Free Apo Research Articles

NADP/H binding nearly doubles the stability of a Mycobacterium drug target: an unfolding study

Mycobacterium Aspartate beta semialdehyde dehydrogenase (ASADH) was studied using various spectroscopic techniques and size exclusion chromatography to examine the unfolding of free (apo) and NADP/H-bound (holo) forms of ASADH. Non-cooperative guanidinium chloride (GdnHCl)-induced unfolding of the apo ASADH was discovered, and no partially folded intermediate structures were stabilized. On the other hand, it was observed that GdnHCl’s unfolding of holoenzyme was a cooperative process without any stable intermediate structure. The native form of holoenzyme is found to be stable against the lower concentration of GdnHCl only (namely up to 1.25 M GdnHCl). The tryptophan environment appears to unfold cooperatively in case of the holoenzyme and is in well coordination with the overall unfolding of the holoenzyme. The presence of NADP/H shows a stabilizing effect on the tryptophan environment as well as on the native NADP/H-bound enzyme. values reveal nearly two-fold (∼1.9) conformationally more stable folded holoenzyme compared to its native apo state. The Cm for the apo and holo forms of ASADH are 1.3 and 1.9 M, respectively. Novel drug leads targeting the NADP/H binding domain of ASADH could offer promising drugs against extremely infective Mycobacterium tuberculosis. Communicated by Ramaswamy H. Sarma

Potent reduction of plasma lipoprotein (a) with an antisense oligonucleotide in human subjects does not affect ex vivo fibrinolysis

It is postulated that lipoprotein (a) [Lp(a)] inhibits fibrinolysis, but this hypothesis has not been tested in humans due to the lack of specific Lp(a) lowering agents. Patients with elevated Lp(a) were randomized to antisense oligonucleotide [IONIS-APO(a)Rx] directed to apo(a) (n = 7) or placebo (n = 10). Ex vivo plasma lysis times and antigen concentrations of plasminogen, factor XI, plasminogen activator inhibitor 1, thrombin activatable fibrinolysis inhibitor, and fibrinogen at baseline, day 85/92/99 (peak drug effect), and day 190 (3 months off drug) were measured. The mean ± SD baseline Lp(a) levels were 477.3 ± 55.9 nmol/l in IONIS-APO(a)Rx and 362.1 ± 89.9 nmol/l in placebo. The mean± SD percentage change in Lp(a) for IONIS-APO(a)Rx was -69.3 ± 12.2% versus -5.4 ± 6.9% placebo (P < 0.0010) at day 85/92/99 and -15.6 ± 8.9% versus 3.2 ± 12.2% (P = 0.003) at day 190. Clot lysis times and coagulation/fibrinolysis-related biomarkers showed no significant differences between IONIS-APO(a)Rx and placebo at all time points. Clot lysis times were not affected by exogenously added Lp(a) at concentrations up to 200 nmol/l to plasma with very low (12.5 nmol/l) Lp(a) levels, whereas recombinant apo(a) had a potent antifibrinolytic effect. In conclusion, potent reductions of Lp(a) in patients with highly elevated Lp(a) levels do not affect ex vivo measures of fibrinolysis; the relevance of any putative antifibrinolytic effects of Lp(a) in vivo needs further study.

Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy

The signaling protein calmodulin (CaM) undergoes a well-known change in secondary structure upon binding Ca2+, but the structural plasticity of the Ca2+-free apo state is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58 °C that are assigned to melting of the C- and N-terminal domains, respectively, but the molecular mechanism of domain unfolding is unknown. We report temperature-jump time-resolved infrared (IR) spectroscopy experiments designed to target the first steps in the C-terminal domain melting transition of human apo-CaM. A comparison of the nonequilibrium relaxation of apo-CaM with the more thermodynamically stable holo-CaM, with 4 equiv of Ca2+ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix destabilization. These observations enable the assignment of previously reported dynamics of CaM on hundreds of microsecond time scales to thermally activated melting, producing a complete mechanism for thermal unfolding of CaM.

Structural and dynamic responses of calcium ion binding loop residues in metallo-proteins

Conformational changes in bio-molecular systems are fundamental to several biological processes. It is important to study changes in responses of underlying microscopic variables, like dihedral angles as conformational change takes place. We perform all-atom simulations and modelling via Langevin equation to illustrate the changes in structural and dynamic responses of dihedral angles of calcium ion binding residues of different proteins in metal ion free (apo) and bound (holo) states. The equilibrium distributions of dihedral angles in apo- and holo-states represent structural response. Our studies show the presence of dihedrals with multiple peaks (isomeric states) separated by barrier heights is more frequent in apo- than in holo-state. The relaxation time-scale of dihedral fluctuations is found to increase linearly with decreasing barrier height due to more frequent barrier re-crossing events. The slow kinetic response of the dihedrals also contributes to slowing down of macro-scale fluctuations, which may be useful to understand kinetics of various bio-molecular processes.

Molecular-Level Profiling of Human Serum Transferrin Protein through Assessment of Nanopore-Based Electrical and Chemical Responsiveness.

In this study, we investigated the voltage and pH responsiveness of human serum transferrin (hSTf) protein using silicon nitride (Si xN y) nanopores. The Fe(III)-rich holo form of hSTf was dominant when pH > pI, while the Fe(III)-free apo form was dominant when pH < pI. The translocations of hSTf were purely in an electrophoretic sense, thus depended on its pI and the solution pH. With increasing voltage, voltage driven protein unfolding became prominent which was indicated by the trends associated with change in conductance, due to hSTf translocation, and in the excluded electrolyte volume. Additionally, analysis of the translocation events of the pure apo form of hSTf showed a clear difference in the event population compared to that of the holo form. The results obtained demonstrate the successful application of nanopore devices to distinguish between the holo and apo forms of hSTf in a mixture and to analyze its folding and unfolding phenomenon over a range of pH and applied voltages.

Quantifying Secondary Structure Changes in Calmodulin Using 2D-IR Spectroscopy.

Revealing the details of biomolecular processes in solution needs tools that can monitor structural dynamics over a range of time and length scales. We assess the ability of 2D-IR spectroscopy in combination with multivariate data analysis to quantify changes in secondary structure of the multifunctional calcium-binding messenger protein Calmodulin (CaM) as a function of temperature and Ca2+ concentration. Our approach produced quantitative agreement with circular dichroism (CD) spectroscopy in detecting the domain melting transitions of Ca2+-free (apo) CaM (reduction in α-helix structure by 13% (CD) and 15% (2D)). 2D-IR also allows accurate differentiation between melting transitions and generic heating effects observed in the more thermally stable Ca2+-bound (holo) CaM. The functionally relevant random-coil-α-helix transition associated with Ca2+ uptake that involves just 7-8 out of a total of 148 amino acid residues was clearly detected. Temperature-dependent Molecular Dynamics (MD) simulations show that apo-CaM exists in dynamic equilibrium with holo-like conformations, while Ca2+ uptake reduces conformational flexibility. The ability to combine quantitative structural insight from 2D-IR with MD simulations thus offers a powerful approach for measuring subtle protein conformational changes in solution.

The molecular mechanism behind resistance of the kinase FLT3 to the inhibitor quizartinib.

Fms-like tyrosine kinase 3 (FLT3) is a receptor tyrosine kinase that is a drug target for leukemias. Several potent inhibitors of FLT3 exist, and bind to the inactive form of the enzyme. Unfortunately, resistance due to mutations in the kinase domain of FLT3 limits the therapeutic effects of these inhibitors. As in many other cases, it is not straightforward to explain why certain mutations lead to drug resistance. Extensive fully atomistic molecular dynamics (MD) simulations of FLT3 were carried out with an inhibited form (FLT-quizartinib complex), a free (apo) form, and an active conformation. In all cases, both the wild type (wt) proteins and two resistant mutants (D835F and Y842H) were studied. Analysis of the simulations revealed that impairment of protein-drug interactions cannot explain the resistance mutations in question. Rather, it appears that the active state of the mutant forms is perturbed by the mutations. It is therefore likely that perturbation of deactivation of the protein (which is necessary for drug binding) is responsible for the reduced affinity of the drug to the mutants. Importantly, this study suggests that it is possible to explain the source of resistance by mutations in FLT3 by an analysis of unbiased MD simulations.

Backbone resonance assignments of complexes of human voltage-dependent sodium channel NaV1.2 IQ motif peptide bound to apo calmodulin and to the C-domain fragment of apo calmodulin.

Human voltage-gated sodium channel NaV1.2 has a single pore-forming α-subunit and two transmembrane β-subunits. Expressed primarily in the brain, NaV1.2 is critical for initiation and propagation of action potentials. Milliseconds after the pore opens, sodium influx is terminated by inactivation processes mediated by regulatory proteins including calmodulin (CaM). Both calcium-free (apo) CaM and calcium-saturated CaM bind tightly to an IQ motif in the C-terminal tail of the α-subunit. Our thermodynamic studies and solution structure (2KXW) of a C-domain fragment of apo 13C,15N- CaM (CaMC) bound to an unlabeled peptide with the sequence of rat NaV1.2 IQ motif showed that apo CaMC (a) was necessary and sufficient for binding, and (b) bound more favorably than calcium-saturated CaMC. However, we could not monitor the NaV1.2 residues directly, and no structure of full-length CaM (including the N-domain of CaM (CaMN)) was determined. To distinguish contributions of CaMN and CaMC, we used solution NMR spectroscopy to assign the backbone resonances of a complex containing a 13C,15N-labeled peptide with the sequence of human NaV1.2 IQ motif (NaV1.2IQp) bound to apo 13C,15N-CaM or apo 13C,15N-CaMC. Comparing the assignments of apo CaM in complex with NaV1.2IQp to those of free apo CaM showed that residues within CaMC were significantly perturbed, while residues within CaMN were essentially unchanged. The chemical shifts of residues in NaV1.2IQp and in the C-domain of CaM were nearly identical regardless of whether CaMN was covalently linked to CaMC. This suggests that CaMN does not influence apo CaM binding to NaV1.2IQp.

Cu/Zn Superoxide Dismutase Forms Amyloid Fibrils under Near-Physiological Quiescent Conditions: The Roles of Disulfide Bonds and Effects of Denaturant.

Cu/Zn superoxide dismutase (SOD1) forms intracellular aggregates that are pathological indicators of amyotrophic lateral sclerosis. A large body of research indicates that the entry point to aggregate formation is a monomeric, metal-ion free (apo), and disulfide-reduced species. Fibril formation by SOD1 in vitro has typically been reported only for harsh solvent conditions or mechanical agitation. Here we show that monomeric apo-SOD1 in the disulfide-reduced state forms fibrillar aggregates under near-physiological quiescent conditions. Monomeric apo-SOD1 with an intact intramolecular disulfide bond is highly resistant to aggregation under the same conditions. A cysteine-free variant of SOD1 exhibits fibrillization behavior and fibril morphology identical to those of disulfide-reduced SOD1, firmly establishing that intermolecular disulfide bonds or intramolecular disulfide shuffling are not required for aggregation and fibril formation. The decreased lag time for fibril formation resulting from reduction of the intramolecular disulfide bond thus primarily reflects the decreased stability of the folded state relative to partially unfolded states, rather than an active role of free sulfhydryl groups in mediating aggregation. Addition of urea to increase the amount of fully unfolded SOD1 increases the lag time for fibril formation, indicating that the population of this species does not dominate over other factors in determining the onset of aggregation. Our results contrast with previous results obtained for agitated samples, in which case amyloid formation was accelerated by denaturant. We reconcile these observations by suggesting that denaturants destabilize monomeric and aggregated species to different extents and thus affect nucleation and growth.

Conformational heterogeneity in CCR7 undergoes transitions to specific states upon ligand binding

Ligand-binding to G protein-coupled receptors (GPCRs) acts as the local driving force that initiates signal transduction through the receptor and mediates its conformational transitions and interactions with various intracellular effectors. In a recent study, We have shown that the binding of ligands CCL19 and CCL21 to CCR7 induces biased triggering of side chain-based molecular switches, which coordinate concerted transmembrane helical domain motions and transitioning of the receptor to distinct conformational states (Gaieb, Z., D.D. Lo, and D. Morikis. 2016. Molecular Mechanism of Biased Ligand Conformational Changes in CC Chemokine Receptor 7. Journal of Chemical Information and Modeling. 56: 1808–1822, DOI: 10.1021/acs.jcim.6b00367). To complement our previous study, we compare the results of the free (apo) CCR7 microsecond molecular dynamics simulations to those of the ligand-bound CCR7, and show that the apo receptor is found in conformational heterogeneity that only exhibits random fluctuations and lacks the coordinated helical motions seen in ligand-bound receptors. We conclude that ligand binding is responsible for coordinating the stochastic conformational nature of CCR7 into specific conformational states, initiated and propagated by specific physicochemical events.

FRET Based Mapping of Calmodulin within the Ryanodine Receptor

Using time-resolved fluorescence resonance energy transfer (TR-FRET) and multi-site-directed labeling of calmodulin (CaM) and FKBP12.6, we further resolve the structural basis underlying CaM regulation of skeletal and cardiac ryanodine receptor isoforms (RyR1 and RyR2) at relaxed and contracting [Ca2+]. Although cryo-EM and FRET-based mapping place Ca2+-bound CaM in a similar location on RyR1 and RyR2, the position of Ca2+-free (apo) CaM remains controversial - cryo-EM suggests a large shift in the centers of mass between apo- and Ca-CaM states, but this was not observed in previous FRET studies. Using TR-FRET, we resolved structural states of CaM bound to RyR1 and RyR2 in isolated sarcoplasmic reticulum membranes at 0.03 and 30 micromolar Ca2+. Donor fluorophores were targeted to the cytoplasmic assembly of RyR1 or RyR2 by pre-incubating sarcoplasmic reticulum vesicles with fluorescent FKBP12.6 labeled at one of five well dispersed sites (D-FKBP). FRET was measured in the presence of CaM labeled with an acceptor fluorophore attached to one of four sites (A-CaM) for each distance measurement. The donor-acceptor distances, calculated from fluorescence decay waveforms, were used to trilaterate the acceptor probe loci within RyR. On both RyR1 and RyR2, we detect a Ca2+-driven decrease in separation between CaM lobes, suggesting a more compact Ca2+-bound CaM, relative to apo-CaM, structure. However, these Ca2+-driven shifts in fluorophore positions are not as dramatic as the large shift previously proposed. We also observe isoform specific differences, as CaM's binding location appears to be rotated down and slightly inward on RyR2 relative to RyR1. This work was supported by NIH grants R01HL092097 (to RLC/DMB) and R37AG26160 (to DDT), and by a Postdoctoral Fellowship from the American Heart Association 16POST31010019 (to RTR).

Acylation of lysine residues in human plasma high density lipoprotein increases stability and plasma clearance in vivo

Although human plasma high density lipoproteins (HDL) concentrations negatively correlate with atherosclerotic cardiovascular disease, underlying mechanisms are unknown. Thus, there is continued interest in HDL structure and functionality. Numerous plasma factors disrupt HDL structure while inducing the release of lipid free apolipoprotein (apo) AI. Given that HDL is an unstable particle residing in a kinetic trap, we tested whether HDL could be stabilized by acylation with acetyl and hexanoyl anhydrides, giving AcHDL and HexHDL respectively. Lysine analysis with fluorescamine showed that AcHDL and HexHDL respectively contained 11 acetyl and 19 hexanoyl groups. Tests with biological and physicochemical perturbants showed that HexHDL was more stable than HDL to perturbant-induced lipid free apo AI formation. Like the reaction of streptococcal serum opacity factor against HDL, the interaction of HDL with its receptor, scavenger receptor class B member 1 (SR-B1), removes CE from HDL. Thus, we tested and validated the hypothesis that selective uptake of HexHDL-[3H]CE by Chinese Hamster Ovary cells expressing SR-B1 is less than that of HDL-[3H]CE; thus, selective SR-B1 uptake of HDL-CE depends on HDL instability. However, in mice, plasma clearance, hepatic uptake and sterol secretion into bile were faster from HexHDL-[3H]CE than from HDL-[3H]CE. Collectively, our data show that acylation increases HDL stability and that the reaction of plasma factors with HDL and SR-B1-mediated uptake are reduced by increased HDL stability. In vivo data suggest that HexHDL promotes charge-dependent reverse cholesterol transport, by a mechanism that increases hepatic sterol uptake via non SR-B1 receptors, thereby increasing bile acid output.

(1)H, (13)C and (15)N resonance assignments for the response regulator CheY3 from Rhodobacter sphaeroides.

Rhodobacter sphaeroides has emerged as a model system for studies of the complex chemotaxis pathways that are a hallmark of many non-enteric bacteria. The genome of R. sphaeroides encodes two sets of flagellar genes, fla1 and fla2, that are controlled by three different operons. Each operon encodes homologues of most of the proteins required for the well-studied E. coli chemotaxis pathway. R. sphaeroides has six homologues of the response regulator CheY that are localized to and are regulated by different clusters of chemosensory proteins in the cell and have different effects on chemotaxis. CheY6 is the major CheY stopping the fla1 flagellar motor and associated with a cytoplasmically localised chemosensory pathway. CheY3 and CheY4 are associated with a membrane localised polar chemosensory cluster, and can bind to but not stop the motor. CheY6 and either CheY3 or CheY4 are required for chemotaxis. We are using NMR spectroscopy to characterise and compare the structure and dynamics of CheY3 and CheY6 in solution. We are interested in defining the conformational changes that occur upon activation of these two proteins and to identify differences in their properties that can explain the different functions they play in chemotaxis in R. sphaeroides. Here we present the 1H, 13C and 15N assignments for CheY3 in its active, inactive and Mg2+-free apo form. These assignments provide the starting point for detailed investigations of the structure and function of CheY3.

FRET-Based Mapping of Calmodulin within the Ryanodine Receptor

Using time-resolved fluorescence resonance energy transfer (TR-FRET) and multi-site-directed labeling of calmodulin (CaM) and FKBP12.6, we further resolve the structural basis underlying CaM regulation of skeletal and cardiac ryanodine receptor isoforms (RyR1 and RyR2) at relaxed and contracting [Ca2+]. Although cryo-EM and FRET-based mapping place Ca2+-bound CaM in a similar location on RyR1 and RyR2, the position of Ca2+-free (apo) CaM remains controversial - cryo-EM suggests a large shift in the centers of mass between apo- and Ca-CaM states, but this was not observed in previous FRET studies. Using TR-FRET, we resolved structural states of CaM bound to RyR1 and RyR2 in isolated sarcoplasmic reticulum membranes at 0.03 and 30 micromolar Ca2+. Donor fluorophores were targeted to the cytoplasmic assembly of RyR1 or RyR2 by pre-incubating sarcoplasmic reticulum vesicles with fluorescent FKBP12.6 labeled at one of five well dispersed sites (D-FKBP). FRET was measured in the presence of CaM labeled with an acceptor fluorophore attached to one of four sites (A-CaM) for each distance measurement. The donor-acceptor distances, calculated from fluorescence decay waveforms, were used to trilaterate the acceptor probe loci within RyR. On both RyR1 and RyR2, we detect a Ca2+-driven decrease in separation between CaM lobes, suggesting a more compact Ca2+-bound CaM, relative to apo-CaM, structure. However, these Ca2+-driven shifts in fluorophore positions are not as dramatic as the large shift previously proposed. We also observe isoform specific differences, as CaM's binding location appears to be rotated down and slightly inward on RyR2 relative to RyR1. This work was supported by NIH grants R01HL092097 (to RLC/DMB) and R37AG26160 (to DDT), and by a Postdoctoral Fellowship from the American Heart Association 16POST31010019 (to RTR).

Conformational thermodynamics guided structural reconstruction of biomolecular fragments.

Computational prediction of structure for macromolecular fragments is a formidable challenge. Here we show that the differences in conformational thermodynamics, computed using the equilibrium distribution of dihedral angles from molecular dynamics simulation, can identify the better model for the missing residues in the metal ion free (apo) skeletal muscle Troponin C (TnC). We use the model to understand Troponin I interaction with calcium (Ca(2+)) ion bound TnC. Our method to compare conformational thermodynamics between different models can be easily generalized to any macromolecule to understand the structure and function even if experimental structures are not resolved.

Destabilization of the dimer interface is a common consequence of diverse ALS‐associated mutations in metal free SOD1

Neurotoxic misfolding of Cu, Zn-superoxide dismutase (SOD1) is implicated in causing amyotrophic lateral sclerosis, a devastating and incurable neurodegenerative disease. Disease-linked mutations in SOD1 have been proposed to promote misfolding and aggregation by decreasing protein stability and increasing the proportion of less folded forms of the protein. Here we report direct measurement of the thermodynamic effects of chemically and structurally diverse mutations on the stability of the dimer interface for metal free (apo) SOD1 using isothermal titration calorimetry and size exclusion chromatography. Remarkably, all mutations studied, even ones distant from the dimer interface, decrease interface stability, and increase the population of monomeric SOD1. We interpret the thermodynamic data to mean that substantial structural perturbations accompany dimer dissociation, resulting in the formation of poorly packed and malleable dissociated monomers. These findings provide key information for understanding the mechanisms and energetics underlying normal maturation of SOD1, as well as toxic SOD1 misfolding pathways associated with disease. Furthermore, accurate prediction of protein-protein association remains very difficult, especially when large structural changes are involved in the process, and our findings provide a quantitative set of data for such cases, to improve modelling of protein association.

'LDL-C' = LDL-C + Lp(a)-C: implications of achieved ultra-low LDL-C levels in the proprotein convertase subtilisin/kexin type 9 era of potent LDL-C lowering.

The measurement that is termed 'LDL-cholesterol' (LDL-C) includes the cholesterol content of lipoprotein(a) [Lp(a)-C], which can contribute approximately 30-45% to measured LDL-C levels as a percentage of its mass. We review the implications of achieved very low LDL-C levels in patients treated with potent LDL-C-lowering agents in the context of varying Lp(a) levels. Combination therapy with statins, ezetimibe, and proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors can lower LDL-C to unprecedentedly low levels. Recent PCSK9 trials have shown that routine achievement of mean LDL-C less than 50 mg/dl is feasible, along with the modest reductions in Lp(a). Many patients will achieve LDL-C less than 25 mg/dl with concomitantly elevated Lp(a) levels that contribute substantially to the measured 'LDL-C'. Therefore, it is possible that some of these patients may have little to no circulating LDL-C. As the new era of ultralow LDL-C levels ensues, it is imperative to understand the contribution of Lp(a)-C to measured LDL-C and the consequences of achieving ultralow or potentially absent LDL-C in the setting of elevated Lp(a) levels and possibly free apo(a). We review this concept and suggest avenues of research, including analyses of existing datasets in current clinical trials and new research studies, to understand its pathophysiological and clinical significance.

Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH.

Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca(2+)-triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca(2+)-bound holo s2b (1.4 Å resolution, R = 15.0%, Rfree = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, Rfree = 20.7%), as well as of Ca(2+)-free apo s2a (1.8 Å resolution, R = 20.7%, Rfree = 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, Rfree = 21.2%; 1.6 Å resolution, R = 16.2%, Rfree = 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca(2+) pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3. B-factor analyses suggest that in the presence of Ca(2+) the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca(2+) binding. Conserved residues not only interact with Ca(2+), but also position the Ca(2+)-interacting water molecule. Ca(2+) aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca(2+) binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

NMR Structure Reveals Novel Interactions between Intrinsically Disordered PEP-19 and Calmodulin

Background: PEP-19 has no known intrinsic activity other than binding predominately to the C-domain of calmodulin (C-CaM), yet it is implicated in numerous cellular processes. We showed that an acidic sequence in PEP-19 is required to greatly increase the rates of Ca2+ binding to C-CaM. Importantly, the acidic sequence is also required for PEP-19 to sensitize HeLa cells to ATP-induced Ca2+ release. Goal: The goal of the current study was to determine the high-resolution NMR solution structure of the PEP-19/apo C-CaM complex.Results: Apo C-CaM adopts a semi-open conformation when bound to PEP-19, with the helices E and F of Ca2+ binding site III showing the greatest change in angle relative to free apo C-CaM. The conformation of Ca2+ binding loop III is similar to that in free apo C-CaM, but loop IV adopts a different conformation with increased conformational exchange when bound to PEP-19. Residues 1-29 in PEP-19 remain disordered when bound to C-CaM, and are thus accessible for potential interactions with other proteins. The IQ motif in PEP-19 adopts a well-defined alpha helix that binds to a hydrophobic groove in apo C-CaM. The C-terminal part of the acidic sequence is alpha helical, but the N-terminal portion (aa 28-36) forms loop and coil structures that are stabilized by interactions between Ile32 and Met34 in PEP-19 and hydrophobic residues in Ca2+ binding site III of C-CaM. This allows acid side chains in PEP-19 to extend toward the solvent to greatly increase negative charge density near site III of C-CaM.Conclusions: The structure suggests that the acidic sequence in PEP-19 modulates Ca2+ binding to site III of C-CaM by direct interactions and/or electrostatic steering of Ca2+, but that allosteric effects increase conformational exchange to modulate Ca2+ binding to site IV.

The crystal structure of archaeal serine hydroxymethyltransferase reveals idiosyncratic features likely required to withstand high temperatures.

Serine hydroxymethyltransferases (SHMTs) play an essential role in one-carbon unit metabolism and are used in biomimetic reactions. We determined the crystal structure of free (apo) and pyridoxal-5'-phosphate-bound (holo) SHMT from Methanocaldococcus jannaschii, the first from a hyperthermophile, from the archaea domain of life and that uses H₄MPT as a cofactor, at 2.83 and 3.0 Å resolution, respectively. Idiosyncratic features were observed that are likely to contribute to structure stabilization. At the dimer interface, the C-terminal region folds in a unique fashion with respect to SHMTs from eubacteria and eukarya. At the active site, the conserved tyrosine does not make a cation-π interaction with an arginine like that observed in all other SHMT structures, but establishes an amide-aromatic interaction with Asn257, at a different sequence position. This asparagine residue is conserved and occurs almost exclusively in (hyper)thermophile SHMTs. This led us to formulate the hypothesis that removal of frustrated interactions (such as the Arg-Tyr cation-π interaction occurring in mesophile SHMTs) is an additional strategy of adaptation to high temperature. Both peculiar features may be tested by designing enzyme variants potentially endowed with improved stability for applications in biomimetic processes.