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Some Macromolecular Mechanisms previously studied by the members of our group

Intermolecular Mechanisms


The mechanism of single-stranded DNA-binding protein recognition by DNA polymerase III

Naue et al., (2011) Nucleic Acids Res. 39(4), 1398-1407



 

Design and optimization of a protein nanomachine for biohybrid devices

 

Amrute-Nayak et al., (2010) Angew. Chem. Int. Ed. 49, 312-316.



The mechanism of pentabromopseudilin inhibition of myosin motor activity

 


Fedorov et al., (2009)  Nature Struct. & Mol. Biol. 16, 80-88.
Protein Data Bank accession codes: 2JJ9, 2JHR



The mechanism of higher assembly of ssDNA-binding proteins in complex with ssDNA

Witte et al., (2008) Biophys. J., 94(6), 2269-2279.



The mechanism of tRNA binding to the translation initiation factor 2

 Nikonov et al., (2007) J. Mol. Biol. 373(2), 328-336.
Protein Data Bank accession codes: 2PLF and 2PMD



Mechanism of biological assembly in ssDNA-binding proteins



Fedorov et al., (2006) Nucleic Acids Res 34, 6708-6717.
Protein Data Bank accession codes: 2IHE and 2IHF



Molecular mechanism of actomyosin-based motility

Geeves et al., (2005) CMLS, Cell. Mol. Life Sci. 62, 1462-1477.



Specific inhibition of human Nitric Oxide Synthase targeting the tetrahydrobiopterin binding site

Matter et al., (2005) J. Med. Chem., 48(15), 4783-4792.
Protein Data Bank accession codes: 1ZVI and 1ZVL



Rational basis for isoform specificity and inhibition of Nitric Oxide Synthases

Fedorov et al., (2004) PNAS  101, 5892-5897.
Protein Data Bank accession codes: 1VAG and 1VAF



Conformational flexibility of the active site of Nitric Oxide Synthases as a source of specific inhibition

Fedorov et al., (2003) J. Biol. Chem. 278, 45818-45825.
Protein Data Bank accession codes: 1QW6, 1QWC, 1QW4 and 1QW5



The mechanisms of 23S rRNA and mRNA binding to the ribosomal protein L1

Our L1 structure on the front-page of Science
Our L1 structure played an important role in interpreting the electron density of protuberance area of the 50S ribosomal subunit in the Nobel Prize winning work of Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A. “The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution.” (2000) Science 289 (5481), 905-920.

Nevskaya et al., (2002) Acta Cryst. D58, 1023-1029.
Nevskaya et al., (2000) Structure with Folding & Design. 8(4), 363-371.
Protein Data Bank accession codes: 1CJS and 1DWU

 

Mechanism of specific protein-rRNA recognition within ribosome

Fedorov et al., (2001) Acta Cryst. D57, 968-976.
Protein Data Bank accession code: 1FEU


Interaction mechanism of Ypt/Rab proteins
 

Rak et al., (2000) The EMBO Journal 19(19), 5105-5113.
Protein Data Bank accession code: 1FKM

 

Intramolecular Mechanisms


Molecular mechanism of translation initiation factor 2

Stolboushkina et al., (2008) J. Mol. Biol. 382, 680-691.
Protein Data Bank accession code: 3CW2


Mechanism of a light-induced signaling  switch Phot-LOV1

Fedorov et al., (2003) Biophysical J. 84, 2474-2482.
Domratcheva et al., (2006) J. Chem. Theory Comput. 2(6), 1565 – 1574.
Protein Data Bank accession codes: 1N9L, 1N9N, 1N9O


Irreversible Photoreduction of Flavin in Phot-LOV1 Photoreceptor

Kottke et al., (2003) Biochemistry 42, 9854-9862.


Molecular mechanisms of ribosomal protein L30

Fedorov et al., (1999). Acta Cryst. D55, 1827-1833.
Protein Data Bank accession code: 1BXY