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| BioNMR of peptides and proteins |
Design and characterization of Trp-cage miniproteins
| | Trp-cage miniproteins are the smallest known proteins with a stable fold wthout disulfides. Our goal is to map the key residue-residue contacts
responsible for its stability designing variants and investigating them by NMR- and CD-spectroscopy. Our findings show that the 9-16 salt bridge is
integrated into the cooperativity network of the molecule rather than being an isolated stabilizing factor.
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| | A Trp-cage miniprotein with key stabilizing residues highlighted
| Cooperation: Dr. Gábor Tóth, Department of Medicinal Chemistry,
University of Szeged, Hungary
Selected publications
Petra Rovó, Viktor Farkas, Orsolya Hegyi, Orsolya Szolomájer-Csikós, Gábor K. Tóth, András Perczel:
Cooperativity network of Trp-cage miniproteins: probing salt-bridges.
J. Pept. Sci. (2011), in press
[abstract]
Péter Hudáky, Pál Stráner, Viktor Farkas, Györgyi Váradi, Gábor Tóth, András Perczel:
Cooperation between a salt bridge and the hydrophobic core triggers fold stabilization in a Trp-cage miniprotein
Biochemistry (2008) 47:1007-1016.
[abstract]
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Characterization of intrinsically disordered proteins and their interactions
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Calpastatin is a functionally disordered inhibitor of the intracellular calcium-regulated cysteine protease calpain. Using chemnical shift mapping and relaxation studies we have shown that the functional segments of calpastatin exhibit characteristic local structural preferences with reduced mobility. Calpain binding is tripartite with flexible linkers between the contact point allowing high speed and specificity of target binding.
The plant dehydrin ERD14 is a functionally disordered stress protein expressed during dehydration. Chemical shift and relaxation analysis revealed that this 185 residue long protein is fully disordered under native conditions with short regions of slight helical propensity, suggested to correspond to preformed structural elements indispensable for biological function.
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| | Summary of NMR analysis of the intrinsic flexibility of calpastatin
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Cooperation: Dr. Péter Tompa, Laboratory of Intrinsically Disordered Proteins,
Institute of Enzymology, Budapest
Selected publications
Róbert Kiss, Zoltán Bozóky, Dénes Kovács, Gergely Róna, Péter Friedrich, Péter Dvortsák, Rudinger Weisemann, Péter Tompa, András Perczel:
Calcium-induced tripartite binding of intrinsically disordered calpastatin to its cognate enzyme, calpain
FEBS Lett. (2008) 582:2149-2154.
[abstract]
Róbert Kiss, Dénes Kovács, Péter Tompa, András Perczel:
Local structural preferences of calpastatin, the intrinsically unstructured protein inhibitor of calpain
Biochemistry (2008) 47:6936-6945.
[abstract]
Bianka Szalainé-Ágoston, Dénes Kov&aaciute;cs, Pér Tompa, András Perczel:
Full backbone assignment and dynamics of the intrinsically disordered dehydrin ERD14
Biomol. NMR Assign. (2011), in press
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Structure, dynamics and activiy of small serine protease inhibitors
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SGCI (Schistocerca gregaria chymotrypsin inhibitor) and SGTI
(Sch. gregaria trypsin inhibitor) are small, 35-residue
peptides isolated from the desert locust, Schistocerca
gregaria. Both are highly flexible on he picosecond-nanosecond time scale with
S2 values around 0.7. Conformational ensembles reflecting the fast time-scale dynamics
of these canonical inhibitors include structures highly similar to he enzyme-bound state. Thus, rather than being
classic examples of the rigid lock-and-key mechanism as widely accepted, these inhibitors rather exhibit
nanosecond-timescale conformer selection.
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| Scheme of nanosecond-timescale conformational selection in SGCI
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Cooperation: Prof. László Gráf, Department of Biochemistry,
Eötvös Loránd University, Budapest
Selected publications
Zoltán Gáspári, Péter Várnai, Balázs Szappanos, András Perczel:
Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action
FEBS Lett., (2010) 584:203-206.
[abstract]
Zoltán Gáspári, Borbála Szenthe, András Patthy, William M. Westler, László Gráf and András Perczel:
Local binding with globally distributed changes in a small protease inhibitor upon enzyme binding
FEBS J. (2006) 273:1831-1842.
[abstract]
Borbála Szenthe, Zoltán Gáspári, Attila Nagy, András Perczel and László Gráf:
Same fold with different mobility: backbone dynamics of small protease inhibitors from the desert locust, Schistocerca gregaria
Biochemistry, (2004) 43(12): 3376-3384.
[abstract]
Structures determined
SGCI: [1KGM]
SGCI[L30K, K31M]: [1KIO]
SGTI: [1KJ0]
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Generation and analysis of dynamic structural ensembles
| Internal dynamics is an intrinsic property of all proteins and is a key determinant of biological function.
To analyze states accessible during the internal fluctuations, dynamic structural ensembles, i.e. conformer sets representing the experimentally determined dynamics up to a given time scale can be generated. Such ensembles represent novel models of protein structures and need to be analyzed differently than conventional single-structure models. We have set up a web server capable of analyzing such ensembles as a whole and have also shown that even basic structural features such as solvent accessibilty of residues etc. may vary considerably between members of such ensembles.
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| | Scheme of the CoNSEnsX approach for the analysis of dynamic structural ensembles
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Cooperation: Sándor Pongor, Protein Structure and Bioinformatics Group,
ICGEB Trieste, Italy
Selected publications
Annamária F. Ángyán, Balázs Szappanos, András Perczel, Zoltán Gáspári:
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data
BMC Strut. Biol. (2010) 10:39
[abstract]
[full text]
Zoltán Gáspári, Annamária F. Ángyán, Somdutta Dhir, Dino Franklin, András Perczel, Alessandro Pintar, Sándor Pongor:
Probing dynamic protein ensembles with atomic proximity measures
Curr. Prot. Pept. Sci. (2010) 11:512-522.
[abstract]
The CCP1-CCP2 module pair of human C1r
| C1r, the first protease of the classical pathway of the complement system, is a modular protein containing, among others, two CCP (complement control protein) modules and a serine protease (SP) domain at the C-terminus. The inter- and intramodular flexibility of the CCP modules s proposed to play a central role in the autoactivation of this modular protease. Our NMR studies on the single CCP2 and the tandem CCP1-CCP2 constructs revealed that the CCP2 module has a well-folded structure in solution whereas the CCP1 module is much less-defined and more flexible. We showed that the CCP2 module stabilizes the CCP1 module through a well defined interface. Our results suggest that the CCP1 module and not the intermodular interface is the key flexible element of the region studied.
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| | Interaction surfaces of CCP1 and CCP2 of human C1r
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Cooperation: Dr. Péter Závodszky and Dr. Péter Gál, Structural Biophysics Group,
Institute of Enzymology, Budapest
Publications
András Láng, Katalin Szilágyi, Balázs Major, Péter Gál,
Péter Závodszky and András Perczel:
Intermodule cooperativity in the structure and dynamics of consecutive complement control modules in human C1r: structural biology.
FEBS J. (2010) 277:3986-3998.
[abstract]
András Láng, Balázs Major, Katalin Szilágyi, Zoltán Gáspári, Péter Gál, Péter Závodszky, András Perczel:
Interaction between separated consecutive complement control modules of human C1r: implications for dimerization of the full-length protease.
FEBS Lett. (2010) 584:4565-4569.
[abstract]
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| Location and mode of myosin binding of the Dynein Light Chain
A 10 kD dynein light chain (DLC) has been previously shown to bind to the tail of myosin Va (myo5a). It is assumed that DLC functions as a cargo-binding and/or regulatory subunit of both motor proteins.
NMR spectroscopy together with molecular docking simulations suggests that a short synthetic peptide of DBD binds to the surface grooves on DLC2, similarly to other known binding partners of DLCs. We hypothesize that DLC2 brings together the two DBDs of the myoVa heavy chains in an asymmetric manner, leaving one of the binding sites of the DLC2 dimer free to interact with a cargo or regulatory proteins.
Cooperation: Dr. László Nyitray, Department of Biochemistry,
Eötvös Loránd University, Budapest
Publications
Zsuzsa Hódi, Attila Németh, László Radnai, Csaba Hetényi, Katalin Schlett, Andrea Bodor, András Perczel, and László Nyitray:
Alternatively spliced exon B of myosin Va is essential for binding the tail-associated light chain shared by dynein
Biochemistry (2006) 45:12582-12595.
[abstract]
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