Non-Additive Effects of Binding Site Mutations in Calmodulin

Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity

Cell membranes are incredibly complex environments containing hundreds of components. Despite substantial advances in the past decade, fundamental questions related to lipid-lipid interactions and heterogeneity persist. This review explores the complexity of lipid membranes, showcasing recent advances in vibrational spectroscopy to characterize the structure, dynamics, and interactions at the membrane interface. We include an overview of modern techniques such as surface-enhanced infrared spectroscopy as a steady-state technique with single-bilayer sensitivity, two-dimensional sum-frequency generation spectroscopy, and two-dimensional infrared spectroscopy to measure time-evolving structures and dynamics with femtosecond time resolution. Furthermore, we discuss the potential of multiscale molecular dynamics (MD) simulations, focusing on recently developed simulation algorithms, which have emerged as a powerful approach to interpret complex spectra. We highlight the ongoing challenges in studying heterogeneous environments in multicomponent membranes via current vibrational spectroscopic techniques and MD simulations. Overall, this review provides an up-to-date comprehensive overview of the powerful combination of vibrational spectroscopy and simulations, which has great potential to illuminate lipid-lipid, lipid-protein, and lipid-water interactions in the intricate conformational landscape of cell membranes.

Exploring the Li+ transporting mutant of NCX_Mj for assigning ion binding sites of mitochondrial NCLX

The plasma membrane (NCX) and mitochondrial (NCLX) Na⁺/Ca²⁺ exchangers are structurally related proteins, although they operate under strictly different ionic conditions and membrane potentials. In contrast with NCX, NCLX can transport either Li⁺ or Na⁺ in exchange for Ca²⁺. Whereas the crystal structure of the archaeal NCX (NCX_Mj) describes the binding sites for alternative binding of 3Na⁺ or 1Ca²⁺, these features remain elusive for NCLX due to the lack of structural information. To elucidate the ion-binding features of mitochondrial NCLX, we analyzed here the Li⁺-transporting NCLX_Mj mutant, produced by replacing the ion-coordinating residues in the archaeal NCX (NCX_Mj) to match the ion-coordinating residues of human NCLX. The NCLX_Mj-mediated Na⁺/Ca²⁺ or Li⁺/Ca²⁺ exchange rates are insensitive to varying voltage, consistent with an electroneutral ion exchange. Molecular dynamics (MD) simulations revealed that NCLX_Mj contains two novel Li⁺ binding sites with four ion-coordinating residues, derived from the three Na⁺ binding sites of NCX_Mj. The ion-coordination modes, observed in the MD simulations, were further supported by two-dimensional infrared (2D IR) spectroscopy and by testing the mutational effects on the ion fluxes. Collectively, our results revealed a structural basis for Li⁺ binding and electroneutral transport (2Na⁺/Li⁺:1Ca²⁺) by NCLX_Mj, meaning that the NCLX-mediated electroneutral transport may predefine mitochondrial Ca²⁺ and Na⁺ signaling to modulate cellular functions.

Engineering lanmodulin's selectivity for actinides over lanthanides by controlling solvent coordination and second-sphere interactions

Developing chelators that combine high affinity and selectivity for lanthanides and/or actinides is paramount for numerous industries, including rare earths mining, nuclear waste management, and cancer medicine. In particular, achieving selectivity between actinides and lanthanides is notoriously difficult. The protein lanmodulin (LanM) is one of Nature's most selective chelators for trivalent actinides and lanthanides. However, mechanistic understanding of LanM's affinity and selectivity for f-elements remains limited. In order to decipher, and possibly improve, the features of LanM's metal-binding sites that contribute to this actinide/lanthanide selectivity, we characterized five LanM variants, substituting the aspartate residue at the 9th position of each metal-binding site with asparagine, histidine, alanine, methionine, and selenomethionine. Spectroscopic measurements with lanthanides (Nd3+ and Eu3+) and actinides (243Am3+ and 248Cm3+) reveal that, contrary to the behavior of small chelator complexes, metal-coordinated water molecules enhance LanM's affinity for f-elements and pH-stability of its complexes. Furthermore, the results show that the native aspartate does not coordinate the metal directly but rather hydrogen bonds to coordinated solvent. By tuning this first-sphere/second-sphere interaction, the asparagine variant nearly doubles LanM's selectivity for actinides versus lanthanides. This study not only clarifies the essential role of coordinated solvent for LanM's physiological function and separation applications, but it also demonstrates that LanM's preference for actinides over lanthanides can be further improved. More broadly, it demonstrates how biomolecular scaffolds possess an expanded repertoire of tunable interactions compared to most small-molecule ligands - providing an avenue for high-performance LanM-based actinide/lanthanide separation methods and bio-engineered chelators optimized for specific medical isotopes.

Proton-modulated interactions of ions with transport sites of prokaryotic and eukaryotic NCX prototypes

The cytosolic pH decline from 7.2 to 6.9 results in 90% inactivation of mammalian Na⁺/Ca²⁺ exchangers (NCXs) due to protons interactions with regulatory and transport domains ("proton block"). Remarkably, the pH titration curves of mammalian and prokaryotic NCXs significantly differ, even after excluding the allosteric effects through regulatory domains. This is fascinating since "only" three (out of twelve) ion-coordinating residues (T50S, E213D, and D240N) differ between the archaeal NCX_Mj and mammalian NCXs although they contain either three or two carboxylates, respectively. To resolve the underlying mechanisms of pH-dependent regulation, the ion-coordinating residues of NCX_Mj were mutated to imitate the ion ligation arrays of mammalian NCXs; the mutational effects were tested on the ion binding/transport by using ion-flux assays and two-dimensional infrared (2D IR) spectroscopy. Our analyses revealed that two deprotonated carboxylates ligate 3Na⁺ or 1Ca²⁺ in NCX prototypes with three or two carboxylates. The Na⁺/Ca²⁺ exchange rates of NCX_Mj reach saturation at pH 5.0, whereas the Na⁺/Ca²⁺ exchange rates of the cardiac NCX1.1 gradually increase even at alkaline pHs. The T50S replacement in NCX_Mj "recapitulates" the pH titration curves of mammalian NCX by instigating an alkaline shift. Proteolytic shaving of regulatory CBD domains activates NCX1.1, although the normalized pH-titration curves are comparable in trypsin treated and untreated NCX1.1. Thus, the T50S-dependent alkaline shift sets a dynamic range for "proton block" function at physiological pH, whereas the CBDs (and other regulatory modes) modulate incremental changes in the transport rates rather than affect the shape of pH dependent curves.

Probing Lanmodulin's Lanthanide Recognition via Sensitized Luminescence Yields a Platform for Quantification of Terbium in Acid Mine Drainage

Lanmodulin is the first natural, selective macrochelator for f elements-a protein that binds lanthanides with picomolar affinity at 3 EF hands, motifs that instead bind calcium in most other proteins. Here, we use sensitized terbium luminescence to probe the mechanism of lanthanide recognition by this protein as well as to develop a terbium-specific biosensor that can be applied directly in environmental samples. By incorporating tryptophan residues into specific EF hands, we infer the order of metal binding of these three sites. Despite lanmodulin's remarkable lanthanide binding properties, its coordination of approximately two solvent molecules per site (by luminescence lifetime) and metal dissociation kinetics (k_off = 0.02-0.05 s^-1, by stopped-flow fluorescence) are revealed to be rather ordinary among EF hands; what sets lanmodulin apart is that metal association is nearly diffusion limited (k_on ≈ 10⁹ M^-1 s^-1). Finally, we show that Trp-substituted lanmodulin can quantify 3 ppb (18 nM) terbium directly in acid mine drainage at pH 3.2 in the presence of a 100-fold excess of other rare earths and a 100 000-fold excess of other metals using a plate reader. These studies not only yield insight into lanmodulin's mechanism of lanthanide recognition and the structures of its metal binding sites but also show that this protein's unique combination of affinity and selectivity outperforms synthetic luminescence-based sensors, opening the door to rapid and inexpensive methods for selective sensing of individual lanthanides in the environment and in-line monitoring in industrial operations.

CH Mode Mixing Determines the Band Shape of the Carboxylate Symmetric Stretch in Apo-EDTA, Ca2+-EDTA, and Mg2+-EDTA

The infrared spectra of EDTA complexed with Ca²⁺ and Mg²⁺ contain, to date, unidentified vibrational bands. This study assigns the peaks in the linear and two-dimensional infrared spectra of EDTA, with and without either Ca²⁺ or Mg²⁺ ions. Two-dimensional infrared spectroscopy and DFT calculations reveal that, in both the presence and absence of ions, the carboxylate symmetric stretch and the terminal CH bending vibrations mix. We introduce a method to calculate participation coefficients that quantify the contribution of the carboxylate symmetric stretch, CH wag, CH twist, and CH scissor in the 1400-1550 cm^-1 region. With the help of participation coefficients, we assign the 1400-1430 cm^-1 region to the carboxylate symmetric stretch, which can mix with CH modes. We assign the 1000-1380 cm^-1 region to CH twist modes, the 1380-1430 cm^-1 region to wag modes, and the 1420-1650 cm^-1 region to scissor modes. The difference in binding geometry between the carboxylate-Ca²⁺ and carboxylate-Mg²⁺ complex manifests as new diagonal and cross-peaks between the mixed modes in the two complexes. The small Mg²⁺ ion binds EDTA tighter than the Ca²⁺ ion, which causes a redshift of the COO symmetric stretches of the sagittal carboxylates. Energy decomposition analysis further characterizes the importance of electrostatics and deformation energy in the bound complexes.

Infrared spectroscopy probes ion binding geometries

Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.

Low-Frequency Protein Motions Coupled to Catalytic Sites

This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.

[Effect of calmodulin and its mutants on binding to NaV1.2 IQ]

OBJECTIVE

To investigate the effect of calmodulin (CaM) and its mutants on binding to voltage-gated Na channel isoleucine-glutamine domain (Na_V1.2 IQ).

METHODS

The cDNA of Na_V1.2 IQ was constructed by PCR technique, CaM mutants CaM₁₂, CaM₃₄ and CaM₁₂₃₄ were constructed with Quickchange^TM site-directed mutagenesis kit (QIAGEN). The binding of Na_V1.2 IQ to CaM and CaM mutants under calcium and calcium free conditions were detected by pull-down assay.

RESULTS

Na_V1.2 IQ and CaM were bound to each other at different calcium concentrations, while GST alone did not bind to CaM. The binding affinity of CaM and Na_V1.2 IQ at [Ca²⁺]-free was greater than that at 100 nmol/L [Ca²⁺] (P < 0.05). In the absence of calcium, the binding amount of CaM wild-type to Na_V1.2 IQ was greater than that of its mutant, and the binding affinity of CaM₁₂₃₄ to Na_V1.2 IQ was the weakest among the three mutants (P < 0.05).

CONCLUSIONS

The binding ability of CaM and CaM mutants to Na_V1.2 IQ is Ca²⁺-dependent. This study has revealed a new mechanism of Na_V1.2 regulated by CaM, which would be useful for the study of ion channel related diseases.

The Chemistry of Lanthanides in Biology: Recent Discoveries, Emerging Principles, and Technological Applications

The essential biological role of rare earth elements lay hidden until the discovery in 2011 that lanthanides are specifically incorporated into a bacterial methanol dehydrogenase. Only recently has this observation gone from a curiosity to a major research area, with the appreciation for the widespread nature of lanthanide-utilizing organisms in the environment and the discovery of other lanthanide-binding proteins and systems for selective uptake. While seemingly exotic at first glance, biological utilization of lanthanides is very logical from a chemical perspective. The early lanthanides (La, Ce, Pr, Nd) primarily used by biology are abundant in the environment, perform similar chemistry to other biologically useful metals and do so more efficiently due to higher Lewis acidity, and possess sufficiently distinct coordination chemistry to allow for selective uptake, trafficking, and incorporation into enzymes. Indeed, recent advances in the field illustrate clear analogies with the biological coordination chemistry of other metals, particularly CaII and FeIII, but with unique twists-including cooperative metal binding to magnify the effects of small ionic radius differences-enabling selectivity. This Outlook summarizes the recent developments in this young but rapidly expanding field and looks forward to potential future discoveries, emphasizing continuity with principles of bioinorganic chemistry established by studies of other metals. We also highlight how a more thorough understanding of the central chemical question-selective lanthanide recognition in biology-may impact the challenging problems of sensing, capture, recycling, and separations of rare earths.