Journal Issue - Volume 11 Issue 11 (November 2002)
Structural and nucleotide‐binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function
- Cosmin Saveanu, Simona Miron, Tudor Borza, Constantin T. Craescu, Gilles Labesse, Cristina Gagyi, Aurel Popescu, Francis Schaeffer, Abdelkader Namane, Christine Laurent‐Winter, Octavian Bârzu, Anne‐Marie Gilles
- Published in Wiley Interscience on Dec 31, 2008
- DOI: 10.1110/ps.0217502 (p 2551-2560)
Abstract Structural genomics is a new approach in functional assignment of proteins identified via whole‐genome sequencing programs. Its rationale is that nonhomologous proteins performing similar or related biological functions might have similar tertiary structure. We used dye pseudoaffinity chromatography, two‐dimensional gel electrophoresis, and mass spectrometry to identify two novel Escherichia coli nucleotide‐binding...
Immunochemical pulsed‐labeling characterization of intermediates during hen lysozyme oxidative folding
- Nicole M. Jarrett, Lisa Djavadi‐Ohaniance, Richard C. Willson, Hideki Tachibana, Michel E. Goldberg
- Published in Wiley Interscience on Dec 31, 2008
- DOI: 10.1110/ps.0221802 (p 2584-2595)
Abstract Previous studies have shown that reduced hen egg white lysozyme refolds and oxidizes according to a linear model, in which the number of disulfide bonds increases sequentially. In this study, we describe the kinetics of native tertiary structure formation during the oxidative‐renaturation of reduced hen egg white lysozyme, as monitored using an immunochemical pulsed‐labeling method based on enzyme‐linked immunosorbent assay...
Characterization of the LDL‐A module mutants of Tva, the subgroup A Rous sarcoma virus receptor, and the implications in protein folding
- Qing‐Yin Wang, Balaji Manicassamy, Xuemei Yu, Klavs Dolmer, Peter G.W. Gettins, Lijun Rong
- Published in Wiley Interscience on Dec 31, 2008
- DOI: 10.1110/ps.0219802 (p 2596-2605)
Abstract Tva is the cellular receptor for subgroup A Rous sarcoma virus (RSV‐A), and the viral receptor function is solely determined by a 40‐residue motif called the LDL‐A module of Tva. In this report, an integral approach of molecular, biochemical, and biophysical techniques was used to examine the role of a well‐conserved tryptophan of the LDL‐A module of Tva in protein folding and ligand binding. We show that substitution of...
Molecular dynamics of the FixJ receiver domain: movement of the β4–α4 loop correlates with the in and out flip of Phe101
- Philippe Roche, Liliane Mouawad, David Perahia, Jean‐Pierre Samama, Daniel Kahn
- Published in Wiley Interscience on Dec 31, 2008
- DOI: 10.1110/ps.0218802 (p 2622-2630)
Abstract FixJ is a two‐domain response regulator involved in nitrogen fixation in Sinorhizobium meliloti. Recent X‐ray characterization of both the native (unphosphorylated) and the active (phosphorylated) states of the protein identify conformational changes of the β4–α4 loop and the conserved residue Phe101 as the key switches in activation. These structures also allowed investigation of the transition between conformations of this...
Prediction of the disulfide‐bonding state of cysteines in proteins at 88% accuracy
- Pier Luigi Martelli, Piero Fariselli, Luca Malaguti, Rita Casadio
- Published in Wiley Interscience on Dec 31, 2008
- DOI: 10.1110/ps.0219602 (p 2735-2739)
Abstract The task of predicting the cysteine‐bonding state in proteins starting from the residue chain is addressed by implementing a new hybrid system that combines a neural network and a hidden Markov model (hidden neural network). Training is performed using 4136 cysteine‐containing segments extracted from 969 nonhomologous proteins of well‐resolved three‐dimensional structure. After a 20‐fold cross‐validation procedure, the...
