A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein-Ligand Binding.

Relative binding free energy (RBFE) simulation is a rigorous approach to the calculation of quantitatively accurate binding free energy values for protein-ligand binding in which a reference binder is gradually converted to a target binder through alchemical transformation during the simulation. The success of such simulations relies on being able to accurately sample the correct conformational phase space for each alchemical state; however, this becomes a challenge when a significant conformation change occurs between the reference and target binder-receptor complexes. Increasing the simulation time and using enhanced sampling methods can be helpful, but effects can be limited, especially when the free energy barrier between conformations is high or when the correct target complex conformation is difficult to find and maintain.

inhibition of co-expressed DIPs and Dprs shapes neural development.

In , two interacting adhesion protein families, Dprs and DIPs, coordinate the assembly of neural networks. While intercellular DIP/Dpr interactions have been well characterized, DIPs and Dprs are often co-expressed within the same cells, raising the question as to whether they also interact in . We show, in cultured cells and that DIP-α and DIP-δ can interact in with their ligands, Dpr6/10 and Dpr12, respectively.

Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations.

Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations.

Astrocyte morphogenesis requires self-recognition.

Self-recognition is a fundamental cellular process across evolution and forms the basis of neuronal self-avoidance1-4. Clustered protocadherins (Pcdh), comprising a large family of isoform-specific homophilic recognition molecules, play a pivotal role in neuronal self-avoidance required for mammalian brain development5-7. The probabilistic expression of different Pcdh isoforms confers unique identities upon neurons and forms the basis for neuronal processes to discriminate between self and non-self5,6,8.

Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity.

The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of RBD mutations that have been frequently observed in infected individuals and probe binding affinity changes to ACE2 using surface plasmon resonance (SPR) measurements and free energy perturbation (FEP) calculations. Our SPR results are largely in accord with previous studies but discrepancies do arise due to differences in experimental methods and to protocol differences even when a single method is used.

Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules.

Neurons in the developing brain express many different cell adhesion molecules (CAMs) on their surfaces. CAM-binding affinities can vary by more than 200-fold, but the significance of these variations is unknown. Interactions between the immunoglobulin superfamily CAM DIP-α and its binding partners, Dpr10 and Dpr6, control synaptic targeting and survival of Drosophila optic lobe neurons.

Sorting of cadherin-catenin-associated proteins into individual clusters.

The cytoplasmic tails of classical cadherins form a multiprotein cadherin-catenin complex (CCC) that constitutes the major structural unit of adherens junctions (AJs). The CCC in AJs forms junctional clusters, "E clusters," driven by and interactions in the cadherin ectodomain and stabilized by α-catenin-actin interactions. Additional proteins are known to bind to the cytoplasmic region of the CCC.

DIP/Dpr interactions and the evolutionary design of specificity in protein families.

Differential binding affinities among closely related protein family members underlie many biological phenomena, including cell-cell recognition. Drosophila DIP and Dpr proteins mediate neuronal targeting in the fly through highly specific protein-protein interactions. We show here that DIPs/Dprs segregate into seven specificity subgroups defined by binding preferences between their DIP and Dpr members.

-endocytosis elicited by nectins transfers cytoplasmic cargo, including infectious material, between cells.

Here, we show that cells expressing the adherens junction protein nectin-1 capture nectin-4-containing membranes from the surface of adjacent cells in a -endocytosis process. We find that internalized nectin-1-nectin-4 complexes follow the endocytic pathway. The nectin-1 cytoplasmic tail controls transfer: its deletion prevents -endocytosis, while its exchange with the nectin-4 tail reverses transfer direction.

Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins.

Binding between DIP and Dpr neuronal recognition proteins has been proposed to regulate synaptic connections between lamina and medulla neurons in the Drosophila visual system. Each lamina neuron was previously shown to express many Dprs. Here, we demonstrate, by contrast, that their synaptic partners typically express one or two DIPs, with binding specificities matched to the lamina neuron-expressed Dprs.

Interactions between the Ig-Superfamily Proteins DIP-α and Dpr6/10 Regulate Assembly of Neural Circuits.

Drosophila Dpr (21 paralogs) and DIP proteins (11 paralogs) are cell recognition molecules of the immunoglobulin superfamily (IgSF) that form a complex protein interaction network. DIP and Dpr proteins are expressed in a synaptic layer-specific fashion in the visual system. How interactions between these proteins regulate layer-specific synaptic circuitry is not known.

Molecular basis of sidekick-mediated cell-cell adhesion and specificity.

Sidekick (Sdk) 1 and 2 are related immunoglobulin superfamily cell adhesion proteins required for appropriate synaptic connections between specific subtypes of retinal neurons. Sdks mediate cell-cell adhesion with homophilic specificity that underlies their neuronal targeting function. Here we report crystal structures of Sdk1 and Sdk2 ectodomain regions, revealing similar homodimers mediated by the four N-terminal immunoglobulin domains (Ig1-4), arranged in a horseshoe conformation.

Understanding boron through size-selected clusters: structure, chemical bonding, and fluxionality.

Boron is an interesting element with unusual polymorphism. While three-dimensional (3D) structural motifs are prevalent in bulk boron, atomic boron clusters are found to have planar or quasi-planar structures, stabilized by localized two-center-two-electron (2c-2e) σ bonds on the periphery and delocalized multicenter-two-electron (nc-2e) bonds in both σ and π frameworks. Electron delocalization is a result of boron's electron deficiency and leads to fluxional behavior, which has been observed in B13(+) and B19(-).

Theoretical study of the Si(5-n)(BH)n2- and Na(Si(5-n)(BH)n)- (n = 0-5) systems.

The potential energy surfaces of the Na(Si(5-n)(BH)(n))(-) and Si(5-n)(BH)(n)(2-) (n = 0-5) systems have been explored in detail. We established that all the global minimum structures of anionic and dianionic systems can be obtained by substitution of one or more silicon atoms of the global minima of NaSi(5)(-) and Si(5)(2-) for B-H units. The conservation of the overall structure upon isoelectronic substitution was shown to be due to the preservation of the chemical bonding pattern.

B22- and B23-: all-boron analogues of anthracene and phenanthrene.

Clusters of boron atoms exhibit intriguing size-dependent structures and chemical bonding that are different from bulk boron and may lead to new boron-based nanostructures. We report a combined photoelectron spectroscopic and ab initio study of the 22- and 23-atom boron clusters. The joint experimental and theoretical investigation shows that B(22)(-) and B(23)(-) possess quasi-planar and planar structures, respectively.

B13+ : a photodriven molecular Wankel engine.

Revved-up rotary: A molecular Wankel motor, the dual-ring structure B(13)(+), is driven by circularly-polarized infrared electromagnetic radiation. Calculations show that this illumination leads to a guided unidirectional rotation of the outer ring, which is achieved with rotational frequency of the order of 300 GHz.

A photoelectron spectroscopy and ab initio study of B21-: negatively charged boron clusters continue to be planar at 21.

The structures and chemical bonding of the B(21)(-) cluster have been investigated by a combined photoelectron spectroscopy and ab initio study. The photoelectron spectrum at 193 nm revealed a very high adiabatic electron binding energy of 4.38 eV for B(21)(-) and a congested spectral pattern.

All-boron analogues of aromatic hydrocarbons: B17- and B18-.

We have investigated the structural and electronic properties of the B(17)(-) and B(18)(-) clusters using photoelectron spectroscopy (PES) and ab initio calculations. The adiabatic electron detachment energies of B(17)(-) and B(18)(-) are measured to be 4.23 ± 0.

Deciphering the mystery of hexagon holes in an all-boron graphene α-sheet.

Boron could be the next element after carbon capable of forming 2D-materials similar to graphene. Theoretical calculations predict that the most stable planar all-boron structure is the so-called α-sheet. The mysterious structure of the α-sheet with peculiar distribution of filled and empty hexagons is rationalized in terms of chemical bonding.

Planarization of B7- and B12- clusters by isoelectronic substitution: AlB6- and AlB11-.

Small boron clusters have been shown to be planar from a series of combined photoelectron spectroscopy and theoretical studies. However, a number of boron clusters are quasiplanar, such as B(7)(-) and B(12)(-). To elucidate the nature of the nonplanarity in these clusters, we have investigated the electronic structure and chemical bonding of two isoelectronic Al-doped boron clusters, AlB(6)(-) and AlB(11)(-).

Unravelling phenomenon of internal rotation in B13+ through chemical bonding analysis.

We describe and explain the fluxionality of B(13)(+). The chemical bonding analysis shows that the inner triangle of B(13)(+) is bound to the peripheral ring by delocalized bonds only, allowing a quasi-free rotation of the inner ring.

Flattening a puckered cyclohexasilane ring by suppression of the pseudo-Jahn-Teller effect.

We report the experimental and theoretical characterization of neutral Si(6)X(12) (X = Cl, Br) molecules that contain D(3d) distorted six-member silicon rings due to a pseudo-Jahn-Teller (PJT) effect. Calculations show that filling the intervenient molecular orbitals with electron pairs of adduct suppresses the PJT effect in Si(6)X(12), with the Si(6) ring becoming planar (D(6h)) upon complex formation. The stabilizing role of electrostatic and covalent interactions between positively charged silicon atoms and chlorine atoms of the subject [Si(6)Cl(14)](2-) dianionic complexes is discussed.

Chemical bonding and aromaticity in trinuclear transition-metal halide clusters.

Trinuclear transition-metal complexes such as Re(3)X(9) (X = Cl, Br, I), with their uniquely featured structure among metal halides, have posed intriguing questions related to multicenter electron delocalization for several decades. Here we report a comprehensive study of the technetium halide clusters [Tc(3)(μ-X)(3)X(6)](0/1-/2-) (X = F, Cl, Br, I), isomorphous with their rhenium congeners, predicted from density functional theory calculations. The chemical bonding and aromaticity in these clusters are analyzed using the recently developed adaptive natural density partitioning method, which indicates that only [Tc(3)X(9)](2-) clusters exhibit aromatic character, stemming from a d-orbital-based π bond delocalized over the three metal centers.