Structural and time-resolved mechanistic investigations of protein hydrolysis by the acidic proline-specific endoprotease from Aspergillus niger

Proline-specific endoproteases have been successfully used in, for example, the in-situ degradation of gluten, the hydrolysis of bitter peptides, the reduction of haze during beer production, and the generation of peptides for mass spectroscopy and proteomics applications. Here we present the crystal structure of the extracellular proline-specific endoprotease from Aspergillus niger (AnPEP), a member of the S28 peptidase family with rarely observed true proline-specific endoprotease activity. Family S28 proteases have a conventional Ser-Asp-His catalytic triad, but their oxyanion-stabilizing hole shows a glutamic acid, an amino acid not previously observed in this role. Since these enzymes have an acidic pH optimum, the presence of a glutamic acid in the oxyanion hole may confine their activity to an acidic pH. Yet, considering the presence of the conventional catalytic triad, it is remarkable that the A. niger enzyme remains active down to pH 1.5. The determination of the primary cleavage site of cytochrome c along with molecular dynamics-assisted docking studies indicate that the active site pocket of AnPEP can accommodate a reverse turn of approximately 12 amino acids with proline at the S1 specificity pocket. Comparison with the structures of two S28-proline-specific exopeptidases reveals not only a more spacious active site cavity but also the absence of any putative binding sites for amino- and carboxyl-terminal residues as observed in the exopeptidases, explaining AnPEP's observed endoprotease activity.

Neural underpinnings of freezing-related dynamic balance control in people with Parkinson's disease

INTRODUCTION

People with Parkinson's disease (PD) with freezing of gait (FOG; freezers) show impaired dynamic balance and experience falls more frequently compared to those without (non-freezers). Here, we explore the neural underpinnings of these freezing-related balance problems.

METHODS

12 freezers, 16 non-freezers and 14 controls performed a dynamic balance task in the lab. The next day, the same task was investigated in the MRI-scanner through motor imagery (MI). A visual imagery (VI) control task was also performed. Imagery engagement was determined by comparing the performance times between the dynamic balance task, and its MI- and VI-variants. Balance-related brain activations in regions of interest were contrasted between groups based on an MI > rest versus VI > rest contrast.

RESULTS

Freezers and non-freezers were matched for age, cognition and disease severity. Similar performance times between the balance control task and the MI-conditions revealed excellent imagery engagement. Compared to non-freezers, freezers showed decreased activation in regions of interest located in the left mesencephalic locomotor region (MLR; p = 0.006), right anterior cerebellum (p = 0.017) and cerebellar vermis (p < 0.001). Intriguingly, non-freezers showed higher activations in the cerebellar vermis than controls (p = 0.010).

CONCLUSION

Overall, we showed that decreased activation in the left MLR, and cerebellar regions in freezers relative to non-freezers could explain why dynamic balance is more affected in freezers. As non-freezers displayed increased cerebellar vermis activation compared to controls, it is possible that freezers show an inability to recruit sufficient compensatory cerebellar activity for effective dynamic balance control.

The Effect of a Multidisciplinary Blended Learning Program on Palliative Care Knowledge for Health Care Professionals Involved in the Care for People with Parkinson's Disease

BACKGROUND

Parkinson's disease (PD) is an increasingly prevalent and progressive degenerative disease. Palliative care for PD should be integrated into the routine care for people with PD. However, PD health care professionals typically lack knowledge of palliative care, highlighting the necessity of educational programs in this field.

OBJECTIVE

To determine the effectiveness of a multidisciplinary blended learning program for health care professionals specialized in PD in the Netherlands.

METHODS

We used a pre-posttest intervention design. The intervention consisted of an e-learning in combination with an online network meeting in which the participating health care professionals discussed palliative care for PD with specialists from the field of palliative care. Outcome variables included self-rated level of knowledge (scale 1-10), familiarity with specialized palliative care services (5-point Likert scale) and the validated End-of-Life Professional Caregiver Survey (EPCS).

RESULTS

A total of 1029 participants from sixteen different disciplines, all active in the care for people with PD, with a mean age of 45 years and 13 years of working experience, followed the blended learning program. Self-rated level of knowledge improved from 4.75 to 5.72 (0.96; p < 0.001; 95% CI change = [0.85 . . . 1.08]. Familiarity with palliative care services also increased by 1.06 (from 1.85 to 2.90; p=<0.001; 95% CI change = [1.00 . . . 1.12]).

CONCLUSION

A blended learning program can improve self-rated knowledge about palliative care and its services. Such programs might be a first step towards optimal integration of palliative care expertise and services within PD-care.

The Role of Tryptophan in π Interactions in Proteins: An Experimental Approach

In proteins, the amino acids Phe, Tyr, and especially Trp are frequently involved in π interactions such as π–π, cation−π, and CH−π bonds. These interactions are often crucial for protein structure and protein–ligand binding. A powerful means to study these interactions is progressive fluorination of these aromatic residues to modulate the electrostatic component of the interaction. However, to date no protein expression platform is available to produce milligram amounts of proteins labeled with such fluorinated amino acids. Here, we present a Lactococcus lactis Trp auxotroph-based expression system for efficient incorporation (≥95%) of mono-, di-, tri-, and tetrafluorinated, as well as a methylated Trp analog. As a model protein we have chosen LmrR, a dimeric multidrug transcriptional repressor protein from L. lactis. LmrR binds aromatic drugs, like daunomycin and riboflavin, between Trp96 and Trp96′ in the dimer interface. Progressive fluorination of Trp96 decreased the affinity for the drugs 6- to 70-fold, clearly establishing the importance of electrostatic π–π interactions for drug binding. Presteady state kinetic data of the LmrR–drug interaction support the enthalpic nature of the interaction, while high resolution crystal structures of the labeled protein–drug complexes provide for the first time a structural view of the progressive fluorination approach. The L. lactis expression system was also used to study the role of Trp68 in the binding of riboflavin by the membrane-bound riboflavin transport protein RibU from L. lactis. Progressive fluorination of Trp68 revealed a strong electrostatic component that contributed 15–20% to the total riboflavin-RibU binding energy.

Impaired Weight-Shift Amplitude in People with Parkinson's Disease with Freezing of Gait

BACKGROUND

People with Parkinson's disease and freezing of gait (FOG; freezers) suffer from pronounced postural instability. However, the relationship between these phenomena remains unclear and has mostly been tested in paradigms requiring step generation.

OBJECTIVE

To determine if freezing-related dynamic balance deficits are present during a task without stepping and determine the influence of dopaminergic medication on dynamic balance control.

METHODS

Twenty-two freezers, 16 non-freezers, and 20 healthy age-matched controls performed mediolateral weight-shifts at increasing frequencies when following a visual target projected on a screen (MELBA task). The amplitude and phase shift differences between center of mass and target motion were measured. Balance scores (Mini-BESTest), 360° turning speed and the freezing ratio were also measured. Subjects with Parkinson's disease were tested ON and partial OFF (overnight withdrawal) dopaminergic medication.

RESULTS

Freezers had comparable turning speed and balance scores to non-freezers and took more levodopa. Freezers produced hypokinetic weight-shift amplitudes throughout the MELBA task compared to non-freezers (p = 0.002), which were already present at task onset (p < 0.001). Freezers also displayed an earlier weight-shift breakdown than controls when OFF-medication (p = 0.008). Medication improved mediolateral weight-shifting in freezers and non-freezers. Freezers decreased their freezing ratio in response to medication.

CONCLUSION

Hypokinetic weight-shifting proved a marked postural control deficit in freezers, while balance scores and turning speed were similar to non-freezers. Both weight-shift amplitudes and the freezing ratio were responsive to medication in freezers, suggesting axial motor vigor is levodopa-responsive. Future work needs to test whether weight-shifting and freezing severity can be further ameliorated through training.

Application of microbial 3-ketosteroid Δ1-dehydrogenases in biotechnology

3-Ketosteroid Δ¹-dehydrogenase catalyzes the 1(2)-dehydrogenation of 3-ketosteroid substrates using flavin adenine dinucleotide as a cofactor. The enzyme plays a crucial role in microbial steroid degradation, both under aerobic and anaerobic conditions, by initiating the opening of the steroid nucleus. Indeed, many microorganisms are known to possess one or more 3-ketosteroid Δ¹-dehydrogenases. In the pharmaceutical industry, 3-ketosteroid Δ¹-dehydrogenase activity is exploited to produce Δ¹-3-ketosteroids, a class of steroids that display various biological activities. Many of them are used as active pharmaceutical ingredients in drug products, or as key precursors to produce pharmaceutically important steroids. Since 3-ketosteroid Δ¹-dehydrogenase activity requires electron acceptors, among other considerations, Δ¹-3-ketosteroid production has been industrially implemented using whole-cell fermentation with growing or metabolically active resting cells, in which the electron acceptors are available, rather than using the isolated enzyme. In this review we discuss biotechnological applications of microbial 3-ketosteroid Δ¹-dehydrogenases, covering commonly used steroid-1(2)-dehydrogenating microorganisms, the bioprocess for preparing Δ¹-3-ketosteroids, genetic engineering of 3-ketosteroid Δ¹-dehydrogenases and related genes for constructing new, productive industrial strains, and microbial fermentation strategies for enhancing the product yield. Furthermore, we also highlight the recent development in the use of isolated 3-ketosteroid Δ¹-dehydrogenases combined with a FAD cofactor regeneration system. Finally, in a somewhat different context, we summarize the role of 3-ketosteroid Δ¹-dehydrogenase in cholesterol degradation by Mycobacterium tuberculosis and other mycobacteria. Because the enzyme is essential for the pathogenicity of these organisms, it may be a potential target for drug development to combat mycobacterial infections.

Thalamic morphology predicts the onset of freezing of gait in Parkinson's disease

The onset of freezing of gait (FOG) in Parkinson's disease (PD) is a critical milestone, marked by a higher risk of falls and reduced quality of life. FOG is associated with alterations in subcortical neural circuits, yet no study has assessed whether subcortical morphology can predict the onset of clinical FOG. In this prospective multimodal neuroimaging cohort study, we performed vertex-based analysis of grey matter morphology in fifty-seven individuals with PD at study entry and two years later. We also explored the behavioral correlates and resting-state functional connectivity related to these local volume differences. At study entry, we found that freezers (N = 12) and persons who developed FOG during the course of the study (converters) (N = 9) showed local inflations in bilateral thalamus in contrast to persons who did not (non-converters) (N = 36). Longitudinally, converters (N = 7) also showed local inflation in the left thalamus, as compared to non-converters (N = 36). A model including sex, daily levodopa equivalent dose, and local thalamic inflation predicted conversion with good accuracy (AUC: 0.87, sensitivity: 88.9%, specificity: 77.8%). Exploratory analyses showed that local thalamic inflations were associated with larger medial thalamic sub-nuclei volumes and better cognitive performance. Resting-state analyses further revealed that converters had stronger thalamo-cortical coupling with limbic and cognitive regions pre-conversion, with a marked reduction in coupling over the two years. Finally, validation using the PPMI cohort suggested FOG-specific non-linear evolution of thalamic local volume. These findings provide markers of, and deeper insights into conversion to FOG, which may foster earlier intervention and better mobility for persons with PD.

Relationship of Agaricus bisporus mannose-binding protein to lectins with β-trefoil fold

Agaricus bisporus mannose-binding protein (Abmb) was discovered as part of the mushroom tyrosinase (PPO3) complex, but its function in the mushroom has remained obscure. The protein has a β-trefoil structure that is common for Ricin-B-like lectins. Indeed, its closest structural homologs are the hemagglutinin components of botulinum toxin (HA-33) and the Ricin-B-like lectin from Clitocybe nebularis (CNL), both of which bind galactose, and actinohivin, a recently discovered mannose-binding lectin from actinomycetes. Here we show that Abmb is evolutionarily related to them, which are lectins with a β-trefoil fold. We also show for the first time that Abmb can exhibit typical lectin agglutination activity but only when in the complex with mushroom tyrosinase. This is unexpected and unique because the two proteins are not evolutionarily related and have different activities. Lectin and tyrosinase major role in defense mechanism as well as Abmb and PPO3 gene regulation during the early stages of the development of mushroom fruiting bodies suggested that Abmb has likely a function in defense against bacterial infection and/or insect-induced damage.

Functional neuroimaging of human postural control: A systematic review with meta-analysis

Postural instability is a strong risk factor for falls that becomes more prominent with aging. To facilitate treatment and prevention of falls in an aging society, a thorough understanding of the neural networks underlying postural control is warranted. Here, we present a systematic review of the functional neuroimaging literature of studies measuring posture-related neural activity in healthy subjects. Study methods were overall heterogeneous. Eleven out of the 14 studies relied on postural simulation in a supine position (e.g. motor imagery). The key nodes of human postural control involved the brainstem, cerebellum, basal ganglia, thalamus and several cortical regions. An activation likelihood estimation meta-analysis revealed that the anterior cerebellum was consistently activated across the wide range of postural tasks. The cerebellum is known to modulate the brainstem nuclei involved in the control of posture. Hence, this systematic review with meta-analysis provides insight into the neural correlates which underpin human postural control and which may serve as a reference for future neural network and region of interest analyses.

The New Freezing of Gait Questionnaire: Unsuitable as an Outcome in Clinical Trials?

BACKGROUND

Freezing of gait (FOG) is a common gait deficit in Parkinson's disease. The New Freezing of Gait Questionnaire (NFOG-Q) is a widely used and valid tool to quantify freezing of gait severity. However, its test-retest reliability and minimal detectable change remain unknown.

OBJECTIVE

To determine the test-retest reliability and responsiveness of the NFOG-Q.

METHODS

Two groups of freezers, involved in 2 previous rehabilitation trials, completed the NFOG-Q at 2 time points (T1 and T2), separated by a 6-week control period without active intervention. Sample 1 (N = 57) was measured in ON and sample 2 (N = 14) in OFF. We calculated various reliability statistics for the NFOG-Q scores between T1 and T2 as well as correlation coefficients with clinical descriptors to explain the variability between time points.

RESULTS

In sample 1 the NFOG-Q showed modest reliability (intraclass correlation coefficient = 0.68 [0.52-0.80]) without differences between T1 and T2. However, a minimal detectable change of 9.95 (7.90-12.27) points emerged for the total score (range 28 points, relative minimal detectable change of 35.5%). Sample 2 showed largely similar results. We found no associations between cognitive-related or disease severity-related outcomes and variability in NFOG-Q scores.

CONCLUSIONS

We conclude that the NFOG-Q is insufficiently reliable or responsive to detect small effect sizes, as changes need to go beyond 35% to surpass measurement error. Therefore, we warrant caution in using the NFOG-Q as a primary outcome in clinical trials. These results emphasize the need for robust and objective freezing of gait outcome measures.

The role and mechanism of microbial 3-ketosteroid Δ1-dehydrogenases in steroid breakdown

3-Ketosteroid Δ¹-dehydrogenases are FAD-dependent enzymes that catalyze the introduction of a double bond between the C1 and C2 atoms of the A-ring of 3-ketosteroid substrates. These enzymes are found in a large variety of microorganisms, especially in bacteria belonging to the phylum Actinobacteria. They play a critical role in the early steps of the degradation of the steroid core. 3-Ketosteroid Δ¹-dehydrogenases are of particular interest for the etiology of some infectious diseases, for the production of starting materials for the pharmaceutical industry, and for environmental bioremediation applications. Here we summarize and discuss the biochemical and enzymological properties of these enzymes, their microbial sources, and their natural diversity. The three-dimensional structure of a 3-ketosteroid Δ¹-dehydrogenase in connection with the enzyme mechanism is highlighted.

Functional MRI to Study Gait Impairment in Parkinson's Disease: a Systematic Review and Exploratory ALE Meta-Analysis

PURPOSE OF REVIEW

Whilst gait impairment is a main cause for disability in Parkinson's disease (PD), its neural control remains poorly understood. We performed a systematic review and meta-analysis of neuroimaging studies of surrogate features of gait in PD.

FINDINGS

Assessing the results from PET or SPECT scans after a period of actual walking as well as fMRI during mental imagery or virtual reality (VR) gait paradigms, we found a varying pattern of gait-related brain activity. Overall, a decrease in activation of the SMA during gait was found in PD compared to elderly controls. In addition, the meta-analysis showed that the most consistent gait-related activation was situated in the cerebellar locomotor region (CLR) in PD. Despite methodological heterogeneity, the combined neuroimaging studies of gait provide new insights into its neural control in PD, suggesting that CLR activation likely serves a compensatory role in locomotion.

Towards understanding neural network signatures of motor skill learning in Parkinson's disease and healthy aging

In the past decade, neurorehabilitation has been shown to be an effective therapeutic supplement for patients with Parkinson's disease (PD). However, patients still experience severe problems with the consolidation of learned motor skills. Knowledge on the neural correlates underlying this process is thus essential to optimize rehabilitation for PD. This review investigates the existing studies on neural network connectivity changes in relation to motor learning in healthy aging and PD and critically evaluates the imaging methods used from a methodological point of view. The results indicate that despite neurodegeneration there is still potential to modify connectivity within and between motor and cognitive networks in response to motor training, although these alterations largely bypass the most affected regions in PD. However, so far training-related changes are inferred and possible relationships are not substantiated by brain-behavior correlations. Furthermore, the studies included suffer from many methodological drawbacks. This review also highlights the potential for using neural network measures as predictors for the response to rehabilitation, mainly based on work in young healthy adults. We speculate that future approaches, including graph theory and multimodal neuroimaging, may be more sensitive than brain activation patterns and model-based connectivity maps to capture the effects of motor learning. Overall, this review suggests that methodological developments in neuroimaging will eventually provide more detailed knowledge on how neural networks are modified by training, thereby paving the way for optimized neurorehabilitation for patients.

Balancing between the two: Are freezing of gait and postural instability in Parkinson's disease connected?

Postural instability and freezing of gait (FoG) are key features of Parkinson's disease (PD) closely related to falls. Growing evidence suggests that co-existing postural deficits could influence the occurrence and severity of FoG. To date, the exact nature of this interrelationship remains largely unknown. We analyzed the complex interaction between postural instability and gait disturbance by comparing the findings available in the posturographic literature between patients with and without FoG. Results showed that FoG and postural instability are intertwined, can influence each other behaviorally and may coincide neurologically. The most common FoG-related postural deficits included weight-shifting impairments, and inadequate scaling and timing of postural responses most apparent at forthcoming postural changes under time constraints. Most likely, a negative cycle of combined and more severe postural deficits in people with FoG will enhance postural stability breakdown. As such, the wide brain network deficiencies involved in FoG may also concurrently influence postural stability. Future work needs to examine whether training interventions targeting both symptoms will have extra clinical benefits on fall frequency.

Structural basis of product inhibition by arabinose and xylose of the thermostable GH43 β-1,4-xylosidase from Geobacillus thermoleovorans IT-08

Complete degradation of the xylan backbone of hemicellulosic plant cell walls requires the synergistic action of endo-xylanases and β-1,4-xylosidases. While endo-xylanases produce xylooligosaccharides from xylan, β-1,4-xylosidases degrade the xylooligosaccharides into xylose monomers. The glycoside hydrolase family 43 β-1,4-xylosidase from Geobacillus thermoleovorans IT-08 is a promising, heat stable catalyst for the saccharification of hemicellulosic material into simple fermentable sugars, but it is competitively inhibited by its products arabinose and xylose. As a first step to help overcome this problem, we elucidated crystal structures of the enzyme in the unliganded form and with bound products, at 1.7-2.0 Å resolution. The structures are very similar to those of other enzymes belonging to glycoside hydrolase family 43. Unexpectedly, the monosaccharides are bound in very different ways. Arabinose preferentially binds in subsite -1, while xylose exclusively interacts with subsite +1. These structures and sugar binding preferences suggest ways for improving the catalytic performance of the enzyme by rational mutational design.

Structure and Function of Human Tyrosinase and Tyrosinase-Related Proteins

Melanin is the main pigment responsible for the color of human skin, hair and eye. Its biosynthesis requires three melanogenic enzymes, tyrosinase (TYR), and the tyrosinase-related proteins TYRP1 and TYRP2. The difficulty of isolating pure and homogeneous proteins from endogenous sources has hampered their study, and resulted in many contradictory findings regarding their physiological functions. In this review, we summarize recent advances on the structure and function of TYR and TYRPs by virtue of the crystal structure of human TYRP1, which is the first available structure of a mammalian melanogenic enzyme. This structure, combined with tyrosinase structures from other lower eukaryotes and mutagenesis studies of key active site residues, sheds light on the mechanism of TYR and TYRPs. Furthermore, a TYRP1-based homology model of TYR provides a high-quality platform to map and analyze albinism-related mutations, as well as the design of specific antimelanogenic compounds. Finally, we provide perspectives for future structure/function studies of TYR and TYRPs.

Study of response of Swiss Webster mice to light subunit of mushroom tyrosinase

The light subunit of mushroom, Agaricus bisporus, tyrosinase (LSMT), has been identified as an extrinsic component of the enzyme. Its function is unknown, but it can cross an epithelial cell layer, which suggests that it can be absorbed by the intestine. A similar capability has been demonstrated for the HA-33 component of the progenitor toxin from Clostridium botulinum, which is the closest structural homolog of LSMT. Unlike HA-33, LSMT appears to be non-immunogenic as shown by preliminary tests in Swiss Webster mice. We investigated the immunogenicity and histopathology of LSMT in mice to determine its safety in vivo. LSMT did not evoke generation of antibodies after prolonged periods of intraperitoneal administration. Histopathological observations confirmed the absence of responses in organs after twelve weekly administrations of LSMT. We found that LSMT is not toxic and is less immunogenic than the C. botulinum HA-33 protein, which supports further research and development for pharmaceutical application.

Structure of Human Tyrosinase Related Protein 1 Reveals a Binuclear Zinc Active Site Important for Melanogenesis

Tyrosinase‐related protein 1 (TYRP1) is one of three tyrosinase‐like glycoenzymes in human melanocytes that are key to the production of melanin, the compound responsible for the pigmentation of skin, eye, and hair. Difficulties with producing these enzymes in pure form have hampered the understanding of their activity and the effect of mutations that cause albinism and pigmentation disorders. Herein we show that the typical tyrosinase‐like subdomain of TYRP1 contains two zinc ions in the active site instead of copper ions as found in tyrosinases, which explains why TYRP1 does not exhibit tyrosinase redox activity. In addition, the structures reveal for the first time that the Cys‐rich subdomain, which is unique to vertebrate melanogenic proteins, has an epidermal growth factor‐like fold and is tightly associated with the tyrosinase subdomain. Our structures suggest that most albinism‐related mutations of TYRP1 affect its stability or activity.

Clinical balance scales indicate worse postural control in people with Parkinson's disease who exhibit freezing of gait compared to those who do not: A meta-analysis

Postural instability and freezing of gait (FOG) are key features of Parkinson's disease (PD) that are closely related to falls. Uncovering the postural control differences between individuals with and without FOG contributes to our understanding of the relationship between these phenomena. The objective of this meta-analysis was to investigate whether postural control deficits, as detected by clinical balance scales, were more apparent in FOG+ compared to FOG-. Furthermore, we aimed to identify whether different scales were equally sensitive to detect postural control deficits and whether medication affected postural control differentially in each subgroup. Relevant articles were identified via five electronic databases. We performed a meta-analysis on nine studies which reported clinical balance scale scores in 249 freezers and 321 non-freezers. Methodological analysis showed that in 5/9 studies disease duration differed between subgroups. Despite this drawback, postural control was found to be significantly worse in FOG+ compared to FOG-. All included clinical balance scales were found to be sufficiently sensitive to detect the postural control differences. Levodopa did not differentially affect postural control (p=0.21), as in both medication states FOG+ had worse postural stability than FOG-. However, this finding warrants a cautious interpretation given the limitations of the studies included. From subscore analysis, we found that reactive and dynamic postural control were the most affected postural control systems in FOG+. We conclude that our findings provide important evidence for pronounced postural instability in individuals with FOG, which can be easily picked up with clinical evaluation tools. Posturographic measures in well-matched subgroups are needed to highlight the exact nature of these deficits.

Large-Scale Recombinant Expression and Purification of Human Tyrosinase Suitable for Structural Studies

Human tyrosinase (TYR) is a glycoprotein that initiates the first two reactions in the melanin biosynthesis pathway. Mutations in its encoding gene cause Oculocutaneous Albinism type I (OCA1), the most severe form of albinism, which is a group of autosomal recessive disorders characterized by reduced or absent production of melanin in skin, hair and eyes. Despite extensive structural and characterization studies of its homologues in lower eukaryotic organisms, the catalytic mechanism of human TYR and the molecular basis of OCA1 are largely unknown. In this work, we have carried out a large-scale recombinant expression of TYR that has enabled us to obtain high yields of pure and active protein, required for crystallization trials and screening of skin whitening agents, which is highly demanded in the cosmetic industry. Addition of an N-terminal honeybee melittin signal peptide for secretion of the produced protein into the (protein-free) medium, as well as a cleavable His-tag at the C-terminus, was crucial for increasing the yield of pure protein. We have successfully crystallized two TYR variants, in both glycosylated and deglycosylated forms, showing preliminary X-ray diffraction patterns at 3.5 Å resolution. Hence, we have established an expression and purification protocol suitable for the crystal structure determination of human TYR, which will give unique atomic insight into the nature and conformation of the residues that shape the substrate binding pocket that will ultimately lead to efficient compound design.

Structural Basis of the Substrate Range and Enantioselectivity of Two (S)-Selective ω-Transaminases

ω-Transaminases are enzymes that can introduce an amino group in industrially interesting compounds. We determined crystal structures of two (S)-selective ω-transaminases, one from Arthrobacter sp. (Ars-ωTA) and one from Bacillus megaterium (BM-ωTA), which have 95% identical sequences but somewhat different activity profiles. Substrate profiling measurements using a range of (R)- and (S)-substrates showed that both enzymes have a preference for substrates with large, flat cyclic side groups, for which the activity of BM-ωTA is generally somewhat higher. BM-ωTA has a preference for (S)-3,3-dimethyl-2-butylamine significantly stronger than that of Ars-ωTA, as well as a weaker enantiopreference for 1-cyclopropylethylamine. The crystal structures showed that, as expected for (S)-selective transaminases, both enzymes have the typical transaminase type I fold and have spacious active sites to accommodate largish substrates. A structure of BM-ωTA with bound (R)-α-methylbenzylamine explains the enzymes' preference for (S)-substrates. Site-directed mutagenesis experiments revealed that the presence of a tyrosine, instead of a cysteine, at position 60 increases the relative activities on several small substrates. A structure of Ars-ωTA with bound l-Ala revealed that the Arg442 side chain has been repositioned to bind the l-Ala carboxylate. Compared to the arginine switch residue in other transaminases, Arg442 is shifted by six residues in the amino acid sequence, which appears to be a consequence of extra loops near the active site that narrow the entrance to the active site.

Postural motor learning in people with Parkinson's disease

Protective postural responses to external perturbations are hypokinetic in people with Parkinson's disease (PD), and improving these responses may reduce falls. However, the ability of people with PD to improve postural responses with practice is poorly understood. Our objective was to determine whether people with PD can improve protective postural responses similarly to healthy adults through repeated perturbations, and whether improvements are retained or generalize to untrained perturbations. Twelve healthy adults and 15 people with PD underwent 25 forward and 25 backward translations of the support surface, eliciting backward, and forward protective steps, respectively. We assessed whether: (1) performance improved over one day of practice, (2) changes were retained 24 h later, and (3) improvements generalized to untrained (lateral) postural responses. People with PD and healthy adults improved postural response characteristics, including center of mass displacement after perturbations (p < 0.001), margin of stability at first footfall (p = 0.001), step latency (p = 0.044), and number of steps (p = 0.001). However, unlike controls, improvements in people with PD occurred primarily in the first block of trials. Improvements were more pronounced during backward protective stepping than forward, and with the exception of step latency, were retained 24 h later. Improvements in forward-backward stepping did not generalize to lateral protective stepping. People with PD can improve protective stepping over the course of 1 day of perturbation practice. Improvements were generally similar to healthy adults, and were retained in both groups. Perturbation practice may represent a promising approach to improving protective postural responses in people with PD; however, additional research is needed to understand how to enhance generalization.

Crystal structure of recombinant tyrosinase-binding protein MtaL at 1.35 Å resolution

Mushroom tyrosinase-associated lectin-like protein (MtaL) binds to mature Agaricus bisporus tyrosinase in vivo, but the exact physiological function of MtaL is unknown. In this study, the crystal structure of recombinant MtaL is reported at 1.35 Å resolution. Comparison of its structure with that of the truncated and cleaved MtaL present in the complex with tyrosinase directly isolated from mushroom shows that the general β-trefoil fold is conserved. However, differences are detected in the loop regions, particularly in the β2-β3 loop, which is intact and not cleaved in the recombinant MtaL. Furthermore, the N-terminal tail is rotated inwards, covering the tyrosinase-binding interface. Thus, MtaL must undergo conformational changes in order to bind mature mushroom tyrosinase. Very interestingly, the β-trefoil fold has been identified to be essential for carbohydrate interaction in other lectin-like proteins. Comparison of the structures of MtaL and a ricin-B-like lectin with a bound disaccharide shows that MtaL may have a similar carbohydrate-binding site that might be involved in glycoreceptor activity.

Older adults can improve compensatory stepping with repeated postural perturbations

The ability to respond quickly and accurately to an external perturbation with a stepping response is critical to avoid falls and this ability is impaired in older, compared to young adults. However, little is known about whether young and older adults improve compensatory stepping responses similarly with practice. This study compares the extent to which young and older adults can improve, retain, and generalize postural compensatory steps in response to external perturbations. Centre of mass displacement, step characteristics and lower leg muscle activation latencies were measured during one training session of compensatory stepping in response to large surface translations in 13 young and 12 older adults. Retention was tested 24 h later. Older adults decreased their center of mass displacements over repeated exposure to large surface translations in both the anterior and posterior directions and retained these improvements. In contrast, young adults only showed adaptation and retention of forward stepping responses. Neither group was able to generalize improvements in stepping responses across directions. These results suggest step training may be beneficial for older adults, however additional, multidirectional training may be necessary to facilitate generalization of postural stepping responses for any direction of a slip or trip.

Ironing out their differences: dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase

Deciphering the structural features that functionally separate ammonia lyases from aminomutases is of interest because it may allow for the engineering of more efficient aminomutases for the synthesis of unnatural amino acids (e.g., β-amino acids). However, this has proved to be a major challenge that involves understanding the factors that influence their activity and regioselectivity differences. Herein, we report evidence of a structural determinant that dictates the activity differences between a phenylalanine ammonia lyase (PAL) and aminomutase (PAM). An inner loop region that closes the active sites of both PAM and PAL was mutated within PAM (PAM residues 77-97) in a stepwise approach to study the effects when the equivalent residue(s) found in the PAL loop were introduced into the PAM loop. Almost all of the single loop mutations triggered a lyase phenotype in PAM. Experimental and computational evidence suggest that the induced lyase features result from inner loop mobility enhancements, which are possibly caused by a 310-helix cluster, flanking α-helices, and hydrophobic interactions. These findings pinpoint the inner loop as a structural determinant of the lyase and mutase activities of PAM.

X-ray crystallographic validation of structure predictions used in computational design for protein stabilization

Protein engineering aimed at enhancing enzyme stability is increasingly supported by computational methods for calculation of mutant folding energies and for the design of disulfide bonds. To examine the accuracy of mutant structure predictions underlying these computational methods, crystal structures of thermostable limonene epoxide hydrolase variants obtained by computational library design were determined. Four different predicted effects indeed contributed to the obtained stabilization: (i) enhanced interactions between a flexible loop close to the N-terminus and the rest of the protein; (ii) improved interactions at the dimer interface; (iii) removal of unsatisfied hydrogen bonding groups; and (iv) introduction of additional positively charged groups at the surface. The structures of an eightfold and an elevenfold mutant showed that most mutations introduced the intended stabilizing interactions, and side-chain conformations were correctly predicted for 72-88% of the point mutations. However, mutations that introduced a disulfide bond in a flexible region had a larger influence on the backbone conformation than predicted. The enzyme active sites were unaltered, in agreement with the observed preservation of catalytic activities. The structures also revealed how a c-Myc tag, which was introduced for facile detection and purification, can reduce access to the active site and thereby lower the catalytic activity. Finally, sequence analysis showed that comprehensive mutant energy calculations discovered stabilizing mutations that are not proposed by the consensus or B-FIT methods.

Effect of introducing a disulphide bond between the A and C domains on the activity and stability of Saccharomycopsis fibuligera R64 α-amylase

Native enzyme and a mutant containing an extra disulphide bridge of recombinant Saccharomycopsis fibuligera R64 α-amylase, designated as Sfamy01 and Sfamy02, respectively, have successfully been overexpressed in the yeast Pichia pastoris KM71H. The purified α-amylase variants demonstrated starch hydrolysis resulting in a mixture of maltose, maltotriose, and glucose, similar to the wild type enzyme. Introduction of the disulphide bridge shifted the melting temperature (TM) from 54.5 to 56 °C and nearly tripled the enzyme half-life time at 65 °C. The two variants have similar kcat/KM values. Similarly, inhibition by acarbose was only slightly affected, with the IC50 of Sfamy02 for acarbose being 40 ± 3.4 μM, while that of Sfamy01 was 31 ± 3.9 μM. On the other hand, the IC50 of Sfamy02 for EDTA was 0.45 mM, nearly two times lower than that of Sfamy01 at 0.77 mM. These results show that the introduction of a disulphide bridge had little effect on the enzyme activity, but made the enzyme more susceptible to calcium ion extraction. Altogether, the new disulphide bridge improved the enzyme stability without affecting its activity, although minor changes in the active site environment cannot be excluded.

Flexibility of truncated and full-length glucansucrase GTF180 enzymes from Lactobacillus reuteri 180

Glucansucrase enzymes synthesize high-molecular-mass extracellular α-glucan polysaccharides from sucrose. Previously, the crystal structure of truncated glucansucrase glucosyltransferase (GTF)180-ΔN from Lactobacillus reuteri 180 (lacking the N-terminal domain) revealed an elongated overall structure with two remote domains (IV and V) extending away from the core. By contrast, a new crystal form of the α-1,6/α-1,3 specific glucansucrase GTF180-ΔN shows an approximate 120(o) rotation of domain V about a hinge located between domains IV and V, giving a much more compact structure than before. Positional variability of domain V in solution is confirmed by small angle X-ray scattering experiments and rigid-body ensemble calculations. In addition, small angle X-ray scattering measurements of full-length GTF180 also provide the first structural data for a full-length glucansucrase, showing that the enzyme has an almost symmetric boomerang-like molecular shape, with a bend likely located between domains IV and V. The ~ 700-residue N-terminal domain, which is not present in the crystal structures, extends away from domain V and the catalytic core of the enzyme. We conclude that, as a result of the hinge region, in solution, GTF180-ΔN (and likely also the full-length GTF180) shows conformational flexibility; this may be a general feature of GH70 glucansucrases.

DATABASE

• Structural data for GTF180-ΔN II have been deposited in the Protein Data Bank under accession code 4AYG.

Crystal structures of two Bacillus carboxylesterases with different enantioselectivities

Naproxen esterase (NP) from Bacillus subtilis Thai I-8 is a carboxylesterase that catalyzes the enantioselective hydrolysis of naproxenmethylester to produce S-naproxen (E>200). It is a homolog of CesA (98% sequence identity) and CesB (64% identity), both produced by B. subtilis strain 168. CesB can be used for the enantioselective hydrolysis of 1,2-O-isopropylideneglycerol (solketal) esters (E>200 for IPG-caprylate). Crystal structures of NP and CesB, determined to a resolution of 1.75Å and 2.04Å, respectively, showed that both proteins have a canonical α/β hydrolase fold with an extra N-terminal helix stabilizing the cap subdomain. The active site in both enzymes is located in a deep hydrophobic groove and includes the catalytic triad residues Ser130, His274, and Glu245. A product analog, presumably 2-(2-hydroxyethoxy)acetic acid, was bound in the NP active site. The enzymes have different enantioselectivities, which previously were shown to result from only a few amino acid substitutions in the cap domain. Modeling of a substrate in the active site of NP allowed explaining the different enantioselectivities. In addition, Ala156 may be a determinant of enantioselectivity as well, since its side chain appears to interfere with the binding of certain R-enantiomers in the active site of NP. However, the exchange route for substrate and product between the active site and the solvent is not obvious from the structures. Flexibility of the cap domain might facilitate such exchange. Interestingly, both carboxylesterases show higher structural similarity to meta-cleavage compound (MCP) hydrolases than to other α/β hydrolase fold esterases.

Crystal structure and site-directed mutagenesis of 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism

3-Ketosteroid Δ(1)-dehydrogenases are FAD-dependent enzymes that catalyze the 1,2-desaturation of 3-ketosteroid substrates to initiate degradation of the steroid nucleus. Here we report the 2.0 Å resolution crystal structure of the 56-kDa enzyme from Rhodococcus erythropolis SQ1 (Δ(1)-KSTD1). The enzyme contains two domains: an FAD-binding domain and a catalytic domain, between which the active site is situated as evidenced by the 2.3 Å resolution structure of Δ(1)-KSTD1 in complex with the reaction product 1,4-androstadiene-3,17-dione. The active site contains four key residues: Tyr(119), Tyr(318), Tyr(487), and Gly(491). Modeling of the substrate 4-androstene-3,17-dione at the position of the product revealed its interactions with these residues and the FAD. The C1 and C2 atoms of the substrate are at reaction distance to the N5 atom of the isoalloxazine ring of FAD and the hydroxyl group of Tyr(318), respectively, whereas the C3 carbonyl group is at hydrogen bonding distance from the hydroxyl group of Tyr(487) and the backbone amide of Gly(491). Site-directed mutagenesis of the tyrosines to phenylalanines confirmed their importance for catalysis. The structural features and the kinetic properties of the mutants suggest a catalytic mechanism in which Tyr(487) and Gly(491) work in tandem to promote keto-enol tautomerization and increase the acidity of the C2 hydrogen atoms of the substrate. With assistance of Tyr(119), the general base Tyr(318) abstracts the axial β-hydrogen from C2 as a proton, whereas the FAD accepts the axial α-hydrogen from the C1 atom of the substrate as a hydride ion.

AcmD, a homolog of the major autolysin AcmA of Lactococcus lactis, binds to the cell wall and contributes to cell separation and autolysis

Lactococcus lactis expresses the homologous glucosaminidases AcmB, AcmC, AcmA and AcmD. The latter two have three C-terminal LysM repeats for peptidoglycan binding. AcmD has much shorter intervening sequences separating the LysM repeats and a lower iso-electric point (4.3) than AcmA (10.3). Under standard laboratory conditions AcmD was mainly secreted into the culture supernatant. An L. lactis acmAacmD double mutant formed longer chains than the acmA single mutant, indicating that AcmD contributes to cell separation. This phenotype could be complemented by plasmid-encoded expression of AcmD in the double mutant. No clear difference in cellular lysis and protein secretion was observed between both mutants. Nevertheless, overexpression of AcmD resulted in increased autolysis when AcmA was present (as in the wild type strain) or when AcmA was added to the culture medium of an AcmA-minus strain. Possibly, AcmD is mainly active within the cell wall, at places where proper conditions are present for its binding and catalytic activity. Various fusion proteins carrying either the three LysM repeats of AcmA or AcmD were used to study and compare their cell wall binding characteristics. Whereas binding of the LysM domain of AcmA took place at pHs ranging from 4 to 8, LysM domain of AcmD seems to bind strongest at pH 4.

Crystal structure of α-1,4-glucan lyase, a unique glycoside hydrolase family member with a novel catalytic mechanism

α-1,4-Glucan lyase (EC 4.2.2.13) from the red seaweed Gracilariopsis lemaneiformis cleaves α-1,4-glucosidic linkages in glycogen, starch, and malto-oligosaccharides, yielding the keto-monosaccharide 1,5-anhydro-D-fructose. The enzyme belongs to glycoside hydrolase family 31 (GH31) but degrades starch via an elimination reaction instead of hydrolysis. The crystal structure shows that the enzyme, like GH31 hydrolases, contains a (β/α)8-barrel catalytic domain with B and B' subdomains, an N-terminal domain N, and the C-terminal domains C and D. The N-terminal domain N of the lyase was found to bind a trisaccharide. Complexes of the enzyme with acarbose and 1-dexoynojirimycin and two different covalent glycosyl-enzyme intermediates obtained with fluorinated sugar analogues show that, like GH31 hydrolases, the aspartic acid residues Asp(553) and Asp(665) are the catalytic nucleophile and acid, respectively. However, as a unique feature, the catalytic nucleophile is in a position to act also as a base that abstracts a proton from the C2 carbon atom of the covalently bound subsite -1 glucosyl residue, thus explaining the unique lyase activity of the enzyme. One Glu to Val mutation in the active site of the homologous α-glucosidase from Sulfolobus solfataricus resulted in a shift from hydrolytic to lyase activity, demonstrating that a subtle amino acid difference can promote lyase activity in a GH31 hydrolase.

Biocatalytic and structural properties of a highly engineered halohydrin dehalogenase

Two highly engineered halohydrin dehalogenase variants were characterized in terms of their performance in dehalogenation and epoxide cyanolysis reactions. Both enzyme variants outperformed the wild-type enzyme in the cyanolysis of ethyl (S)-3,4-epoxybutyrate, a conversion yielding ethyl (R)-4-cyano-3-hydroxybutyrate, an important chiral building block for statin synthesis. One of the enzyme variants, HheC2360, displayed catalytic rates for this cyanolysis reaction enhanced up to tenfold. Furthermore, the enantioselectivity of this variant was the opposite of that of the wild-type enzyme, both for dehalogenation and for cyanolysis reactions. The 37-fold mutant HheC2360 showed an increase in thermal stability of 8 °C relative to the wild-type enzyme. Crystal structures of this enzyme were elucidated with chloride and ethyl (S)-3,4-epoxybutyrate or with ethyl (R)-4-cyano-3-hydroxybutyrate bound in the active site. The observed increase in temperature stability was explained in terms of a substantial increase in buried surface area relative to the wild-type HheC, together with enhanced interfacial interactions between the subunits that form the tetramer. The structures also revealed that the substrate binding pocket was modified both by substitutions and by backbone movements in loops surrounding the active site. The observed changes in the mutant structures are partly governed by coupled mutations, some of which are necessary to remove steric clashes or to allow backbone movements to occur. The importance of interactions between substitutions suggests that efficient directed evolution strategies should allow for compensating and synergistic mutations during library design.

Structure of the α-1,6/α-1,4-specific glucansucrase GTFA from Lactobacillus reuteri 121

The reuteransucrase GTFA from Lactobacillus reuteri 121, which belongs to glycosyl hydrolase family GH70, synthesizes branched α-glucans with both α-1,6- and α-1,4-glycosidic linkages (reuteran) from sucrose. The crystal structure of GTFA-ΔN, a 118 kDa fragment of GTFA comprising residues 745-1763 and including the catalytic domain, was determined at 3.6 Å resolution by molecular replacement. The crystals have large solvent channels and an unusually high solvent content of 85%. GTFA-ΔN has the same domain arrangement and domain topologies as observed in previously determined GH70 glucansucrase structures. The architecture of the GTFA-ΔN active site and binding pocket confirms that glucansucrases have a conserved substrate specificity for sucrose. However, this first crystal structure of an α-1,6/α-1,4-specific glucansucrase shows that residues from conserved sequence motif IV (1128-1136 in GTFA-ΔN) contribute to the acceptor-binding subsites and that they display differences compared with other structurally characterized glucansucrases. In particular, the structure clarifies the importance of residues following the transition-state stabilizer for product specificity, and especially residue Asn1134, which is in a position to interact with sugar units in acceptor subsite +2.

Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches

Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (K(D)). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.

Structure and catalytic mechanism of 3-ketosteroid-Delta4-(5α)-dehydrogenase from Rhodococcus jostii RHA1 genome

3-Ketosteroid Δ4-(5α)-dehydrogenases (Δ4-(5α)-KSTDs) are enzymes that introduce a double bond between the C4 and C5 atoms of 3-keto-(5α)-steroids. Here we show that the ro05698 gene from Rhodococcus jostii RHA1 codes for a flavoprotein with Δ4-(5α)-KSTD activity. The 1.6 Å resolution crystal structure of the enzyme revealed three conserved residues (Tyr-319, Tyr-466, and Ser-468) in a pocket near the isoalloxazine ring system of the FAD co-factor. Site-directed mutagenesis of these residues confirmed that they are absolutely essential for catalytic activity. A crystal structure with bound product 4-androstene-3,17-dione showed that Ser-468 is in a position in which it can serve as the base abstracting the 4β-proton from the C4 atom of the substrate. Ser-468 is assisted by Tyr-319, which possibly is involved in shuttling the proton to the solvent. Tyr-466 is at hydrogen bonding distance to the C3 oxygen atom of the substrate and can stabilize the keto-enol intermediate occurring during the reaction. Finally, the FAD N5 atom is in a position to be able to abstract the 5α-hydrogen of the substrate as a hydride ion. These features fully explain the reaction catalyzed by Δ4-(5α)-KSTDs.