Characterization and regulation of MT1‐MMP cell surface‐associated activity

Quantitative assessment of MT1‐MMP cell surface‐associated proteolytic activity remains undefined. Presently, MT1‐MMP was stably expressed and a cell‐based FRET assay developed to quantify activity toward synthetic collagen‐model triple‐helices. To estimate the importance of cell surface localization and specific structural domains on MT1‐MMP proteolysis, activity measurements were performed using a series of membrane‐anchored MT1‐MMP mutants and compared directly with those of soluble MT1‐MMP. MT1‐MMP activity (kcat/KM) on the cell surface was 4.8‐fold lower compared with soluble MT1‐MMP, with the effect largely manifested in kcat. Deletion of the MT1‐MMP cytoplasmic tail enhanced cell surface activity, with both kcat and KM values affected, while deletion of the hemopexin‐like domain negatively impacted KM and increased kcat. Overall, cell surface localization of MT1‐MMP restricts substrate binding and protein‐coupled motions (based on changes in both kcat and KM) for catalysis. Comparison of soluble and cell surface‐bound MT2‐MMP revealed 12.9‐fold lower activity on the cell surface. The cell‐based assay was utilized for small molecule and triple‐helical transition state analog MMP inhibitors, which were found to function similarly in solution and at the cell surface. These studies provide the first quantitative assessments of MT1‐MMP activity and inhibition in the native cellular environment of the enzyme.MT1‐MMP was stably expressed and a cell‐based FRET assay developed to quantify activity toward synthetic collagen‐model triple‐helices. Activity measurements were performed using a series of membrane‐anchored MT1‐MMP mutants and compared directly with those of soluble MT1‐MMP. Cell surface localization of MT1‐MMP was found to restrict substrate binding and protein‐coupled motions for catalysis. Small molecule and triple‐helical transition state analog MMP inhibitors were found to function similarly in solution and at the cell surface.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150520/1/cbdd13450.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150520/2/cbdd13450_am.pd

Trapping One Electron between Three Beryllium Atoms: Very Strong One-Electron Three-Center Bonds

The ability of a set of beryllium-substituted cyclohexane derivatives to trap electrons was determined by evaluating their electron affinities at the G4(MP2) level of theory. The nature of bonding and the effect of the different substituents attached to beryllium were studied by different computational methods (quantum theory of atoms in molecules, electron localization function, natural bond orbital, and analysis of the spin density), revealing the existence of a one-electron/Be cyclic bonding in trisubstituted species. This peculiar bond is the key for the high electron affinity values found in the tri-BeX derivatives (X=F, Cl, CN), such as the triberyllium cyano derivatives of cyclohexane, reaching values of 294 kJ mol, only marginally smaller than the values reported for tetracyanoethylene (305 kJ mol) and for some fullerenes (306 kJ mol).This work was performed with financial support from the Ministerio de Economía, Industria y Competitividad (project CTQ2015- 63997-C2), by the COST Action CM1204 and Comunidad Autónoma de Madrid (S2013/MIT2841, Fotocarbon). Thanks are also given to the CTI (CSIC) for their continued computational support.Peer Reviewe

Clustering of Electron Deficient B- and Be-Containing Analogues: In the Fight for Tetracoordination, Beryllium Takes the Lead

Despite being neighbors in the periodic table and highly electron-deficient elements, beryllium and boron can lead to complexes with distinctive peculiarities. CCSD(T) calculations using 6-31+G(d,p) and aug-cc-pVTZ basis sets on B3LYP optimized geometries with the same basis set expansions have been carried out to characterize the structures, bonding and stability of (BeX) : (BX) (n=0,1,2; m=0,1,2; X=F, Cl, CN, NC, CCH) complexes. The differences between Be and B are already manifested in their dimerization patterns, since (BeX) homodimers are very stable, BeX : BX heterodimers are systematically less stable than Be-homodimers, and (BX) homodimers are in almost all cases not prone to form. This trend is a reflection of the strongly electropositive nature of Be compared with B. Larger clusters exhibit the same behavior, as no stable BeX(BX) trimers can be found with two BX monomers being neighbors. Conversely, all (BeX)(BX) trimers present, as a global minimum, a structure in which the two BeX monomers are bonded, whereas for the (BeX)(BX) tetramers the (BeX) subunit is at the center of the cluster. The relevance of this binding pattern in the global stability is supported by an excellent correlation between the stabilization energies and the number of Be−Be and Be−B interactions the clusters present, with a clear preference for maximizing facing Be subunits. One obvious consequence is that the stability of the complexes increases dramatically with their size in a fashion that can be easily predicted.This work was carried out with financial support from the projectsPGC2018-094644-B-C21,PGC2018-094644-B-C22 and PID2019-110091GB-I00(MICINN)of the Ministerio de Ciencia, Innovación y Universidades of Spain.Thanks are also given to the CTI (CSIC)and to the Centro de Computación Científica of the UAM(CCC-UAM)for the generous allocation of computer time and for their continued technical suppor

Weak interactions get strong: synergy between tetrel and alkaline-earth bonds

Weak and strong noncovalent interactions such as tetrel bonds and alkaline-earth bonds, respectively, cooperate and get reinforced when acting together in ternary complexes of general formula RN··· SiHF···MY, where MY is a Be or Mg derivative and RN is a N-containing Lewis base with different hybridization patterns. Cooperativity has been studied in the optimized MP2/aug′-cc-pVTZ ternary complexes by looking at changes on geometries, binding energies, Si NMR chemical shifts, and topological features according to the atoms in molecules theoretical framework. Our study shows that cooperativity in terms of energy is in general significant: more than 40 kJ/mol, and up to 83.6 kJ/mol in the most favorable case. The weakest the isolated interaction, the strongest the reinforcement in the ternary complex; in this sense, the tetrel bond is shortened enormously, between 0.3 and 0.6 Å. This dramatic reinforcement of the tetrel bond is also nicely reflected in the positive variations of the Si chemical shifts in all the ternary complexes. At the same time the ternary complexes are characterized by the presence of totally planar silyl group, due to the pentacoordination of the Si atom. Both the hybridization of the N base and the geometry imposed by the alkaline-earth ligands have a strong influence on the binding energies, as they modify the donor ability of N and the Lewis acid character of the alkaline-earth metal.Financial support from the Ministerio de Ciencia, Innovación y Universidades (Projects PGC2018-094644-B-C21, PGC2018- 094644-B-C22, and CTQ2016-76061-P)) and Comunidad de Madrid (P2018/EMT-4329 AIRTEC-CM) is acknowledged. The authors want to thank the CTI (CSIC) and the CCCUAM (Centro de Computación Cientifíca at the Universidad Autónoma de Madrid) for the computational resources.Peer Reviewe

On predicting bonding patterns of small clusters of alkaline-earth (Be, Mg) and triel (B, Al) fluorides: a balance between atomic size and electron-deficient character

The structures, bonding and stability of (MF):(M¿F) (M = Be, Mg; M¿ = B, Al; m = 0,1,2; n = 0,1,2) clusters were obtained at the B3LYP/aug-cc-pVTZ level of theory. To understand trends across this set of closely related atoms, an analysis of the results obtained using atoms in molecules (AIM), electron localisation function (ELF) and electron density shift (EDS) approaches, permits to identify subtle dissimilarities when the first-row elements, Be and B, are replaced by the second-row counterparts, Mg and Al. For dimers this replacement involves an increase in the bonding enthalpies as a direct consequence of a much larger ionic character of the derivatives including second-row elements. For trimers and tetramers, rather stable structures involving penta-coordinated aluminium atoms are formed, which are not found for the B-containing analogues. In all clusters investigated the electronic environment around each monomer does not change significantly neither with nature of the monomers interacting with it or with the size of the cluster, though some small cooperative effects are observed when analyzing the binding enthalpies. The important consequence is that the stability of larger clusters can be easily predicted through a statistical treatment of the values obtained for the smaller ones.This work was supported by Ministerio de Ciencia, Innovación y Universidades of Spain: [Grant Number PID2019-110091GB- I00, PID2021-125207NB-C31, PID2021-125207NB-C32

Relativistic effects on NMR parameters of halogen-bonded complexes

Relativistic effects are found to be important for the estimation of NMR parameters in halogen-bonded complexes, mainly when they involve the heavier elements, iodine and astatine. A detailed study of 60 binary complexes formed between dihalogen molecules (XY with X, Y = F, Cl, Br, I and At) and four Lewis bases (NH, HO, PH and SH) was carried out at the MP2/aug-cc-pVTZ/aug-cc-pVTZ-PP computational level to show the extent of these effects. The NMR parameters (shielding and nuclear quadrupolar coupling constants) were computed using the relativistic Hamiltonian ZORA and compared to the values obtained with a non-relativistic Hamiltonian. The results show a mixture of the importance of the relativistic corrections as both the size of the halogen atom and the proximity of this atom to the basic site of the Lewis base increase.Financial support from the Ministerio de Ciencia, Innovación y Universidades (projects PGC2018-094644-B-C21, PGC2018-094644-B-C22 and CTQ2016-76061-P) and Comunidad de Madrid (P2018/EMT-4329 AIRTEC-CM). The authors want to thank the CTI (CSIC) for the computational resources

Are Anions of Cyclobutane Beryllium Derivatives Stabilized through Four-Center One-Electron Bonds?

High-level G4 ab initio calculations allowed us to show that CH(BeX) (X = H, Cl) derivatives behave as rather efficient electron capturers due to their ability to trap the extra electron through the formation of a four-membered beryllium ring. This finding is in agreement with previous work showing the ability of highly electron-deficient atoms, such as beryllium, to lead to multicenter one-electron bonds. In our particular case, the formation of the four-center bond is characterized, in very good harmony, by different topological methods such as quantum theory of atoms in molecules (QTAIM), the electron localization function (ELF), and the noncovalent interactions (NCI) approach and is accompanied by large electron affinity values, around 300 kJ·mol, in the gas phase. Preliminary results may anticipate that the ability of groups of beryllium atoms to trap electrons decays on going to bigger systems.Financial support from the Ministerio de Ciencia, Innovación y Universidades (projects PGC2018-094644-B-C21, PGC2018- 094644-B-C22, and CTQ2016-76061-P) is acknowledged. M. M. Montero-Campillo is grateful to the Ministerio de Ciencia, Innovación y Universidades, from Spain for her JoséCastillejo International Mobility grant at the Laboratoire of Chimie Thèorique (Sorbonne Universitè) in Paris. Thanks are also given to the CTI (CSIC) and the Centro de Computación Cientifí ca of the UAM (CCC-UAM) for their continued computational support

Modeling interactions between an amino acid and a metal dication: Cysteine-calcium(II) Reactions in the gas phase

The gas‐phase interactions between Ca2+ and cysteine (Cys) have been investigated through the use of electrospray ionization/mass spectrometry techniques and B3LYP/6‐311++G(3df,2p)//B3LYP/6‐311+G(d,p) density functional theory computations. The unimolecular collision‐activated decomposition of [Ca(Cys)]2+ is dominated by the loss of ammonia, a Coulomb explosion yielding NH4+ and [CaC3H3O2S]+, and the loss of H2S. The detection of lighter [C3H3OS]+ monocations indicates that the [CaC3H4O2S]2+ doubly charged species produced by the loss of ammonia undergo a subsequent Coulomb explosion yielding [C3H3OS]++CaOH+. This [C3H3OS]+ cation finally decomposes into [C2H3S]++CO. Alternatively, the aforementioned [CaC3H4O2S]2+ dications may also lead to lighter [CaCO2]2+ and [CaC2H4S]2+ dications by the loss of C2H4S and CO2, respectively. A detailed theoretical exploration of the Ca2+/Cys potential‐energy surface indicates that the salt‐bridge structures, in which the metal dication interacts with the carboxylate group of the zwitterionic form of cysteine, are at the origin of the different reaction pathways leading to the observed product ions, even though they lie higher in energy than the charge‐solvated adduct in which the metal interacts simultaneously with the carbonyl oxygen, the amino, and the SH group of its canonical form. The interaction between the metal cation and the base is essentially electrostatic, with a calculated binding energy of 560 kJ mol−1.This study was supported by the DGI Projects (no. CTQ2012‐35513‐C02), by the Project MADRISOLAR2 (Ref. S2009PPQ/1533) of the Comunidad Autónoma de Madrid, and by Consolider on Molecular Nanoscience (no. CSC2007‐00010).Peer Reviewe

Periodic trends in bond dissociation energies. A theoretical study

Bond dissociation energies (BDEs) of all possible A-X single bonds involving the first- and second-row atoms, from Li to Cl, where the free valences are saturated by hydrogens, have been estimated through the use of the G3-theory and at the B3LYP/6-311+G(3df,2pd)//B3LYP/6-31G(2df,p) DFT level of theory. BDEs exhibit a periodical behavior. The A-X (A = Li, Be, B, Na, Mg, Al, and Si) BDEs show a steady increase along the first and the second row of the periodic table as a function of the atomic number Z(X). For A-X bonds involving electronegative atoms (A = C, N, O, F, P, S, and Cl) the bond energies achieve a maximum around Z(X) = 5. The same behavior is observed when BDEs are plotted against the electronegativity χ(X) of the atom X. Thus, for A-X bonds (A = Li, Be, B, Na, Mg, Al, Si), the BDEs for a fixed A increases, grosso modo, as the electronegativity differences between X and A increase, with some exceptions, which reflect the differences in the relaxation energies of the radicals produced upon the bond cleavage. A similar trend, albeit less pronounced, is found for single A-X bonds, where A = C, N, O, F, P, S, and Cl. However, there is an additional feature embodied in the enhancement of the strength of the A-boron bonds due to the ability of boron to act as a strong electron acceptor. The trends in bond lengths and charge densities at the bond critical points are in line with the aforementioned behavior. © 2005 American Chemical Society.Peer Reviewe