Academic literature on the topic 'Triosephosphate Isomerase Barrel'

Background.Amyloid secondary structure relies on the intermolecular assembly of polypeptide chains through main-chain interaction. According to this, all proteins have the potential to form amyloid structure, nevertheless, in nature only few proteins aggregate into toxic or functional amyloids. Structural characteristics differ greatly among amyloid proteins reported, so it has been difficult to link the fibrillogenic propensity with structural topology. However, there are ubiquitous topologies not represented in the amyloidome that could be considered as amyloid-resistant attributable to structural features, such is the case of TIM barrel topology.Methods.This work was aimed to study the fibrillogenic propensity of human triosephosphate isomerase (HsTPI) as a model of TIM barrels. In order to do so, aggregation of HsTPI was evaluated under native-like and destabilizing conditions. Fibrillogenic regions were identified by bioinformatics approaches, protein fragmentation and peptide aggregation.Results.We identified four fibrillogenic regions in the HsTPI corresponding to theβ3,β6,β7y α8 of the TIM barrel. From these, theβ3-strand region (residues 59–66) was highly fibrillogenic. In aggregation assays, HsTPI under native-like conditions led to amorphous assemblies while under partially denaturing conditions (urea 3.2 M) formed more structured aggregates. This slightly structured aggregates exhibited residual cross-βstructure, as demonstrated by the recognition of the WO1 antibody and ATR-FTIR analysis.Discussion.Despite the fibrillogenic regions present in HsTPI, the enzyme maintained under native-favoring conditions displayed low fibrillogenic propensity. This amyloid-resistance can be attributed to the three-dimensional arrangement of the protein, whereβ-strands, susceptible to aggregation, are protected in the core of the molecule. Destabilization of the protein structure may expose inner regions promotingβ-aggregation, as well as the formation of hydrophobic disordered aggregates. Being this last pathway kinetically favored over the thermodynamically more stable fibril aggregation pathway.

Triosephosphate isomerase (TIM), a central enzyme in the glycolytic pathway, has been the subject of extensive structural and mechanistic investigations over the past 30 years. The TIM barrel is the prototype of the (β/α)8 barrel fold, which is one of the most extensively used structural motifs in enzymes. Mechanistic studies on TIM from a variety of sources have emphasized the importance of loop 6 dynamics for enzyme activity. Several conserved residues in TIM have been investigated by extensive site-directed mutagenesis of the enzyme from yeast, chicken, and trypanosoma. The cloning and sequencing of the TIM gene from the malarial parasite Plasmodium falciparum in 1993 revealed the unexpected mutation of a hitherto conserved residue serine (S96) to phenylalanine (F96). Subsequent results from the genome sequencing programs of Plasmodium falciparum, Plasmodium vivax, and Plasmodium yoelii confirmed the presence of the S96F mutation in malarial parasites. The crystal structure of PfTIM and several inhibitor complexes, including a high-resolution (1.1 Å) structure of the PfTIM 2-phosphoglycerate complex, revealed that loop 6 had a propensity to remain open, even in several ligand bound structures. Furthermore, both open and closed forms could be characterized for the same complex. Since glycolysis is the primary source of ATP for the malarial parasite during the intraerythrocytic stage, glycolytic enzymes present themselves as potential targets for inhibitors. Two distinct approaches have been explored. The use of dimer interface peptides, which interfere with assembly, has proved promising. Inactivation of the enzyme by modification of a cysteine (C13) residue, which lies close to the active site residue, lysine (K12) is another potential strategy. The differential reactivity, of the four-cysteine residues, at positions 13, 126, 196, and 217 in each subunit has been established using electrospray ionization mass spectrometry. Studies of single tryptophan mutants (W11F and W168F) of PfTIM provide a probe to study folding, stability, and inhibitor interactions.

ABSTRACTThe β-1,4-endoglucanase (EC 3.2.1.4) from the hyperthermophilic archaeonPyrococcus horikoshii(EGPh) has strong hydrolyzing activity toward crystalline cellulose. When EGPh is used in combination with β-glucosidase (EC 3.2.1.21), cellulose is completely hydrolyzed to glucose at high temperature, suggesting great potential for EGPh in bioethanol industrial applications. The crystal structure of EGPh shows a triosephosphate isomerase (TIM) (β/α)8-barrel fold with an N-terminal antiparallel β-sheet at the opposite side of the active site and a very short C-terminal sequence outside of the barrel structure. We describe here the function of the peripheral sequences outside of the TIM barrel core structure. Sequential deletions were performed from both N and C termini. The activity, thermostability, and pH stability of the expressed mutants were assessed and compared to the wild-type EGPh enzyme. Our results demonstrate that the TIM barrel core is essential for enzyme activity and that the N-terminal β-sheet is critical for enzyme thermostability. Bioinformatics analyses identified potential key residues which may contribute to enzyme hyperthermostability.

Equilibrium folding of rat liver BHMT (betaine–homocysteine methyltransferase), a TIM (triosephosphate isomerase)-barrel tetrameric protein, has been studied using urea as denaturant. A combination of activity measurements, tryptophan fluorescence, CD and sedimentation-velocity studies suggested a multiphasic process including two intermediates, a tetramer (I4) and a monomer (J). Analysis of denaturation curves for single- and six-tryptophan mutants indicated that the main changes leading to the tetrameric intermediate are related to alterations in the helix α4 of the barrel, as well as in the dimerization arm. Further dissociation to intermediate J included changes in the loop connecting the C-terminal α-helix of contact between dimers, disruption of helix α4, and initial alterations in helix α7 of the barrel, as well as in the dimerization arm. Evolution of the monomeric intermediate continued through additional perturbations in helix α7 of the barrel and the C-terminal loop. Our data highlight the essential role of the C-terminal helix in dimer–dimer binding through its contribution to the increased stability shown by BHMT as compared with other TIM barrel proteins. The results are discussed in the light of the high sequence conservation shown by betaine–homocysteine methyltransferases and the knowledge available for other TIM-barrel proteins.

Triosephosphate isomerase (TIM) barrel proteins have not only a conserved architecture that supports a myriad of enzymatic functions, but also a conserved folding mechanism that involves on- and off-pathway intermediates. Although experiments have proven to be invaluable in defining the folding free-energy surface, they provide only a limited understanding of the structures of the partially folded states that appear during folding. Coarse-grained simulations employing native centric models are capable of sampling the entire energy landscape of TIM barrels and offer the possibility of a molecular-level understanding of the readout from sequence to structure. We have combined sequence-sensitive native centric simulations with small-angle X-ray scattering and time-resolved Förster resonance energy transfer to monitor the formation of structure in an intermediate in the Sulfolobus solfataricus indole-3-glycerol phosphate synthase TIM barrel that appears within 50 μs and must at least partially unfold to achieve productive folding. Simulations reveal the presence of a major and 2 minor folding channels not detected in experiments. Frustration in folding, i.e., backtracking in native contacts, is observed in the major channel at the initial stage of folding, as well as late in folding in a minor channel before the appearance of the native conformation. Similarities in global and pairwise dimensions of the early intermediate, the formation of structure in the central region that spreads progressively toward each terminus, and a similar rate-limiting step in the closing of the β-barrel underscore the value of combining simulation and experiment to unravel complex folding mechanisms at the molecular level.

N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) toN-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host–pathogen interactions. In this study, atomic resolution structures of NanA fromFusobacterium nucleatum(FnNanA) in ligand-free and ligand-bound forms are reported at 2.32 and 1.76 Å resolution, respectively. F. nucleatumis a Gram-negative pathogen that causes gingival and periodontal diseases in human hosts. Like other bacterialN-acetylneuraminate lyases, FnNanA also shares the triosephosphate isomerase (TIM)-barrel fold. As observed in other homologous enzymes, FnNanA forms a tetramer. In order to characterize the structure–function relationship, the steady-state kinetic parameters of the enzyme are also reported.

ABSTRACT Three catabolic enzymes, UlaD, UlaE, and UlaF, are involved in a pathway leading to fermentation of l-ascorbate under anaerobic conditions. UlaD catalyzes a β-keto acid decarboxylation reaction to produce l-xylulose-5-phosphate, which undergoes successive epimerization reactions with UlaE (l-xylulose-5-phosphate 3-epimerase) and UlaF (l-ribulose-5-phosphate 4-epimerase), yielding d-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway. We describe here crystallographic studies of UlaE from Escherichia coli O157:H7 that complete the structural characterization of this pathway. UlaE has a triosephosphate isomerase (TIM) barrel fold and forms dimers. The active site is located at the C-terminal ends of the parallel β-strands. The enzyme binds Zn2+, which is coordinated by Glu155, Asp185, His211, and Glu251. We identified a phosphate-binding site formed by residues from the β1/α1 loop and α3′ helix in the N-terminal region. This site differs from the well-characterized phosphate-binding motif found in several TIM barrel superfamilies that is located at strands β7 and β8. The intrinsic flexibility of the active site region is reflected by two different conformations of loops forming part of the substrate-binding site. Based on computational docking of the l-xylulose 5-phosphate substrate to UlaE and structural similarities of the active site of this enzyme to the active sites of other epimerases, a metal-dependent epimerization mechanism for UlaE is proposed, and Glu155 and Glu251 are implicated as catalytic residues. Mutation and activity measurements for structurally equivalent residues in related epimerases supported this mechanistic proposal.

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

Hydrogenases use complex metal cofactors to catalyze the reversible formation of hydrogen. In [FeFe]-hydrogenases, the H-cluster cofactor includes a diiron subcluster containing azadithiolate, three CO, and two CN− ligands. During the assembly of the H cluster, the radical S-adenosyl methionine (SAM) enzyme HydG lyses the substrate tyrosine to yield the diatomic ligands. These diatomic products form an enzyme-bound Fe(CO)x(CN)y synthon that serves as a precursor for eventual H-cluster assembly. To further elucidate the mechanism of this complex reaction, we report the crystal structure and EPR analysis of HydG. At one end of the HydG (βα)8 triosephosphate isomerase (TIM) barrel, a canonical [4Fe-4S] cluster binds SAM in close proximity to the proposed tyrosine binding site. At the opposite end of the active-site cavity, the structure reveals the auxiliary Fe-S cluster in two states: one monomer contains a [4Fe-5S] cluster, and the other monomer contains a [5Fe-5S] cluster consisting of a [4Fe-4S] cubane bridged by a μ2-sulfide ion to a mononuclear Fe2+ center. This fifth iron is held in place by a single highly conserved protein-derived ligand: histidine 265. EPR analysis confirms the presence of the [5Fe-5S] cluster, which on incubation with cyanide, undergoes loss of the labile iron to yield a [4Fe-4S] cluster. We hypothesize that the labile iron of the [5Fe-5S] cluster is the site of Fe(CO)x(CN)y synthon formation and that the limited bonding between this iron and HydG may facilitate transfer of the intact synthon to its cognate acceptor for subsequent H-cluster assembly.

Xylanases (EC 3.2.1.8) are glycosyl hydrolases that catalyze the hydrolysis of internal β-1,4 glycosidic bonds of xylan backbones, and have potential economical and environment friendly applications in the paper pulp, food, animal feed, detergent industries, bio-ethanol and bio-energy production systems. A xylanase from Bacillus sp. NG-27 (BSX), which is an extracellular endoxylanase, belonging to glycosyl hydrolase family 10 (GH10), shows optimum activity at a temperature of 70 °C and at a pH 8.5. It has a (β/α)8-triosephosphate isomerase (TIM) barrel fold, which has been studied concerning its function, structural properties, design and evolution. BSX, apart from thermo-alkalophilic features, shows resistance to SDS denaturation and protease K degradation. Hence, BSX serves as an important model system for fundamental understanding of the structure-stability-evolution relations of the ubiquitous TIM barrel fold. While the factors responsible for the thermal stability of GH10 xylanases have been analyzed, the improvement of thermostability of already thermostable enzymes is an important challenge. In general, there are large differences in optimal temperature (Tm) between hyperthermostable proteins with respect to their mesophilic homologs, indicating considerable scope available for introducing novel protein engineering approaches to improve protein stability. Thermostability and thermotolerance are of particular importance for industrial enzymes, because higher operating temperatures allow higher reactivity, higher bioavailability, higher process yield, lower viscosity, and reducing the risk of contamination. Thus, finding enzymes that can function at high temperatures has immense industrial importance and constitutes an active area of research. Earlier studies on enzymatic activity and thermostability of a recombinant BSX (RBSX) with different extreme N-terminus mutants by biochemical/biophysical methods showed that a single amino acid substitution (Val1→Leu) markedly enhanced the thermostability of recombinant xylanase from 70 °C to 75 °C without compromising its catalytic activity and showed higher cooperativity in the thermal unfolding transition. Conversely, substitution of Val1→Ala (V1A) at the same position decreased the stability of the protein from 70 °C to 68 °C. Furthermore, it was observed that substitution of Phe4 by Ala decreased the stability by ~4 °C whereas substitution of Trp6→Ala and Tyr343→Ala decreased the stability by ~10 °C with respect to RBSX. On the other hand, substitution of Phe4 by another aromatic residue Trp (F4W) did not change the stability and activity of RBSX. However, structural details were not available at that time, precluding any structure-based rationalization of stability changes resulting from a single amino acid substitution. The thesis reports the crystal structures of a recombinant xylanase from Bacillus sp. NG-27 (RBSX) and its various N-terminal and C-terminal mutants namely V1A, V1L, F4A, F4W, W6A, and Y343A. The crystal structure of RBSX (PDB ID: 4QCE) was solved at a resolution of 2.35 Å whereas those of V1A mutant (PDB ID: 4QCF) and V1L mutant (PDB ID: 4QDM) were solved at a resolution of 2.26 Å and 1.99 Å respectively. On the other hand, the crystal structure of F4A was solved at a resolution of 2.23 Å whereas F4W, W6A, and Y343A mutants were solved at a resolution of 2.22 Å, 1.67 Å, and 2.30 Å respectively. The availability of experimentally determined RBSX structure and its various mutant structures has enabled a critical examination including from a network perspective, of factors influencing thermal stability. The crystal structures in combination with computational analysis have provided valuable insights into the structural features that govern protein thermostability. The thesis candidate established a link between N-terminal to C-terminal contacts and RBSX thermostability. The study reveals that augmenting N-terminal to C-terminal noncovalent interactions is associated with enhancement of the stability of the enzyme. Perhaps, for the first time, the study provides a network perspective of N-terminal to C-terminal interactions and shows that the stabilizing interactions are not restricted to terminal regions but propagate to different parts of the protein structure. Furthermore, analysis of structures of different aromatic mutants of RBSX and structural bioinformatics studies were combined to understand the role of long-range aromatic cluster in the form of 'aromatic-clique' in the thermal stabilization of proteins. The results highlight an additional source of stability in thermophilic proteins, which could arise due to the prevalence of aromatic-cliques. In addition, the work exemplifies the experimental evidence specifically through long-range aromatic clique, in reiterating the role of interactions between N- and C-termini in protein stabilization. The thesis candidate demonstrated the experimental evidence depicting the role of partially solvent exposed tryptophan residues in shielding a surface pocket, which influenced the solvation of backbone atoms and stability of the RBSX enzyme. The candidate carried out a comprehensive database analysis of available crystal structures to look into the possible role of partially exposed tryptophan in hyperthermophilic proteins. The study provides strong evidence that partially exposed tryptophan side-chain is recruited in hyperthermophilic proteins for occluding potential surface pockets, to provide backbone solvent shielding and local stabilization. The overall structure of this thesis is further explained through a chapter wise description below: Chapter 1 | An introduction and outline of the thesis This chapter starts with a general introduction about the diversity of microorganisms and their ability to thrive in extreme environments such as high temperature. The research on these enterprising organisms offers not just the insights into the resilience of life on earth or possibilities of life elsewhere in the universe but also can provide exciting opportunities for a variety of industrial, environmental, biomedical, and pharmaceutical applications. While the adaptation of the cell inventory is important, it is a challenge for proteins to overcome high temperature in order to remain folded in the correct three-dimensional structure while maintaining adequate flexibility for their desired function. Hence, elucidation of the molecular basis of protein stability at extreme temperature continues to attract researcher over a board range of disciplines. The various structural features responsible for protein stability are outlined and the basic structural and molecular strategies for the adaptation to high temperatures revealed by structure analysis are delineated. Of all potentially deactivating factors of protein stability, temperature is the best studied. A brief outline of the strategies and approaches for the design of proteins to meet the desirable properties such as increased thermal stability are presented whereas the structural features responsible for stability of triosephosphate isomerase (TIM)-barrel fold is outlined under a separate section. Subsequently a short introduction of family 10 (GH10) xylanases, which has the ubiquitous TIM-barrel fold and their classifications are presented. A section is dedicated to describe various thermostable GH10 xylanases, their structural features responsible for stability, and current and potential biotechnological applications. At the end, the scope of the present work is detailed. Chapter 2| Crystallization, Data Collection and Data processing of recombinant BSX (RBSX) and its different variants: Chapter 2 presents the purification of recombinant xylanase from Bacillus sp. NG-27 (RBSX), its N-terminal variants (V1A, V1L), and aromatic variants (F4W, F4A, W6A, and Y343A). The expression and purification of RBSX and its variants were carried out at the laboratory of our collaborator Prof. V. S. Reddy, Plant Transformation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India. Initial crystallization trials were screened by hanging drop vapor diffusion method and micro-batch diffusion method using crystallization-screening kits (Crystal Screen and Crystal Screen 2) from Hampton Research, USA and a laboratory made screen, which was based on reported crystallization condition of native BSX. After a few rounds of trials and optimization of the crystallization condition, diffraction quality rod shaped crystals of recombinant BSX (RBSX) were obtained within ten days, when 2-µl protein solution (10 g/ml) was mixed with 2-µl reservoir solution composed of 0.12 M MgCl2, 0.1 M NaCl, 0.1M Tris-HCl pH 8.5 and 15% PEG 8000. Subsequently, crystal was used for X-ray data collection and it diffracted X-rays to better than 2.2 Å at the home source at cryo-temperature (100 K). RBSX crystals belong to orthorhombic space group P212121 with unit cell parameters a = 54.77 Å, b = 75.65 Å, c = 179.91 Å and α = β = γ =90°. A three-dimensional screening grid was prepared based on crystallization condition of RBSX by carefully varying salt concentration (NaCl and MgCl2 from 10mM to 300mM in the interval of 10mM), different PEG variants (PEG 1000, PEG 3350, PEG 4000, PEG 8000, and PEG 10000) in the range of 5% to 20%. Tris-HCl buffer of pH 8.0 and of pH 8.5 was used in the concentration range of 0.05M and 0.1M respectively. Rod shaped crystals were obtained using hanging drop vapor diffusion method from the condition of 0.1M NaCl, 80mM MgCl2, 0.05M Tris-HCl pH 8.5 and 18 % PEG 8000 and 0.1M NaCl, 60mM MgCl2, 0.1M Tris-HCl pH 8.5 and 16 % PEG 8000 for V1L mutant and V1A mutant respectively. The diffracting crystals of F4A mutant were obtained from the condition of 0.1M NaCl, 140mM MgCl2, 0.05M Tris-HCl pH 8.5 and 15% PEG 8000 by using hanging drop vapor diffusion method. On the other hand, F4W and Y343A, crystals were grown by micro-batch diffusion method containing 1.1-μ1 ratio of protein and crystallization solution of 0.1M NaCl, 120mM MgCl2, 0.1M Tris-HCl pH 8.5 and 18% PEG 8000 and 0.1M NaCl, 150mM MgCl2, 0.1M Tris-HCl pH 8.5 and 15 % PEG 6000 respectively . W6A mutant crystals were grown by hanging drop vapor diffusion method of 0.1M NaCl, 160mM MgCl2, 0.05M Tris-HCl pH 8.5 and 20% PEG 8000. All the crystals were obtained at 20 °C-22 °C in 5-10 days, and were used for diffraction experiments (details in the table below). Table 1 Protein Space a b c α β γ X-ray source PDB group (Å) (Å) (Å) (°) (°) (°) ID RBSX P212121 54.77 75.65 176.91 90 90 90 Home-source 4QCE V1A C2 73.57 80.12 69.90 90 110.81 90 Home-source 4QCF V1L P212121 54.88 76.58 176.73 90 90 90 Synchrotron 4QDM F4W P212121 55.27 77.32 176.75 90 90 90 Home- source 5EB8 F4A P212121 52.62 67.71 181.54 90 90 90 Home- source 5EFF W6A P212121 54.99 76.60 181.54 90 90 90 Synchrotron 5EFD Y343A C2 73.86 80.11 69.21 90 111.19 90 Home- source 5EBA The quality of all dataset was assessed by SFCHECK. The data sets were found appropriate and useful for structure determination as discussed in Chapter 3. Chapter 3 | Molecular Replacement, Model Building, Refinement, validation of recombinant xylanase (RBSX), and different mutant structures: Chapter 3 details the application of molecular replacement method to the structure solution of RBSX structure, N-terminal and aromatic mutants of RBSX, the course of iterative model building and the refinement carried out and the quality of the final protein structure models. The structure solution for all the structures was obtained by the molecular replacement (MR) method with the program PHASER-MR in the PHENIX package using a search model of native-enzyme (2F8Q). The asymmetric unit of RBSX, V1L, F4A, F4W, W6A crystals was expected to contain two molecules whereas V1A and Y343A crystal was expected to contain one molecule as indicated by Matthews’s coefficient calculation. The final round of refinement was carried out with restrained refinement with TLS parameters for all the structures. The most essential refinement statistics of the final model of RBSX, V1A, and V1L mutant structures are given in Table 2 whereas the same for aromatic mutant structures, F4A, F4W, W6A, and Y343A are given in Table 3. Table 2 Refinement Statistics RBSX V1A V1L Resolution (Å) 27.7-2.32 26.8-2.26 40.2-1.96 Rwork / Rfree (%) 17.9/22.7 17.4/22.5 15.2/19.0 Average B-factors (Å2) Protein 21.6 26.3 13.9 Ligand/ion 15.6 26.4 18.74 Water 20.6 27.2 23.2 RMSD Bond distance (Å) 0.007 0.005 0.019 Bond angles (◦) 1.123 0.955 1.802 Luzzati coordinate 0.279 0.269 0.175 error (Å) Working set Table 3 Refinement Statistics F4A F4W W6A Y343A Resolution (Å) 18.15-2.23 18.97-2.22 32.1-1.67 34.03-2.30 Rwork / Rfree (%) 17.8/24.0 16.8/21.0 15.68/18.58 17.8/23.0 Average B-factors (Å2) Protein 13.1 19.5 16.7 26.8 Ligand/ion 14.2 20.0 21.4 26.1 Water 11.5 28.9 25.9 30.7 RMSD Bond distance (Å) 0.0144 0.0088 0.0139 0.0063 Bond angles (◦) 1.593 1.228 1.5995 1.0951 Luzzati coordinate 0.261 0.252 0.176 0.293 error (Å) Working set Chapter 4 | Mutations at the extreme N-terminus modulate thermostability of RBSX: Implications of interactions between termini for stability This chapter details the structural analysis of RBSX and its various extreme N-terminus mutations in relation to their different thermostability scale. Although several factors have been attributed to thermostability, the stabilization strategies used by proteins are still enigmatic. Studies on a RBSX, which has the ubiquitous (β/α)8-TIM (Triosephosphate isomerase) barrel fold showed that just a single mutation, Valine1→Leucine (V1L), though not part of any secondary structural element, markedly enhanced the stability from 70 °C to 75 °C without loss of catalytic activity. Conversely, substitution of Valine1→Alanine (V1A) at the same position decreased the stability of the enzyme from 70 °C to 68 °C. To gain structural insights as to how a single extreme N-terminus mutation can markedly influence the thermostability of the enzyme, the candidate has determined the crystal structure of RBSX and two mutants. Based on computational analysis of their crystal structures including residue interaction network, a link was established between N- to C-terminal contacts and RBSX thermostability. The study reveals that augmenting N- to C-terminal non-covalent interactions is associated with the enhancement of the stability of the enzyme. Perhaps, for the first time, the study provides a network perspective of N-terminal to C-terminal interactions and shows that the stabilizing interactions are not restricted to terminal regions but propagate to different parts of the protein structure. In addition, several lines of evidence were discussed that point to support the structural coupling between the chain termini and implications of stability changes in different proteins. It is proposed that the strategy of mutations at the termini could be exploited with a view to modulate stability without compromising on enzymatic activity, or in general, protein function, in diverse folds where N- and C-termini are in close proximity. Chapter 5 | Role of long-range aromatic cluster in the structural stability of RBSX Chapter 5 describes the different aromatic mutant crystal structures of RBSX namely F4W, F4A, W6A, and Y343A and the structural comparison with the RBSX crystal structure. Systematic studies of different alanine mutations (F4A, W6A, and Y343A) to disrupt this aromatic cluster showed that substitution of Phe4, Trp6, and Y343 by alanine drastically decreased the stability of recombinant BSX (RBSX). It was observed that substitution of Phe4 by Ala (F4A) decreased the RBSX stability by ~5 °C whereas substitutions of Trp6 by Ala (W6A) and Tyr343 by Ala (Y343A) markedly decreased the stability of the enzyme by ~10 °C. On the other hand, substitution of Phe4 by Trp (F4W) did not result any change in its thermal unfolding pattern of the enzyme. We observed that the mutated amino acid residues (Phe4, Trp6, and Tyr343) in the RBSX structure are part of an ‘aromatic-clique’. An aromatic-clique is defined as a cluster of aromatic residues in which each residue interacts with all other residues within the cluster through aromatic interactions. The study reveals that the decreased stability shown by F4A, W6A, and Y343A mutants resulted from cumulative effects in the loss of aromatic interactions and disruption of aromatic-clique, and reduced van der Waal interactions. In addition, the work exemplifies the importance of interactions between N-terminal and C-terminal through aromatic contacts or packing in folding and stability of the TIM-barrel fold protein. The structure based multiple sequence alignment of RBSX with other GH10 xylanase from Bacillus organisms revealed that aromatic-clique of interest is fully conserved in B. halodurans (BHX) and Bacillus firmus (BFX) xylanases, which are thermostable in nature, like RBSX. On the other hand, this aromatic-clique is not conserved in the GH10 xylanases from Bacillus N137, Bacillus alcalophilus, which are reported as thermo-labile in nature. Furthermore, analysis of available crystal structures of different thermostable xylanases from GH10 family showed the prevalence of aromatic-clique that may be playing a critical role in their structure-stability and folding. Lastly, a comprehensive analysis of homologous pairs of proteins from (hyper)thermophilic and mesophilic organisms was carried out and observed the high occurrence of aromatic-cliques in the thermophilic proteins in comparison to their mesophilic homologs. These results highlight an additional source of stability in thermophilic proteins, which can arise due to the prevalence of aromatic-cliques. The findings reported in the thesis provide important lessons for engineering xylanases for industrial applications. The strategy of mutations based on clustering of aromatic pairs in the form of ‘aromatic-clique’ may be effectively applied to other enzymes and provides new insights for engineers to design proteins for biotechnological applications. Chapter 6 | Tryptophan occludes surface pocket: Implications for protein stability Chapter 6 describes the structural feature of a partially exposed tryptophan residue, which effectively occludes a surface pocket and plays a critical role in RBSX thermo-stabilization. As a part our long-standing interest in the structural analysis of thermostable proteins, it was observed that just a single mutation, W6A of a recombinant xylanase (RBSX) from Bacillus sp. NG-27 decreased the stability from 70 °C to 60 °C. To gain structural insights into how a single mutation W6A can remarkably influence the thermostability of the enzyme, we determined the crystal structure of W6A mutant and compared the same with the crystal structure of RBSX. We serendipitously observed that substitution of Trp6 by alanine (W6A) in the protein results a small surface pocket, which was shielded by the bulky side-chain of Trp6 in the native structure. Inspection of the molecular structure of native protein structure revealed that side chain of Trp6 occludes the surface pocket, sterically impeding entry of solvent molecules including water. We demonstrated the experimental evidence depicting how a partially exposed tryptophan, which was shielding a surface pocket (tryptophan-shield), can directly influence the backbone solvation, and modulate the stability of the enzyme. Furthermore, computational analysis of high-resolution structures of hyperthermophilic proteins reveals that bulky and aromatic indole side-chain of tryptophan effectively occludes surface pockets in several hyperthermophilic proteins. The study provides a strong evidence that partially exposed tryptophan side-chain is recruited in hyperthermophilic proteins for occluding potential surface pockets to provide backbone solvent shielding and local stabilization. Chapter 7 | Summary and future direction Chapter 7 summaries the important findings of the present study from the crystal structure and computational analysis of a recombinant xylanase (RBSX) and its various N-terminal and C-terminal mutants and also outlines the future direction of the work. Appendix A details SFCHECK output for the processed data for all the structures reported in the thesis. Appendix B Reprints of the publications