Steric effects on multivalent ligand-receptor binding: exclusion of ligand sites by bound cell surface receptors.

Steric effects can influence the binding of a cell surface receptor to a multivalent ligand. To account for steric effects arising from the size of a receptor and from the spacing of binding sites on a ligand, we extend a standard mathematical model for ligand-receptor interactions by introducing a steric hindrance factor. This factor gives the fraction of unbound ligand sites that are accessible to receptors, and thus available for binding, as a function of ligand site occupancy. We derive expressions for the steric hindrance factor for various cases in which the receptor covers a compact region on the ligand surface and the ligand expresses sites that are distributed regularly or randomly in one or two dimensions. These expressions are relevant for ligands such as linear polymers, proteins, and viruses. We also present numerical algorithms that can be used to calculate steric hindrance factors for other cases. These theoretical results allow us to quantify the effects of steric hindrance on ligand-receptor kinetics and equilibria.     

The cooperative binding of large ligands to a one-dimensional lattice: the steric hindrance effect

The cooperative binding of monomeric ligands to a long lattice of a linear polymer with complete or partial steric hindrance is treated using a matrix method. Results and typical calculations of the model are represented. Non-saturated cooperative binding as well as two-step (biphasic) binding isotherms can be interpreted by the steric hindrance model. This is applicable to the analysis of the binding of surfactants to polymer. The usefulness and the limitation also are discussed.     

Structural analysis of the inhibition of thermolysin by an active-site-directed irreversible inhibitor

The mode of binding of the irreversible thermolysin inhibitor ClCH2CO-DL-(N-OH)Leu-OCH3 [Rasnick, D., & Powers, J.C. (1978) Biochemistry 17, 4363-4369] has been determined by X-ray crystallography at a resolution of 2.3 A and the structure of the covalent complex refined to give a crystallographic residual of 17.0%. This is the first such structural study of an active-site-directed covalent complex of a zinc protease. As anticipated by Rasnick and Powers, the inhibitor alkylates Glu-143 in the thermolysin active site, and the hydroxamic acid moiety coordinates the zinc ion. The formation of the covalent complex is associated with a significant shift in a segment of the polypeptide backbone in the vicinity of the active site. This conformational adjustment appears to be necessary to relieve steric hindrance which would otherwise prevent alkylation of Glu-143. It is suggested that this steric hindrance, which occurs for thermolysin but would not be expected for carboxypeptidase A, accounts for the previously inexplicable difference in reactivity of these two metalloproteases toward N-haloacetyl amino acids. The relevance of this steric hindrance to the mechanism of catalysis is discussed. In agreement with previous results [Kester, W. R., & Matthews, B. W. (1977) Biochemistry 16, 2506-2516], it appears that steric hindrance prevents the direct attack of Glu-143 on the carbonyl carbon of an extended substrate, therefore ruling out the anhydride pathway in thermolysin-catalyzed hydrolysis of polypeptide substrates and their ester analogues.     

Biotreatment of waste gas containing pyridine in a biofilter

Industrial waste gas emissions containing pyridine are generated from pyridine manufacturing industries, and in industrial operations where pyridine is used as a solvent, as an intermediate for synthesis and as a catalyst for a variety of applications. Pyridine has unpleasant fishy odor with an odor index of 2390 and waste gaseous emissions containing pyridine require proper treatment prior to discharge. A biofilter, packed with compost and wood chips and inoculated with Pseudomonas pseudoalcaligenes-KPN for enrichment of pyridine-degrading microorganisms, was operated on a continuous feed basis for a period of more than 2 years. The results indicate that the biofilter medium with optimal moisture content of 68% and an effective bed retention time (EBRT) of 28.50s could degrade pyridine effectively (>99%) at a loading of 434 g pyridine m(-3)h(-1). The treated waste gas was also found to be free from pyridine odor.     

Breast Cancer Cells Adapt Contractile Forces to Overcome Steric Hindrance

Cell migration through the extracellular matrix is governed by the interplay between cell-generated propulsion forces, adhesion forces, and resisting forces arising from the steric hindrance of the matrix. Steric hindrance in turn depends on matrix porosity, matrix deformability, cell size, and cell deformability. In this study, we investigate how cells respond to changes in steric hindrance that arise from altered cell mechanical properties. Specifically, we measure traction forces, cell morphology, and invasiveness of MDA-MB 231 breast cancer cells in three-dimensional collagen gels. To modulate cell mechanical properties, we either decrease nuclear deformability by twofold overexpression of the nuclear protein lamin A or we introduce into the cells stiff polystyrene beads with a diameter larger than the average matrix pore size. Despite this increase of steric hindrance, we find that cell invasion is only marginally inhibited, as measured by the fraction of motile cells and the mean invasion depth. To compensate for increased steric hindrance, cells employ two alternative strategies. Cells with higher nuclear stiffness increase their force polarity, whereas cells with large beads increase their net contractility. Under both conditions, the collagen matrix surrounding the cells stiffens dramatically and carries increased strain energy, suggesting that increased force polarity and increased net contractility are functionally equivalent strategies for overcoming an increased steric hindrance.     

Steric hindrance of growth of filamentous fungi in solid substrate fermentation of wheat straw

Cellulolytic fungi, such as Trichoderma reesei, T. lignorum, and Chaetomium cellulolyticum reach a low packing density of mycelia when grown on straw under conditions of solid substrate fermentation. The low packing density is shown to be caused partially by the geometric limitation of the growth of mycelia in the substrate and particularly in its pores, but the exact contribution of this limitation and other limitations such as mass transfer and substrate availability cannot be easily distinguished. The combined effect of such limitations is called steric hindrance. This steric hindrance is associated with and may be the principal cause of low biomass concentration in SSF.     

Seven coordinate complexes of metal(II) nitrates

ESR spectra at both X and Q band are reported for manganese(II) ions doped into the seven coordinate complexes M(L)₃(NO₃)₂ (M = Co, Ni, Zn or Cd; L = pyridine or substituted pyridine). The zero field splitting parameters D and λ (= E/D) are deduced. All complexes show considerable deviation from cubic symmetry, as can be expected for a seven coordinate structure. The distinctly lower D value of Ni(Mn)(pyridine)₃(NO₃)₂, as compared to the analogous cobalt and zinc complex, suggests a geometry tending towards an octahedral structure. The steric hindrance by the substituent reduces the D value.     

Strategy in drug reseabch. Synthesis and study of the psogestational and ovulation inhibitory activity of a series of 11β-substituted-17α-ethynyl-4-estren-17β-ols

Using the strategy based on the Hansch method which analyses effects of substituents on biological activity in terms of their hydrophobic, electronic and steric effects we selectively synthesised a series of 11β-substituted-17α-ethynyl-4-estren-17β-ols that combine ease of synthesis with good discrimination between these factors aiming at finding the compounds with optimum biological activity in that series. The compounds were tested quantitatively in the Clauberg test (rabbit) and the ovulation inhibition test (rat). The differences in biological activity could reasonably be correlated with two steric effects introduced by the 11β-substituent. These were a change in the overall shape of the 11β-substituent and the angular methyl group, and direct steric hindrance of the steroid-receptor protein binding. Some exceptions were found possibly due to metabolic conversion of these compounds to the corresponding 11β-substituted-17α-ethynyl-l,5,5(10)-estratriene-5, 17β-diols.     

Solid angle as steric parameter of acyclic saturated groups

With the early aim of quantifying steric consequences of chirality, efforts to define a nonempirical steric parameter of chemical groups are reported. Steric hindrance of a reacting center by any acyclic saturated R group has been characterized by a geometric “axial steric parameter”: the solid angle of R. When the group is a “symmetric top substituent” (i.e., when all the terminal atoms are equivalent), the solid angle matches the solid angle of a cone envelope of R. The definition of this cone is compared with Tolman's definition of a ligand cone in organometallic complexes. The chemical significance of this parameter is shown by an excellent correlation with the Dubois' experimental steric parameter E′_s. Modeling steric repulsion by the cone of R, and correcting solid angles for conformational effects, only 3 empirical coefficients are needed to calculate 33 values of E′_s with less than 10% error. The cone model is suggested to be relevant within the limits of random and independent free rotations about all the bonds in the C–R group. A separation between “axial cone steric hindrance” and other steric effects is proposed. The basic model and the corrections proposed allow the conformational features of esters to be discussed.     

Are the 11-oxo-steroids really so hindered towards organometallic compounds?

Allylation of an 11-oxo-steroid, the protected adrenosterone, was studied to examine more closely the steric hindrance of such a ketosteroid. While the beta face exhibits, as well known, a strong steric hindrance, the alpha side appears to be only relatively hindered. A high diastereoselectivity was observed in the addition of crotyl magnesium bromide.     

Antibody binding in proximity to the receptor/glycoprotein complex leads to a basal level of virus neutralization

Hypothetically, antibodies may neutralize enveloped viruses by diverse mechanisms, such as disruption of receptor binding, interference with conformational changes required for virus entry, steric hindrance, or virus aggregation. Here, we demonstrate that retroviral infection mediated by the avian sarcoma-leukosis virus (ASLV-A) envelope glycoproteins can be neutralized by an antibody directed against a functionally unimportant component of a chimeric receptor protein. Thus, the binding of an antibody in proximity to the retroviral envelope glycoprotein-receptor complex, without binding to the entry machinery itself, results in neutralization. This finding provides additional support for the hypothesis that steric hindrance is sufficient for antibody-mediated neutralization of retroviruses.     

Synthesis and cytotoxic activity of A-ring modified betulinic acid derivatives

New A-ring modified betulinic acid derivatives having small steric hindrance were prepared and tested for cytotoxic activity on 3 cancer cell lines: 10 compounds showed stronger cytotoxic activity than betulinic acid. Especially, the compounds bearing 1-ene-3-oxo with electron-withdrawing groups at C2 showed strong cytotoxicity.     

Novel oxazolidinone based compounds as inhibitors of aromatase and the use of the substrate-heme complex approach in the rationalisation of these compounds

The synthesis, biochemical evaluation and molecular modelling of a series of N-alkylated 4-(4(')-aminobenzyl)-2-oxazolidinones is described involving the derivatisation of the starting R- or S-enantiomer of 4-benzyl-2-oxazolidinones. The compounds were tested for human placental aromatase (AR) inhibition in vitro and were found, in general, to be more potent than the standard compound, aminoglutethimide (AG). The inhibitory activity of the compounds was rationalised through the use of the novel substrate-heme complex (SHC) approach and suggests that the S-enantiomer based compounds protrude beyond the C(13), C(17), and C(16) area of the steroid backbone, resulting in steric hindrance with the active site of AR and thus reduced inhibitory activity. The R-enantiomer based compounds do not protrude in the same area and as such are not thought to undergo any steric hindrance and in comparison to the S-enantiomer, possess greater inhibitory activity.     

A method for fast safety screening of explosives in terms of crystal packing and molecular stability

Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide.     

Discovery of 3,3-dimethyl-5-hydroxypipecolic hydroxamate-based inhibitors of aggrecanase and MMP-13

A series of pipecolic hydroxamate inhibitors of MMP-13 and aggrecanase was discovered based on screening known inhibitors of TNF-alpha converting enzyme (TACE). Potency versus aggrecanase was optimized by modification of the benzyloxyarylsulfonamide group. Incorporation of geminal alkyl substitution at the 3-position of the piperidine ring improved metabolic stability, presumably by increasing steric hindrance around the metabolically labile hydroxamic acid. This modification also resulted in dramatic improvement of aggrecanase activity with a slight reduction in selectivity versus MMP-1. Synthesis, structure activity relationships, and strategies to reduce metabolic clearance are described.     

Regioselectivity of enzymatic modification of poly(methyl acrylate)

Enzymes are potentially useful catalysts for polymerization as well as modification of polymers. While lipases have been used previously for polymerization reactions, they have not been used for modification of polymers. In this report, lipases were used to determine regioselective modification of ester functions in a telomer of poly(methyl acrylate). The influence of chain length on the extent of transesterification of methyl acrylate telomers of DP(n) 6-50 was studied by examining the relationship between the extents of enzymic modification to other telomerization parameters. The regioselectivity was observed when the average DP(n) of telomers is in a range of 6-22. At a higher DP(n) (>22), however, the average number of reacting ester functions per telomer strongly deviated from the theoretically predicted value. This phenomenon was suspected as a result of steric hindrance caused by folding of longer telomer chains. To verify this hypothesis, acrylate telomers at a DP(n) ranging from 10 to 42 were synthesized using a shorter telogen, i.e., 2,2'-ethanedithiol. The transesterification of these telomers showed a deviation in a degree of conversion when DP(n) was greater than 10, possibly indicating the inhibition caused by steric hindrance. Therefore, regioselective modification of acrylic polymers, which is difficult to achieve by conventional chemical methods, may be accomplished enzymatically.     

N-Acylation of stimulatory amino acids changes chiral recognition of the fleshfly labellar sugar receptor

Summary N-Acylation changed nonstimulatory Dvaline into a clear stimulant of the sugar receptor of the fleshfly,Boettcherisca peregrina. Of theN-acyl-D-valines, the most stimulatory wasN-acetyl-D-valine. Similar changes into stimulants were also observed in other aliphatic amino acids such as leucine and methionine. Dose-response curves ofN-acetyl-D-valine suggested an increase of binding affinity, compared with that ofN-acetyl-L-valine. By treatment experiment with pronase 10 mg/ml, stimulatoryN-acetyl-D-amino acids were suggested to react with the specific alkyl site (R site), which was presumed to discriminate between L- and D-forms of the amino acids through steric hindrance between its own spatial barrier and D-amino acids (Shimada and Isono 1978; Shimada and Tanimura 1981).This change of chiral recognition cannot be explained by simple steric hindrance at the R site. It means, instead, that a hydrophobic subsite rather than a spatial barrier must be postulated.     

Pretreatment of lipase with soybean oil before immobilization to prevent loss of activity

Lipase was pretreated with soybean oil in order to allow fatty acids to bond to the active site before immobilization. This pretreated lipase exhibited steric hindrance around the active site such that during immobilization, covalent bonds were formed between the carrier and the lipase region far from the active site. The activity of the pretreated lipase immobilized covalently on a silica gel was 530 U/g-matrix, which is 16 times higher than that of the immobilized non-pretreated lipase. In addition, the immobilized lipase activity was maintained at levels exceeding 90% of its original activity after 10 reuses.     

Gating of the ATP-sensitive K+ channel by a pore-lining phenylalanine residue

ATP-sensitive K(+) (K(ATP)) channels are gated by intracellular ATP, proton and phospholipids. The pore-forming Kir6.2 subunit has all essential machineries for channel gating by these ligands. It is known that channel gating involves the inner helix bundle of crossing in which a phenylalanine residue (Phe168) is found in the TM2 at the narrowest region of the ion-conduction pathway in the Kir6.2. Here we present evidence that Phe168-Kir6.2 functions as an ATP- and proton-activated gate via steric hindrance and hydrophobic interactions. Site-specific mutations of Phe168 to a small amino acid resulted in losses of the ATP- and proton-dependent gating, whereas the channel gating was well maintained after mutation to a bulky tryptophan, supporting the steric hindrance effect. The steric hindrance effect, though necessary, was insufficient for the gating, as mutating Phe168 to a bulky hydrophilic residue severely compromised the channel gating. Single-channel kinetics of the F168W mutant resembled the wild-type channel. Small residues increased P(open), and displayed long-lasting closures and long-lasting openings. Kinetic modeling showed that these resulted from stabilization of the channel to open and long-lived closed states, suggesting that a bulky and hydrophobic residue may lower the energy barrier for the switch between channel openings and closures. Thus, it is likely that the Phe168 acts as not only a steric hindrance gate but also potentially a facilitator of gating transitions in the Kir6.2 channel.     

Molecular mechanism of translocation through nuclear pore complexes during nuclear protein import.

The trafficking of macromolecules between cytoplasm and nucleus through nuclear pore complexes is mediated by specific carrier molecules such as members of the importin-beta family. Nuclear pore proteins (nucleoporins) frequently contain sequence repeats based on FG cores and carriers appear to move their cargo through the pores by hopping between successive FG cores. A major question is why some macromolecules are transported while others are not. This selectivity may be generated by the ability to bind FG repeats, a local concentration of carrier-cargo complexes near the entrance to the pore channel, and steric hindrance produced by high concentrations of nucleoporins in the channel.