Lactadherin's Multistate Binding Predicts Stable Membrane-Bound Conformations of Factors V and VIII's C Domains.

Protein binding to negatively charged lipids is essential for maintaining numerous vital cellular processes where its dysfunction can lead to various diseases. One such protein that plays a crucial role in this process is lactadherin, which competes with coagulation factors for membrane binding sites to regulate blood clotting. Despite identifying key binding regions of these proteins through structural and biochemical studies, models incorporating membrane dynamics are still lacking. In this study, we report on the multimodal binding of lactadherin and use it to gain insight into the binding mechanisms of its C domain homologs, factor V and factor VIII. Molecular dynamics simulations enhanced with the highly mobile mimetic model enabled the determination of lactadherin's multimodal binding on membranes that revealed critical interacting residues consistent with prior NMR and mutagenesis data. The binding occurred primarily via two dynamic structural ensembles: an inserted state and an unreported, highly conserved side-lying state driven by a cationic patch. We utilized these findings to analyze the membrane binding domains of coagulation factors V and VIII and identified their preferred membrane-bound conformations. Specifically, factor V's C domains maintained an inserted state, while factor VIII preferred a tilted, side-lying state that permitted antibody binding. Insight into lactadherin's atomistically resolved membrane interactions from a multistate perspective can guide new therapeutic opportunities in treating diseases related to blood coagulation.

Fungicidal amphotericin B sponges are assemblies of staggered asymmetric homodimers encasing large void volumes.

Amphotericin B (AmB) is a powerful but toxic fungicide that operates via enigmatic small molecule-small molecule interactions. This mechanism has challenged the frontiers of structural biology for half a century. We recently showed AmB primarily forms extramembranous aggregates that kill yeast by extracting ergosterol from membranes. Here, we report key structural features of these antifungal 'sponges' illuminated by high-resolution magic-angle spinning solid-state NMR, in concert with simulated annealing and molecular dynamics computations. The minimal unit of assembly is an asymmetric head-to-tail homodimer: one molecule adopts an all-trans C1-C13 motif, the other a C6-C7-gauche conformation. These homodimers are staggered in a clathrate-like lattice with large void volumes similar to the size of sterols. These results illuminate the atomistic interactions that underlie fungicidal assemblies of AmB and suggest this natural product may form biologically active clathrates that host sterol guests.

Bioinformatics-Guided Expansion and Discovery of Graspetides.

Graspetides are a class of ribosomally synthesized and post-translationally modified peptide natural products featuring ATP-grasp ligase-dependent formation of macrolactones/macrolactams. These modifications arise from serine, threonine, or lysine donor residues linked to aspartate or glutamate acceptor residues. Characterized graspetides include serine protease inhibitors such as the microviridins and plesiocin. Here, we report an update to Rapid ORF Description and Evaluation Online (RODEO) for the automated detection of graspetides, which identified 3,923 high-confidence graspetide biosynthetic gene clusters. Sequence and co-occurrence analyses doubled the number of graspetide groups from 12 to 24, defined based on core consensus sequence and putative secondary modification. Bioinformatic analyses of the ATP-grasp ligase superfamily suggest that extant graspetide synthetases diverged once from an ancestral ATP-grasp ligase and later evolved to introduce a variety of ring connectivities. Furthermore, we characterized thatisin and iso-thatisin, two graspetides related by conformational stereoisomerism from Lysobacter antibioticus. Derived from a newly identified graspetide group, thatisin and iso-thatisin feature two interlocking macrolactones with identical ring connectivity, as determined by a combination of tandem mass spectrometry (MS/MS), methanolytic, and mutational analyses. NMR spectroscopy of thatisin revealed a cis conformation for a key proline residue, while molecular dynamics simulations, solvent-accessible surface area calculations, and partial methanolytic analysis coupled with MS/MS support a trans conformation for iso-thatisin at the same position. Overall, this work provides a comprehensive overview of the graspetide landscape, and the improved RODEO algorithm will accelerate future graspetide discoveries by enabling open-access analysis of existing and emerging genomes.

Computational Studies of Relative Stabilities of Low-Spin d6 cis- and trans-[M(en)2X2]+ Complexes (M = Co, Rh, Ir): Steric and Electronic Effects in the Context of the Structural Trans Influence.

Computational studies of low spin d6 cis- and trans-[M(en)2X2]+ complexes (M = Co, Rh, Ir) employing multiple model chemistries find that isomer preferences fall into three categories. Complexes where X is largely a σ-donor (H-, CH3-, CF3-) prefer cis geometries, in keeping with predictions associated with the trans influence series. Complexes where this donor characteristic is augmented by π acceptor behavior (B(CF3)2-, BCl2-, SiCl3-) evince even greater preference for cis geometries. QTAIM charge data suggest this is marked by lower positive charge on the metal in cis complexes. In contrast, complexes where X is a π donor and low in the trans influence series (X = OH-, F-, Cl-, I-) prefer trans geometries to varying degrees. QTAIM calculations indicate that this arises because the cis complexes are destabilized by distortions of the electron density in the M-X bonds. This can be viewed conceptually as resulting from repulsions between lone pair electrons on the ligands. Complexes where the X ligands are moderately trans-influencing and can interact conjugatively (CN-, NC-, NO2-, C≡CH-) prefer trans geometries because they combine destabilization of cis geometries with enhanced stabilization of trans geometries resulting from conjugation.

Estimating Ring Strain Energies of Highly Substituted Cyclohexanes with the Semi-homodesmotic Approach: Why Substantial Ring Strain Exists for Nominally Tetrahedral Ring Carbon Atoms.

Estimation of ring strain energies (RSEs) of substituted cyclohexanes c-C6H(x)R(12-x) (R = F, Cl, Me; x = 0, 2, 4, 8, 10, 12) using homodesmotic reaction methods gives implausible results for highly substituted cases, particularly, c-C6R12. Prior work suggests that this stems from poorly canceled interactions between substituents on the acyclic reference molecules. We apply here our semi-homodesmotic approach that minimizes use of acyclic references and ensures cancellation of intramolecular substituent interactions. The approach provides RSEs that are more consistent with chemical intuition, although they are higher than expected for "strain-free" cyclohexanes. The RSE for c-C6Me12 is predicted to be 11.9 kcal mol(-1). RSEs for halogenated rings rise significantly from 8-9 kcal mol(-1) for c-1,1,2,2-C6H8R4 to 44-50 kcal mol(-1) for c-C6R12 (R = F, Cl). The increase, and accompanying observation of larger RSEs for "adjacent CR2" systems, can be tied to increased bond distances in the rings upon progressive substitution. The sizable RSE for perchlorocyclohexane suggests that it may be susceptible to ring-opening reactions, a facet of its chemistry that is currently unexplored.

A semi-homodesmotic approach for estimating ring strain energies (RSEs) of highly substituted cyclopropanes that minimizes use of acyclic references and cancels steric interactions: RSEs for c-C3R6 that make sense.

Estimation of ring strain energies (RSEs) of substituted cyclopropanes c-C(3)H(x)R(6-x) (R = F, Cl, Me; x = 0, 2, 4) using homodesmotic reaction methods has been plagued by implausible results. Prior work suggests that this stems from poorly canceled interactions between substituents on the acyclic reference molecules. We report a semi-homodesmotic approach that minimizes use of acyclic references, focusing instead on canceling substituent interactions. The method requires employing homodesmotic group equivalent reactions only for disubstituted cyclopropanes and relies solely on absolute energy calculations for more substituted rings. This provides RSEs consistent with chemical intuition regardless of the degree of substitution. We find that RSEs increase with substitution regardless of the electronic nature of R, although the increase is more dramatic when R is electron-withdrawing. The RSEs determined are consistent with QTAIM data, which show that progressive substitution always increases critical path angles. Overall, the semi-homodesmotic approach is simpler than hyperhomodesmotic reaction methods, and gives more trustworthy results.