0A 210 S 215 Y 41L 44D 67N 70R 19 0A 227L 18 4V 210 W 215 F 219 R 41L 67N 74V 98G 11 8I 18 4V 210 W 215 Y 227L 41L 44D 10 3N 11 8I 18 4V...
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Báo cáo "A new formulation for fast calculation of far field force in molecular dynamics simulations " ppt
... approximate the potential field of the original distribution of the particles The difference is that P2 M2 uses the distribution of point charges, while the Anderson’s method uses potential values In the ... order, the charges Qj and the positions Rj = (Rj , θj , φj ) of pseudoparticles must satisfy βm = l 2l + K Qj j =1 Rl +1 j Ylm∗ (θj , φj ) (8) for all (p + 1) combinations of l and m in the range of ... 10 00 200 10 0 10 12 8K N 256K 512 K 1M 2M 4M Number of particles N Figure Comparison of the code A and B Squares are performance of code A on MDGRAPE-2 Circles are that of code B Open and filled symbols...
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Báo cáo y học: " Flexible catalytic site conformations implicated in modulation of HIV-1 protease autoprocessing reactions" pps
... editing 23 References 10 11 12 13 14 15 16 17 18 Loeb DD, Swanstrom R, Everitt L, Manchester M, Stamper SE, Hutchison CA, 3rd: Complete mutagenesis of the HIV- 1 protease Nature 19 89, 340(6232):397-400 ... Conformational analysis of TMC 114 , a novel HIV- 1 protease inhibitor J Chem Inf Model 2008, 48 (1) :99 -10 8 Rose JR, Salto R, Craik CS: Regulation of autoproteolysis of the HIV- 1 and HIV- 2 proteases with ... Antimicrob Agents Chemother 2003, 47 (10 ): 312 3- 312 9 Lefebvre E, Schiffer CA: Resilience to resistance of HIV- 1 protease inhibitors: profile of darunavir AIDS Rev 2008, 10 (3) :13 1 -14 2 Nivesanond K, Peeters...
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Báo cáo y học: "The evolution of HIV-1 reverse transcriptase in route to acquisition of Q151M multi-drug resistance is complex and involves mutations in multiple domains" ppt
... NNRTI E138 Y1 81 V100 F87 V SF 20 I A100 I100 I A100 I100 M230 L I100 A100 I100 A100 I100 Y70 H2 21 N348 N100 10 0 T69 Y100 10 0 I100 I3 L94 I 31 L100 A33 V97 T48 S100 S68 K102 G100 R 61 N100 S123 Other ... 58 .1 ± 14 .2 0.3 218 .9 ± 13 .3 10 0.9 37-RT 219 .7 ± 7.5 25.8 512 0.9 ± 515 .6 30.4 230.9 ± 10 .2 10 6.4 37-Pol 217 .8 ± 18 .1 25.6 2025.3 ± 14 4.2 12 .0 2 31. 5 ± 17 .1 106.7 16 8 .1 ± 6.4 77.5 228.8 ± 6.7 10 5.5 ... V 314 4,332
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Báo cáo khoa học: NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B–NS3 protease ppt
... 4244–4255 ª 2009 The Authors Journal compilation ª 2009 FEBS 4253 NMR analysis of the West Nile virus protease 10 11 12 13 14 15 16 17 18 X.-C Su et al minants of the NS2B cofactor of the West Nile ... NS2B–NS3pro(K96A) and inhibitors and Protons of WNV NS3pro Compound 2a d2 His 51 H Tyr130 Hd Thr132 C!2H3 Thr132 Ha Thr134 C!2H3 Tyr150 Hd Asn152 CbH2 Gly153 HN Val154 C!H3 Ile155 Cd1H3 Tyr1 61 Hd a Compound H1 ... we could not assign the backbone amides of Thr132, NMR analysis of the West Nile virus protease Gly133 and Gly1 51 even in the presence of 1, or 3, and the backbone resonances of neighbouring residues...
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Báo cáo Y học: Modulation of the oligomeric structures of HIV-1 retroviral enzymes by synthetic peptides and small molecules pptx
... HIV- 1 PROTEASE Structure and function of HIV- 1 PR HIV- 1 PR catalyzes the hydrolysis of specific peptide bonds within the HIV- 1 Gag and Gag-Pol polyproteins to generate the various structural and ... assembly of the HIV and HIV proteases Protein Sci 1, 12 44 12 53 19 Franciskovich, J., Houseman, K., Mueller, R & Chmielewski, J (19 93) A systematic evaluation of the inhibition of HIV- 1 protease ... folding in retroviral proteases: crystal structure of a synthetic HIV- 1 protease Science 245, 616 – 6 21 15 Todd, M.J., Semo, N & Freire, E (19 98) The structural stability of the HIV- 1 protease J Mol...
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Molecular dynamics simulations of the tensile and melting behaviours of silicon nanowires
... [30], and in the present simulation the load is along the [11 0] orientation and the resolved shear stress on the (11 1) plane causes the sliding After the formation of the neck, the plastic deformations ... cohesion of the atoms near the surface, as compared with those in the bulk, and the increasing dominance of the surface would decrease the strength of the structure 3.2 The melting properties of the ... [12 ] [13 ] [14 ] [15 ] [16 ] [17 ] [18 ] [19 ] [20] [ 21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [ 31] [32] [33] [34] [35] [36] 689 Y.F Zhang, Y.H Tang, N Wang, et al., Appl Phys Lett 72 (19 98) 18 35...
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the deacons for defense armed resistance and the civil rights movement
... Campaign 10 8 With a Single Bullet 12 9 Victory 15 0 10 Expanding in the Bayou State 16 5 11 Mississippi Chapters 18 4 12 Heading North 216 13 Black Power—Last Days 234 Conclusion: The Myth of Nonviolence ... months of their birth, the Deacons had become the talk of the movement and folk heroes to legions of African Americans in the Deep South The publicity propelled the Deacons into the center of a ... the mean habits of adult society Thomas recalled that sometimes the whites would band together and swoop down on a handful of frolicking blacks, claiming the waters as the spoils of war On other...
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Báo cáo sinh học: " Imperfect DNA mirror repeats in the gag gene of HIV-1 (HXB2) identify key functional domains and coincide with protein structural elements in each of the mature proteins" doc
... 22 21 21 21 21 21 20 19 19 19 19 19 19 19 18 18 18 18 18 18 18 mIMR DNA begin 11 58 13 14 10 87 13 49 74 13 02 17 562 322 478 734 930 10 22 14 04 356 838 11 46 772 11 89 12 53 268 3 61 1238 12 74 990 63 15 9 ... AA 12 61 803 10 8 12 79 300 200 97 14 08 212 226 274 259 11 18 644 11 00 515 11 31 409 918 988 10 51 673 10 66 612 953 12 97 33 733 11 30 21 155 17 0 12 8 346 63 18 4 11 2 15 6 337 38 382 585 667 696 967 10 59 ... 15 9 19 2 305 956 10 60 14 27 468 5 41 886 919 956 13 89 14 61 end mIMR AA begin end Protein function 11 94 13 50 11 22 13 84 10 3 13 29 43 587 346 502 758 954 10 46 14 28 379 8 61 116 9 794 12 11 1274 21 288 381...
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báo cáo hóa học: " Lipopolysaccharide-enhanced transcellular transport of HIV-1 across the blood-brain barrier is mediated by luminal microvessel IL-6 and GM-CSF" potx
... LPS (10 0 µg/mL for hr) added to the luminal chamber significantly increased 13 1 I -HIV- 1 permeability of BMEC monolayers (Fig 1A and 1C) and decreased TEER (Fig 1B and 11 1D) The presence of antibodies ... levels of proinflammatory cytokines/chemokines in the blood of patients with AIDS [12 -14 ] are likely associated with the increase in HIV- 1 infiltration [15 -17 ], while HIV- 1 gp120 and Tat induce the ... infection [9] and penetration of HIV- 1 is independent of the CD4 receptor [10 ] At the early stage, HIV- 1 enters the brain through an intact, normally functioning BBB [11 ] At later stages of infection,...
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báo cáo hóa học:" Substitutions in the Reverse Transcriptase and Protease Genes of HIV-1 Subtype B in Untreated Individuals and Patients Treated With Antiretroviral Drugs" potx
... K70R ( 31. 3) T 215 F (11 .7) V 118 I (25) M184V (76.4) G333A (NA) F77L (0) M41L ( 21. 5) Q151M (3.9) L74V (3.9) E44A/D (5.8) T 215 Y (33.3) V75I (0) L 210 W (25.4) K 219 E (11 .7) E44D (0) K 219 Q (7.8) Q151M (3.9) ... (3.9) T 215 F (11 .7) T 215 Y (33.3) RT (NNRTI) (n = 12 ) V108I (25) Y181C (33.3) G190S (0) P236L (0) Y188C (0) V106A (0) K103N (9.6) Y188H/L (16 .6) M230L (0) P225H (0) L100I (8.3) K103N (8.3) Y188L (9.6) ... absence of Vif, the synthesis of the negative strand of DNA can result in the insertion of a uracil as a result of the deamination of a cytosine, leading to the inclusion of an adenosine instead of...
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báo cáo hóa học:" The HIV-1 Non-subtype B Workgroup: An International Collaboration for the Collection and Analysis of HIV-1 Non-subtype B Data" pot
... 2002, 18 6: 617 -625 Abstract Page of (page number not for citation purposes) Journal of the International AIDS Society 2005, 7: 71 10 11 12 13 14 15 http://www.jiasociety.org/content/7 /1/ 71 Kantor ... non-B HIV- 1 subtypes Currently, the workgroup consists of investigators from 15 sites in 13 countries The goal of the workgroup is to collect and analyze a robust database of sequences and clinical ... analyses of RT and protease sequences from persons infected with nonsubtype B HIV- 1 Program and abstracts of the 10 th Conference on Retroviruses and Opportunistic Infections; February 10 14, 2003;...
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Báo cáo hóa học: "Molecular Dynamics Simulations of the Roller Nanoimprint Process: Adhesion and Other Mechanical Characteristics" pot
... of 0.002° per time step The unit of time step was 10 -15 s The characteristic width and height of the roller tooth were both nm The roller was composed of 11 294 atoms The width and height of the ... doi :10 .11 09/TEPM.2002.807728 M.H Muser, Comput Phys Commun 14 6 (1) , 54 (2002) doi: 10 .10 16/S0 010 -4655(02)00434-4 R Komanduri, N Chandrasekaran, L.M Raff, Phys Rev B 61( 20), 14 007 (19 97) doi :10 .11 03/PhysRevB. 61. 14007 ... Solids 15 3, 235 (20 01) doi :10 .10 80 /10 42 015 010 8 211 842 18 J.M Haile, Molecular Dynamics Simulation: Elementary Methods (Wiley, New York, 19 92) 19 A Ganneapali, S.K Mallapragada, Phys Rev B 66, 10 410 3...
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Báo cáo y học: "Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines" ppsx
... Identification of RANTES, MIP -1 alpha, and MIP -1 beta as the major HIVsuppressive factors produced by CD8+ T cells Science 19 95, 270(5243) :18 11- 1 815 Chitnis CE, Miller LH: Identification of the erythrocyte ... 32 amino acid V3-like peptide of the P vivax RII with the V3 loop of HIV- 1 strain MN To amplify the V3 loop of HIV- 1MN by PCR, PM -1 cells were infected with HIV- 1 MN (donated by Dr James Robinson, ... regions of the env gene of HIV and amplify the region between nucleotides 6884 and 7783, which includes the V3 loop This PCR product then served as template in a nested PCR of the HIV- 1 MN V3...
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Báo cáo khoa học: "Replication and drug resistant mutation of HIV-1 subtype B'''' (Thailand B) variants isolated from HAART treatment individuals in China" pot
... K 219 Q L74V M41L, L74V, T 215 F K65R T69APST M41LM, T 215 Y A62V, K70KN, V75T - T 215 Y K103N, Y181C D67N, K70R, T 215 F, K 219 Q K103N, Y181C V75T V108I, Y181C K103N, Y181C M41L, L74V, T 215 F K101E, Y181C, ... Y181C, G190S K103N, Y181C V108FILV K103N, G190A Y188L G190EV - - G190A V1 V2 R5X4 R5 - V3 V4 V5 V6 V7 V8 V9 V10 V 11 V12 V13 R5X4 R5X4 R5X4 R5X4 R5X4 R5 R5 R5 R5X4 R5X4 R5 T 215 Y D67N, K70R, T 215 F, ... and variants after culture weeks first variants Virus variants tropism fourth variants NRTIs NNRTIs NRTIs NNRTIs K103N K1 01* EKQ, Y181C, G190A K103N, Y181C K103N, Y181C Y181C K103N, Y181C K101E,...
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