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- Rui J. Sousa, Professor;
Ph.D., University of Pittsburgh, 1991.
Telephone: (210) 567-8782 E-mail: sousa@biochem.uthscsa.edu
Conformational mechanisms and dynamics of transcription.
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Telephone: (210) 567-8782 E-mail: sousa@biochem.uthscsa.edu Conformational mechanisms and dynamics of transcription. |
Jiang
J, Maes EG, Taylor AB, Wang L, Hinck AP, Lafer EM, Sousa R.
Structural Basis of J Cochaperone Binding and Regulation of Hsp70.
Mol Cell. 2007 Nov 9;28(3):422-433.
PMID: 17996706
Nayak
D, Guo Q, Sousa R.
Functional architecture of T7 RNA polymerase transcription complexes.
J Mol Biol. 2007 Aug 10;371(2):490-500. Epub 2007 May 31.
PMID: 17580086
Shaner
L, Sousa R, Morano KA.
Characterization of Hsp70 binding and nucleotide exchange by the yeast
Hsp110 chaperone Sse1.
Biochemistry. 2006 Dec 19;45(50):15075-84.
PMID: 17154545
Sousa
R, Lafer EM.
Keep the traffic moving: mechanism of the Hsp70 motor.
Traffic. 2006 Dec;7(12):1596-603. Epub 2006 Oct 6. Review.
PMID: 17026666
Guo
Q, Sousa R.
Translocation by T7 RNA polymerase: a sensitively poised Brownian ratchet.
J Mol Biol. 2006 Apr 21;358(1):241-54. Epub 2006 Feb 14.
PMID: 16516229
Jiang
J, Lafer EM, Sousa R.
Crystallization of a functionally intact Hsc70 chaperone.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Jan 1;62(Pt
1):39-43. Epub 2005 Dec 16.
PMID: 16511258
Jiang
J, Prasad K, Lafer EM, Sousa R.
Structural Basis of Interdomain Communication in the Hsc70 Chaperone.
Mol Cell. 2005 Nov 23;20(4):513-524.
PMID: 16307916
Guo
Q, Nayak D, Brieba LG, Sousa R.
Major conformational changes during T7RNAP transcription initiation
coincide with, and are required for, promoter release.
J Mol Biol. 2005 Oct 21;353(2):256-70.
PMID: 16169559 [PubMed - indexed for MEDLINE]
Guo
Q, Sousa R.
Weakening of the t7 promoter-polymerase interaction facilitates promoter
release.
J Biol Chem. 2005 Apr 15;280(15):14956-61. Epub 2005 Feb 12.
PMID: 15711016
Sousa
R.
Machinations of a maxwellian demon.
Cell. 2005 Jan 28;120(2):155-6.
PMID: 15680319 [PubMed - indexed for MEDLINE]
Guo
Q, Sousa R.
Multiple roles for the T7 promoter nontemplate strand during transcription
initiation and polymerase release.
J Biol Chem. 2005 Feb 4;280(5):3474-82. Epub 2004 Nov 23.
PMID: 15561715 [PubMed - indexed for MEDLINE]
Sousa
R.
On models and methods for studying polymerase translocation.
Methods Enzymol. 2003;371:3-13. No abstract available.
PMID: 14712688 [PubMed - indexed for MEDLINE]
Mukherjee
S, Brieba LG, Sousa R.
Discontinuous movement and conformational change during pausing and
termination by T7 RNA polymerase.
EMBO J. 2003 Dec 15;22(24):6483-93.
PMID: 14657021 [PubMed - indexed for MEDLINE]
Sousa
R, Mukherjee S.
T7 RNA polymerase.
Prog Nucleic Acid Res Mol Biol. 2003;73:1-41. Review. No abstract
available.
PMID: 12882513 [PubMed - indexed for MEDLINE]
Jiang
J, Taylor AB, Prasad K, Ishikawa-Brush Y, Hart PJ, Lafer EM, Sousa R.
Structure-function analysis of the auxilin J-domain reveals an extended
Hsc70 interaction interface.
Biochemistry. 2003 May 20;42(19):5748-53.
PMID: 12741832 [PubMed - indexed for MEDLINE]
Mukherjee
S, Sousa R.
Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular
Reactions.
Biol Proced Online. 2003;5:78-89. Epub 2003 Mar 24.
PMID: 12734553 [PubMed - as supplied by publisher]
Padilla
R, Sousa R.
A Y639F/H784A T7 RNA polymerase double mutant displays superior properties
for synthesizing RNAs with non-canonical NTPs.
Nucleic Acids Res. 2002 Dec 15;30(24):e138.
PMID: 12490729 [PubMed - indexed for MEDLINE]
Mukherjee
S, Brieba LG, Sousa R.
Structural transitions mediating transcription initiation by T7 RNA
polymerase.
Cell. 2002 Jul 12;110(1):81-91.
PMID: 12150999 [PubMed - indexed for MEDLINE]
Brieba
LG, Padilla R, Sousa R.
Role of T7 RNA polymerase His784 in start site selection and initial
transcription.
Biochemistry. 2002 Apr 23;41(16):5144-9.
PMID: 11955062 [PubMed - indexed for MEDLINE]
Sousa
R.
A new level of regulation in transcription elongation? Trends Biochem
Sci. 2001 Dec;26(12):695-7. No abstract available.
PMID: 11738586 [PubMed - indexed for MEDLINE]
Brieba
LG, Sousa R.
T7 promoter release mediated by DNA scrunching.
EMBO J. 2001 Dec 3;20(23):6826-35.
PMID: 11726518 [PubMed - indexed for MEDLINE]
Sousa
R.
T 7 RNA polymerase.
Uirusu. 2001 Jun;51(1):81-94. Review. No abstract available.
PMID: 11565269 [PubMed - indexed for MEDLINE]
Brieba
LG, Sousa R.
The T7 RNA polymerase intercalating hairpin is important for promoter
opening during initiation but not for RNA displacement or transcription
bubble stability during elongation.
Biochemistry. 2001 Apr 3;40(13):3882-90.
PMID: 11300767 [PubMed - indexed for MEDLINE]
Mentesana
PE, Chin-Bow ST, Sousa R, McAllister WT.
Characterization of halted T7 RNA polymerase elongation complexes reveals
multiple factors that contribute to stability.
J Mol Biol. 2000 Oct 6;302(5):1049-62.
PMID: 11183774 [PubMed - indexed for MEDLINE]
Brieba
LG, Gopal V, Sousa R.
Scanning mutagenesis reveals roles for helix n of the bacteriophage
T7 RNA polymerase thumb subdomain in transcription complex stability, pausing,
and termination.
J Biol Chem. 2001 Mar 30;276(13):10306-13. Epub 2000 Dec 21.
PMID: 11124963 [PubMed - indexed for MEDLINE]
Huang
J, Sousa R.
T7 RNA polymerase elongation complex structure and movement.
J Mol Biol. 2000 Oct 27;303(3):347-58.
PMID: 11031112 [PubMed - indexed for MEDLINE]
Huang
J, Brieba LG, Sousa R.
Misincorporation by wild-type and mutant T7 RNA polymerases: identification
of interactions that reduce misincorporation rates by stabilizing the catalytically
incompetent open conformation.
Biochemistry. 2000 Sep 26;39(38):11571-80.
PMID: 10995224 [PubMed - indexed for MEDLINE]
Sousa
R.
Use of T7 RNA polymerase and its mutants for incorporation of nucleoside
analogs into RNA.
Methods Enzymol. 2000;317:65-74. No abstract available.
PMID: 10829272 [PubMed - indexed for MEDLINE]
Brieba
LG, Sousa R.
Roles of histidine 784 and tyrosine 639 in ribose discrimination by
T7 RNA polymerase.
Biochemistry. 2000 Feb 8;39(5):919-23.
PMID: 10653635 [PubMed - indexed for MEDLINE]
Huang
J, Villemain J, Padilla R, Sousa R.
Mechanisms by which T7 lysozyme specifically regulates T7 RNA polymerase
during different phases of transcription.
J Mol Biol. 1999 Oct 29;293(3):457-75.
PMID: 10543943 [PubMed - indexed for MEDLINE]
Gopal
V, Brieba LG, Guajardo R, McAllister WT, Sousa R.
Characterization of structural features important for T7 RNAP elongation
complex stability reveals competing complex conformations and a role for
the non-template strand in RNA displacement.
J Mol Biol. 1999 Jul 9;290(2):411-31.
PMID: 10390341 [PubMed - indexed for MEDLINE]
Guajardo
R, Sousa R.
Characterization of the effects of Escherichia coli replication terminator
protein (Tus) on transcription reveals dynamic nature of the tus block
to transcription complex progression.
Nucleic Acids Res. 1999 Jul 1;27(13):2814-24.
PMID: 10373601 [PubMed - indexed for MEDLINE]
Padilla
R, Sousa R.
Efficient synthesis of nucleic acids heavily modified with non-canonical
ribose 2'-groups using a mutantT7 RNA polymerase (RNAP).
Nucleic Acids Res. 1999 Mar 15;27(6):1561-3.
PMID: 10037823 [PubMed - indexed for MEDLINE]
Villemain
J, Sousa R.
Specificity in transcriptional regulation in the absence of specific
DNA binding sites: the case of T7 lysozyme.
J Mol Biol. 1998 Sep 4;281(5):793-802.
PMID: 9719635 [PubMed - indexed for MEDLINE]
Guajardo
R, Lopez P, Dreyfus M, Sousa R.
NTP concentration effects on initial transcription by T7 RNAP indicate
that translocation occurs through passive sliding and reveal that divergent
promoters have distinct NTP concentration requirements for productive initiation.
J Mol Biol. 1998 Sep 4;281(5):777-92.
PMID: 9719634 [PubMed - indexed for MEDLINE]
Lopez
PJ, Guillerez J, Sousa R, Dreyfus M.
On the mechanism of inhibition of phage T7 RNA polymerase by lac repressor.
J Mol Biol. 1998 Mar 13;276(5):861-75.
PMID: 9566192 [PubMed - indexed for MEDLINE]
Villemain
J, Guajardo R, Sousa R.
Role of open complex instability in kinetic promoter selection by bacteriophage
T7 RNA polymerase.
J Mol Biol. 1997 Nov 14;273(5):958-77.
PMID: 9367784 [PubMed - indexed for MEDLINE]
Huang
Y, Beaudry A, McSwiggen J, Sousa R.
Determinants of ribose specificity in RNA polymerization: effects of
Mn2+ and deoxynucleoside monophosphate incorporation into transcripts.
Biochemistry. 1997 Nov 4;36(44):13718-28.
PMID: 9354643 [PubMed - indexed for MEDLINE]
Huang
Y, Eckstein F, Padilla R, Sousa R.
Mechanism of ribose 2'-group discrimination by an RNA polymerase.
Biochemistry. 1997 Jul 8;36(27):8231-42.
PMID: 9204868 [PubMed - indexed for MEDLINE]
Lopez
PJ, Guillerez J, Sousa R, Dreyfus M.
The low processivity of T7 RNA polymerase over the initially transcribed
sequence can limit productive initiation in vivo.
J Mol Biol. 1997 May 30;269(1):41-51.
PMID: 9192999 [PubMed - indexed for MEDLINE]
Guajardo
R, Sousa R.
A model for the mechanism of polymerase translocation.
J Mol Biol. 1997 Jan 10;265(1):8-19.
PMID: 8995520 [PubMed - indexed for MEDLINE]
Sousa
R.
Structural and mechanistic relationships between nucleic acid polymerases.
Trends Biochem Sci. 1996 May;21(5):186-90. Review.
PMID: 8871404 [PubMed - indexed for MEDLINE]
Makarova
OV, Makarov EM, Sousa R, Dreyfus M.
Transcribing of Escherichia coli genes with mutant T7 RNA polymerases:
stability of lacZ mRNA inversely correlates with polymerase speed.
Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12250-4.
PMID: 8618879 [PubMed - indexed for MEDLINE]
Sousa
R, Padilla R.
A mutant T7 RNA polymerase as a DNA polymerase.
EMBO J. 1995 Sep 15;14(18):4609-21.
PMID: 7556104 [PubMed - indexed for MEDLINE]
Sousa
R, Rose J, Wang BC.
The thumb's knuckle. Flexibility in the thumb subdomain of T7 RNA polymerase
is revealed by the structure of a chimeric T7/T3 RNA polymerase.
J Mol Biol. 1994 Nov 18;244(1):6-12.
PMID: 7966322 [PubMed - indexed for MEDLINE]
Bonner
G, Lafer EM, Sousa R.
Characterization of a set of T7 RNA polymerase active site mutants.
J Biol Chem. 1994 Oct 7;269(40):25120-8.
PMID: 7929200 [PubMed - indexed for MEDLINE]
Bonner
G, Lafer EM, Sousa R.
The thumb subdomain of T7 RNA polymerase functions to stabilize the
ternary complex during processive transcription.
J Biol Chem. 1994 Oct 7;269(40):25129-36.
PMID: 7523379 [PubMed - indexed for MEDLINE]
Sousa
R, Chung YJ, Rose JP, Wang BC.
Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution.
Nature. 1993 Aug 12;364(6438):593-9.
PMID: 7688864 [PubMed - indexed for MEDLINE]
Bonner
G, Patra D, Lafer EM, Sousa R.
Mutations in T7 RNA polymerase that support the proposal for a common
polymerase active site structure.
EMBO J. 1992 Oct;11(10):3767-75.
PMID: 1396570 [PubMed - indexed for MEDLINE]
Zhou
S, Sousa R, Tannery NH, Lafer EM.
Characterization of a novel synapse-specific protein. II. cDNA cloning
and sequence analysis of the F1-20 protein.
J Neurosci. 1992 Jun;12(6):2144-55.
PMID: 1607933 [PubMed - indexed for MEDLINE]
Sousa
R, Tannery NH, Zhou S, Lafer EM.
Characterization of a novel synapse-specific protein. I. Developmental
expression and cellular localization of the F1-20 protein and mRNA.
J Neurosci. 1992 Jun;12(6):2130-43.
PMID: 1607932 [PubMed - indexed for MEDLINE]
Sousa
R, Patra D, Lafer EM.
Model for the mechanism of bacteriophage T7 RNAP transcription initiation
and termination.
J Mol Biol. 1992 Mar 20;224(2):319-34.
PMID: 1560455 [PubMed - indexed for MEDLINE]
Patra
D, Lafer EM, Sousa R.
Isolation and characterization of mutant bacteriophage T7 RNA polymerases.
J Mol Biol. 1992 Mar 20;224(2):307-18.
PMID: 1560454 [PubMed - indexed for MEDLINE]
Sousa
R, Chung YJ, McAllister WT, Wang BC, Lafer EM.
Single crystals of a chimeric T7/T3 RNA polymerase with T3 promoter
specificity and a nonprocessive T7 RNAP mutant.
J Biol Chem. 1990 Dec 15;265(35):21430-2.
PMID: 2254305 [PubMed - indexed for MEDLINE]
Sousa
R, Hrinya Tannery N, Lafer EM.
Two new monoclonal antibodies provide immunohistochemical evidence
for the unique biochemical similarity of the mouse globus pallidus, entopeduncular
nucleus and substantia nigra pars reticulata.
Neuroscience. 1990;34(2):403-10.
PMID: 2333150 [PubMed - indexed for MEDLINE]
Morton
CC, Nussenzweig MC, Sousa R, Sorenson GD, Pettengill OS, Shows TB.
Mapping and characterization of an X-linked processed gene related
to MYCL1.
Genomics. 1989 Apr;4(3):367-75.
PMID: 2541066 [PubMed - indexed for MEDLINE]
Sousa
RJ, Tannery NH, Lafer EM.
In situ hybridization mapping of glucocorticoid receptor messenger
ribonucleic acid in rat brain.
Mol Endocrinol. 1989 Mar;3(3):481-94.
PMID: 2747654 [PubMed - indexed for MEDLINE]
Sousa
R, Rose JP, Chung YJ, Lafer EM, Wang BC.
Single crystals of bacteriophage T7 RNA polymerase.
Proteins. 1989;5(4):266-70.
PMID: 2678097 [PubMed - indexed for MEDLINE]
Lafer
EM, Sousa RJ, Rich A.
Z-DNA-binding proteins in Escherichia coli purification, generation
of monoclonal antibodies and gene isolation.
J Mol Biol. 1988 Sep 20;203(2):511-6.
PMID: 3058987 [PubMed - indexed for MEDLINE]
Lafer
EM, Sousa R, Ali R, Rich A, Stollar BD.
The effect of anti-Z-DNA antibodies on the B-DNA-Z-DNA equilibrium.
J Biol Chem. 1986 May 15;261(14):6438-43.
PMID: 3700399 [PubMed - indexed for MEDLINE]
Lafer
EM, Sousa R, Rich A.
Anti-Z-DNA antibody binding can stabilize Z-DNA in relaxed and linear
plasmids under physiological conditions.
EMBO J. 1985 Dec 30;4(13B):3655-60.
PMID: 4092691 [PubMed - indexed for MEDLINE]
Lafer
EM, Sousa R, Rosen B, Hsu A, Rich A.
Isolation and characterization of Z-DNA binding proteins from wheat
germ.
Biochemistry. 1985 Sep 10;24(19):5070-6.
PMID: 4074677 [PubMed - indexed for MEDLINE]