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PubMed2005

AAA+ proteins: have engine, will work.

The AAA+ (ATPases associated with various cellular activities) family is a large and functionally diverse group of enzymes that are able to induce conformational changes in a wide range of substrate proteins. The family's defining feature is a structurally conserved ATPase domain that assembles into oligomeric rings and undergoes conformational changes during cycles of nucleotide binding and hydrolysis. Here, we review the structural organization of AAA+ proteins, the conformational changes they undergo, the range of different reactions they catalyse, and the diseases associated with their dysfunction.

Adenosine Triphosphatases↗
PubMed2005

A protein folding pathway with multiple folding intermediates at atomic resolution.

Using native-state hydrogen-exchange-directed protein engineering and multidimensional NMR, we determined the high-resolution structure (rms deviation, 1.1 angstroms) for an intermediate of the four-helix bundle protein: Rd-apocytochrome b562. The intermediate has the N-terminal helix and a part of the C-terminal helix unfolded. In earlier studies, we also solved the structures of two other folding intermediates for the same protein: one with the N-terminal helix alone unfolded and the other with a reorganized hydrophobic core. Together, these structures provide a description of a protein folding pathway with multiple intermediates at atomic resolution. The two general features for the intermediates are (i) native-like backbone topology and (ii) nonnative side-chain interactions. These results have implications for important issues in protein folding studies, including large-scale conformation search, -value analysis, and computer simulations.

Biophysical Phenomena↗
PubMed1997

Modified proenzymes as artificial substrates for proteolytic enzymes: colorimetric assay of bacterial collagenase and matrix metalloproteinase activity using modified pro-urokinase.

We describe a new principle for assessment of the activity of proteolytic enzymes of all classes and show the application of this principle for the quantitative assay of bacterial collagenase and human matrix metalloproteinases (MMPs). Central to this new principle is the presence of a proenzyme that can be activated into an active enzyme by a single proteolytic event. The regular activation sequence in the proenzyme is replaced using protein engineering by an artificial sequence recognized by the proteinase to be determined. The latter can act as an activator for the newly engineered proenzyme. In the present paper a simple colorimetric assay for the determination for MMPs is described based on this principle. With the aid of protein engineering, a modified pro-urokinase has been prepared in which the activation sequence normally recognized by plasmin (Pro-Arg-Phe-Lys upward arrowIle-Ile-Gly-Gly) has been replaced by a sequence expected to be recognized and hydrolysed by many MMPs (Arg-Pro-Leu-Gly upward arrowIle-Ile-Gly-Gly). The active urokinase resulting from activation of the modified pro-urokinase by a MMP could be measured either directly, using a specific chromogenic peptide substrate for urokinase, or indirectly via urokinase-catalysed plasminogen activation. The response of the assay to equal molar quantities of active MMPs decreases in the order MMP-2>MMP-9>MMP-1>MMP-3>MMP-7. The detection limit for MMP-9 was below 15 pM, corresponding to 3. 75x10(-15) mol per assay. Using the assay, increased MMP activity was detected in synovial tissue extracts from rheumatoid arthritis patients compared with those from osteoarthritis patients, and in stomach tumour extracts as compared with normal stomach tissue extracts.

Arthritis, Rheumatoid↗
PubMed2006

Engineering of protein thermodynamic, kinetic, and colloidal stability: Chemical Glycosylation with monofunctionally activated glycans.

In this work we establish the relationship between chemical glycosylation and protein thermodynamic, kinetic, and colloidal stability. While there have been reports in the literature that chemical glycosylation modulates protein stability, mechanistic details still remain uncertain. To address this issue, we designed and coupled monofunctional activated glycans (lactose and dextran) to the model protein alpha-chymotrypsin (alpha-CT). This resulted in a series of glycoconjugates with variations in the glycan size and degree of glycosylation. Thermodynamic unfolding, thermal inactivation, and temperature-induced aggregation experiments revealed that chemical glycosylation increased protein thermodynamic (Delta G(25 degrees C)), kinetic (t(1/2)(45 degrees C)), and colloidal stability. These results highlight the potential of chemical glycosylation with monofunctional activated glycans as a technology for increasing the long-term stability of liquid protein formulations for industrial and biotherapeutic applications.

Chemical Engineering↗
PubMed1991

A de novo designed signal peptide cleavage cassette functions in vivo.

Leader peptidase (Lep) is a membrane-bound enzyme of the Escherichia coli inner membrane that serves to remove signal peptides from exported proteins. Statistical and experimental studies of known signal peptides have defined a short C-terminal region that seems to provide the information for correct cleavage by Lep. Based on the patterns of conserved amino acids found in this region, we have designed a signal peptide "cleavage cassette." This cassette is processed at the expected site when introduced after an uncleaved signal peptide. Furthermore, processing is blocked in the predicted manner when the (-3, -1)-rule for signal peptide cleavage is violated. This suggests that current understanding of the sequence requirements for signal peptide cleavage is sufficiently advanced to be used in, e.g. protein engineering applications.

Amino Acid Sequence↗
PubMed1998

Immunoglobulin-cytokine fusion molecules: the new generation of immunomodulating agents.

Advances in the understanding of genetic engineering, protein expression, and Ig function have come together to allow for the rapid synthesis and production of a novel generation of potent immunomodulating reagents. Selective approaches that allow the isolation of desired specificities will be elucidated through meticulous engineering techniques. This, in turn, may eventually result in the fulfillment of the tremendous potential of engineered proteins for therapeutic and diagnostic applications.

Animals↗
PubMed1999

Identification of side-chain clusters in protein structures by a graph spectral method.

This paper presents a novel method to detect side-chain clusters in protein three-dimensional structures using a graph spectral approach. Protein side-chain interactions are represented by a labeled graph in which the nodes of the graph represent the Cbeta atoms and the edges represent the distance between the Cbeta atoms. The distance information and the non-bonded connectivity of the residues are represented in the form of a matrix called the Laplacian matrix. The constructed matrix is diagonalized and clustering information is obtained from the vector components associated with the second lowest eigenvalue and cluster centers are obtained from the vector components associated with the top eigenvalues. The method uses global information for clustering and a single numeric computation is required to detect clusters of interest. The approach has been adopted here to detect a variety of side-chain clusters and identify the residue which makes the largest number of interactions among the residues forming the cluster (cluster centers). Detecting such clusters and cluster centers are important from a protein structure and folding point of view. The crucial residues which are important in the folding pathway as determined by PhiF values (which is a measure of the effect of a mutation on the stability of the transition state of folding) as obtained from protein engineering methods, can be identified from the vector components corresponding to the top eigenvalues. Expanded clusters are detected near the active and binding site of the protein, supporting the nucleation condensation hypothesis for folding. The method is also shown to detect domains in protein structures and conserved side-chain clusters in topologically similar proteins.

Algorithms↗
PubMed1995

Nuclear magnetic resonance characterization of the N-terminal thioredoxin-like domain of protein disulfide isomerase.

A genetically engineered protein consisting of the 120 residues at the N-terminus of human protein disulfide isomerase (PDI) has been characterized by 1H, 13C, and 15N NMR methods. The sequence of this protein is 35% identical to Escherichia coli thioredoxin, and it has been found also to have similar patterns of secondary structure and beta-sheet topology. The results confirm that PDI is a modular, multidomain protein. The last 20 residues of the N-terminal domain of PDI are some of those that are similar to part of the estrogen receptor, yet they appear to be an intrinsic part of the thioredoxin fold. This observation makes it unlikely that any of the segments of PDI with similarities to the estrogen receptor comprise individual domains.

Amino Acid Sequence↗
PubMed2001

Surface characterization of porous, biocompatible protein polymer thin films.

Genetically engineered protein polymer coatings are intended to improve the performance of implantable neural prosthetic devices. To facilitate device integration with tissue, three-dimensionally structured protein polymer films were deposited on the devices using electrostatic atomization and gas-evolution foaming. Periodic features and the length-scale dependence of the surface roughness were identified in topographic data collected using scanning probe microscopy. Using the power spectral density of surface data, the influence of process parameters on the surface roughness of protein polymer thin films was examined. Details of surface topography are known to influence biological behavior, and the method presented was capable of quantifying the evolution of surface features at biologically relevant length scales. This study provides a means for the quantitative exploration of the effects of topography on the performance of these devices and on biocompatibility in general.

Biocompatible Materials↗
PubMed1996

The development of tertiary interactions during the folding of a large protein.

BACKGROUND: We have used protein engineering and relaxation kinetics to examine the order in which secondary structure elements assemble during folding. Aliphatic contacts in the core of a large domain within the monomeric protein phosphoglycerate kinase (PGK) were disrupted in order to map the development of interactions between beta-strand and alpha-helix residues, both near and distant in the sequence. RESULTS: Mutations which break sequence-local alpha-beta contacts destabilize the first identifiable intermediate in folding, showing that these contacts develop early in the folding pathway. In contrast, the removal of sequence-distant alpha-beta interactions has little effect at this stage, but reduces the rate at which the intermediate converts to the native state. Thus, contacts between these remote segments of secondary structure start to form later on in the process, during the rate-limiting transition. CONCLUSIONS: In the case of this large protein domain, our results support the hypothesis that folding proceeds by a hierarchic pathway. Interactions form rapidly between sequence-local groups to produce microdomains before the establishment of the long-range contacts necessary to define the global fold, which proceeds through a highly hydrated transition state.

Circular Dichroism↗
PubMed2000

Mapping protein sequence spaces by recurrence quantification analysis: a case study on chimeric structures.

Recurrence quantification analysis (RQA) was used to characterize the folding properties of 22 chimeric sequences derived from two parent proteins of similar length but different three-dimensional arrangement. A non-linear relation between sequence data and their RQA representation was revealed, which points to new information carried by this method as compared with classical best-alignment methods. This new information is significantly correlated with the folding properties of the hybrid polypeptide chains, as substantiated by careful statistical analysis of the recurrence plots' numerical descriptors, thus encouraging their systematic use to complement sequence data in both proteomics and protein engineering tasks. Even the direct visual screening of the qualitative graphical features of recurrence plots is shown to provide useful hints to discriminate between different recurrence structures of protein sequences.

Amino Acid Sequence↗
PubMed2004

Successful design and synthesis of a polarity-triggered beta-->alpha conformational switch using the side chain interaction index (SCII) as a measure of local structural stability.

Certain sequences within proteins have the ability to undergo an abrupt cooperative conformational switch from beta-strand to helix in response to decreasing polarity of the environment. This behavior was first observed at the CD4 binding site of the envelope glycoprotein gp120 of HIV-1, but evidence has accumulated that polarity-driven beta --> alpha switches may be widespread, serving both to facilitate binding on protein/membrane or protein/protein contact and to signal that docking has occurred. The characteristics identified so far that distinguish switch sequences (a reverse turn at the N-terminus that acts as a helix initiation site, a conserved tryptophan residue downstream, and high potential for both the helix and beta-fold) appear to be necessary but not sufficient, as some otherwise promising sequences found in data bank searches proved not to be capable of cooperative refolding. Analysis of existing switches has led to the development of the side chain interaction index (SCII) as a further parameter characterizing the beta --> alpha polarity-driven switch. Data bank searches using this additional parameter have successfully identified a series of new potential switch sequences. All of them have in common the amino acid tetrad LPCR at the N-terminus and a tryptophan 5-20 residues C-terminal to it. Those with a high SCII as well, when synthesized and tested, exhibited strongly cooperative polarity-driven refolding. Control peptides, containing all other parameters but with a low SCII, did not. Using this new information, an artificial sequence was designed that had a high SCII as well as the initiation site, conserved tryptophan, and high Palpha and Pbeta. When synthesized and tested, this sequence did in fact behave as a conformational switch, refolding cooperatively from beta-fold to helix at a threshold value of 30% TFE. The successful design of a polarity-driven conformational switch opens the possibility of using this motif as a tool in protein engineering.

Adenylyl Cyclases↗
PubMed2005

Role of protein dynamics in reaction rate enhancement by enzymes.

An integrated view of protein structure, dynamics, and function is emerging, where proteins are considered as dynamically active assemblies and internal motions are closely linked to function such as enzyme catalysis. Further, the motion of solvent bound to external regions of protein impacts internal motions and, therefore, protein function. Recently, we discovered a network of protein vibrations in enzyme cyclophilin A, coupled to its catalytic activity of peptidyl-prolyl cis-trans isomerization. Detailed studies suggest that this network, extending from surface regions to active site, is a conserved part of enzyme structure and has a role in promoting catalysis. In this report, theoretical investigations of concerted conformational fluctuations occurring on microsecond and longer time scales within the discovered network are presented. Using a new technique, kinetic energy was added to protein vibrational modes corresponding to conformational fluctuations in the network. The results reveal that protein dynamics promotes catalysis by altering transition state barrier crossing behavior of reaction trajectories. An increase in transmission coefficient and number of productive trajectories with increasing amounts of kinetic energy in vibrational modes is observed. Variations in active site enzyme-substrate interactions near transition state are found to be correlated with barrier recrossings. Simulations also showed that energy transferred from first solvation shell to surface residues impacts catalysis through network fluctuations. The detailed characterization of network presented here indicates that protein dynamics plays a role in rate enhancement by enzymes. Therefore, coupled networks in enzymes have wide implications in understanding allostericity and cooperative effects, as well as protein engineering and drug design.

Binding Sites↗
PubMed2006

Strategy of macromolecular grafting onto a gold substrate dedicated to protein-protein interaction measurements.

Many biotechnology applications use proteins immobilized on surface. For biosensor, the sensing layer is a key component interfacing the transducer and the sample. Strategies employed to activate the bidimensional surface act directly on the performance of the biosensor. In this paper we propose a novel strategy for engineered proteins self-assembly. Our original supramolecular structure allows a direct and fast covalent attachment of proteins onto bare gold substrate through a homobifunctional cross-linker, 1,4-di-([2'-pyridyldithio]propionamido)butane (DPDPB). In this work, engineered proteins and linker-protein complexes were synthesized and characterized by gel electrophoresis, chromatography and spectroscopy experiments. Macromolecular construction "DPDPB-GST tag-GEC1 protein" was conceived in order to guarantee a 2D architecture enhancing the capabilities of the target (tubulin) to recognize its partner (GEC1). Surface plasmon resonance measurements clearly showed potential of this particular self-assembled protein layer compared to a commercial immunosensor interface. At the concentrations tested, the recognition process occurs between tubulin and the immobilized GEC1; moreover enhanced binding was obtained with the home-made 2D sensing layer more than with 3D carboxymethyl dextran matrix.

Biosensing Techniques↗
PubMed2000

Surface grafting onto template-assembled synthetic protein scaffolds in molecular recognition.

Creating functional biological molecules de novo requires a detailed understanding of the intimate relationship between primary sequence, folding mechanism, and packing topology, and remains up to now a most challenging goal in protein design and mimicry. As a consequence, the use of well-defined robust macromolecules as scaffolds for the introduction of function by grafting surface residues has become a major objective in protein engineering and de novo design. In this article, the concept of scaffolds is demonstrated on some selected examples, illustrating that novel types of functional molecules can be generated. Reengineered proteins and, most notably, de novo designed peptide scaffolds exhibiting molecular function, are ideal tools for structure-function studies and as leads in drug design.

Binding Sites↗
PubMed1993

New programs for protein tertiary structure prediction.

Prediction of protein tertiary structure remains an unsolved problem in molecular biology, but a solution to this problem is extremely important for protein engineering and rational drug design. Recent developments in motif recognition and side chain modeling present the prospect of nearly automatic model building for a large fraction of newly determined protein sequences. We review some of these new algorithms and present preliminary results of their application to the prediction of a structure for fasciclin III, a neural adhesion molecule from Drosophila.

Animals↗
PubMed2000

Preliminary study on the cleavage of fusion protein GST-CMIV with palladium(II) complex.

A novel method for post-treatment of gene-engineered proteins is reported. A coden of Cys-His unit is introduced into the N-terminal of cecropin CMIV by using PCR. The gene is expressed in E. coli fused with GST. After purification, the fusion protein is cleaved by [Pd(en)(H2O)2]2+ at the His-Arg bond and the cecropin CMIV with antibacterial activity is obtained. The preliminary results held some promise of success for application of the palladium(II) complex as cleavage agent for the production of peptide drugs from gene-engineering fusion proteins.

Anti-Bacterial Agents↗