Antigen-antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures

The structures of protein antigen-antibody (Ag-Ab) interfaces contain information about how Ab recognize Ag as well as how Ag are folded to present surfaces for Ag recognition. As such, the Ab surface holds information about Ag folding that resides with the Ab-Ag interface residues and how they interact. In order to gain insight into the nature of such interactions, a data set comprised of 53 non-redundant 3D structures of Ag-Ab complexes was analyzed. We assessed the physical and biochemical features of the Ag-Ab interfaces and the degree to which favored interactions exist between amino acid residues on the corresponding interface surfaces. Amino acid compositional analysis of the interfaces confirmed the dominance of TYR in the Ab paratope-containing surface (PCS), with almost two fold greater abundance than any other residue. Additionally TYR had a much higher than expected presence in the PCS compared to the surface of the whole antibody (defined as the occurrence propensity), along with aromatics PHE, TRP, and to a lesser degree HIS and ILE. In the Ag epitope-containing surface (ECS), there were slightly increased occurrence propensities of TRP and TYR relative to the whole Ag surface, implying an increased significance over the compositionally most abundant LYS > ASN > GLU > ASP > ARG. This examination encompasses a large, diverse set of unique Ag-Ab crystal structures that help explain the biological range and specificity of Ag-Ab interactions. This analysis may also provide a measure of the significance of individual amino acid residues in phage display analysis of Ag binding.     

Antigen-antibody interactions and structural flexibility of a femtomolar-affinity antibody

The femtomolar-affinity mutant antibody (4M5.3) generated by directed evolution is interesting because of the potential of antibody engineering. In this study, the mutant and its wild type (4-4-20) were compared in terms of antigen-antibody interactions and structural flexibility to elucidate the effects of directed evolution. For this purpose, multiple steered molecular dynamics (SMD) simulations were performed. The pulling forces of SMD simulations elucidated the regions that form strong attractive interactions in the binding pocket. Structural analysis in these regions showed two important mutations for improving attractive interactions. First, mutation of Tyr102(H) to Ser (sequence numbering of Protein Data Bank entry 1FLR ) played a role in resolving the steric hindrance on the pathway of the antigen in the binding pocket. Second, mutation of Asp31(H) to His played a role in resolving electrostatic repulsion. Potentials of mean force (PMFs) of both the wild type and the mutant showed landscapes that do not include obvious intermediate states and go directly to the bound state. These landscapes were regarded as funnel-like binding free energy landscapes. Furthermore, the structural flexibility based on the fluctuations of the positions of atoms was analyzed. It was shown that the fluctuations in the positions of the antigen and residues in contact with antigen tend to be smaller in the mutant than in the wild type. This result suggested that structural flexibility decreases as affinity is improved by directed evolution. This suggestion is similar to the relationship between affinity and flexibility for in vivo affinity maturation, which was suggested by Romesberg and co-workers [Jimenez, R., et al. (2003) Proc. Natl. Acad. Sci. U.S.A.100, 92-97]. Consequently, the relationship was found to be applicable up to femotomolar affinity levels.     

Antigen-antibody interactions and the anomalous kinetics of arylsulfatase A.

Antibodies against homogeneous rabbit liver arylsulfatase A (aryl-sulfatase sulfohydrolase, EC 3.1.6.1) were produced in a goat and the effects of these antibodies on the kinetic parameters of the enzyme have been studied. The results indicate that the binding of antibody to the enzyme does not alter the enzyme active site, since Km and -ki values are unaffected. However, a small reduction in the enzyme activity was observed as the result of a reduction of V in the enzyme-antibody complex. The binding of antibodies led to a change in the pH-rate profile, giving one broad pH optimum shifted toward higher pH value. The enzyme-antibody complex still showed the characteristic arylsulfatase A anomalous kinetics at pH 5.5, but the inactivation was significantly slower than for the native enzyme. As calculated from quantitative immuno-precipitation data, the native enzyme bound 5--7 molecules of IgG. The number of IgG molecules which bound to the turnover-modified enzyme was reduced to 3--4. The loss of antigenic determinants from the turnover-modified enzyme indicates that significant conformational changes occur during the turnover-induced modification, or that a covalent modification of residues present at the antigenic sites has occurred, or both.     

Prion domains: sequences, structures and interactions

Mammalian and most fungal infectious proteins (also known as prions) are self-propagating amyloid, a filamentous beta-sheet structure. A prion domain determines the infectious properties of a protein by forming the core of the amyloid. We compare the properties of known prion domains and their interactions with the remainder of the protein and with chaperones. Ure2p and Sup35p, two yeast prion proteins, can still form prions when the prion domains are shuffled, indicating a parallel in-register beta-sheet structure.     

Three new supramolecular networks formed via hydrogen bonding interactions: Syntheses, crystal structures and magnetic properties

Three new iron(III) citrate complexes [Fe₂(cit)₂(H₂O)₂](H₂bpa) (1), [Fe₂(cit)₂(H₂O)₂](H₂bpe) (2) and [Fe₄(cit)₄(H₂O)₄](H₂bpp)₂(H₂O) (3) (cit = C(O⁻)(COO⁻)(CH₂COO⁻)₂, bpa = 1,3-bis(4-pyridyl)ethane, bpe = 1,3-bis(4-pyridyl)ethene, bpp = 1,3-bis(4-pyridyl)propane) were synthesized and characterized by elemental analysis, spectroscopic techniques and magnetic properties. Single X-ray diffraction analyses in the 1-3 complexes reveal that the iron ion is six-coordinated and is bound by two deprotonated citrates and a pair of aqua ligands in a distorted octahedral fashion. The anionic complex contains a centro-symmetrical planar of four-membered Fe₂O₂ ring. There are significant contributions to the stabilities of the assembled lattices in 1-3 arising from the protonated pyridine analogue counterions neutralizing the anionic charges of the complexes. The units in the complexes are connected together via hydrogen bonding to form 3D supramolecular networks. The supramolecular structures of 1-2 show alternating and motif linking the anionic moieties which are in turn interwoven with cationic moieties, while 3 shows alternating and motif. The magnetic properties of 1-3 are investigated and discussed in detail.     

Transient protein-protein interactions: structural, functional, and network properties

Transient interactions, which involve protein interactions that are formed and broken easily, are important in many aspects of cellular function. Here we describe structural and functional properties of transient interactions between globular domains and between globular domains, short peptides, and disordered regions. The importance of posttranslational modifications in transient interactions is also considered. We review techniques used in the detection of the different types of transient protein-protein interactions. We also look at the role of transient interactions within protein-protein interaction networks and consider their contribution to different aspects of these networks.     

The SRS 3D module: integrating structures, sequences and features

In this paper we present SRS 3D, a new service that allows users to easily and rapidly find all related structures for a given target sequence; structures can then be viewed together with sequences, alignments and sequence features (currently from UniProt, InterPro and PDB). Extensive user feedback confirms that SRS 3D is intuitive and useful especially for those not expert in structures. AVAILABILITY: An SRS 3D server is provided at http://srs3d.ebi.ac.uk/.     

Analyzing and visualizing residue networks of protein structures

The study of individual amino acid residues and their molecular interactions in protein structures is crucial for understanding structure-function relationships. Recent work has indicated that residue networks derived from 3D protein structures provide additional insights into the structural and functional roles of interacting residues. Here, we present the new software tools RINerator and RINalyzer for the automatized generation, 2D visualization, and interactive analysis of residue interaction networks, and highlight their use in different application scenarios.     

Hydrothermal synthesis, crystal structures and properties of new Fe, Co, Ni, and Zn complexes with 6-quinolinecarboxylate: Interplay of coordinative and noncovalent interactions

Reactions of Fe^II, Co^II, Ni^II, and Zn^II salts with 6-quinolinecarboxylic acid (HL) under the hydrothermal conditions afford three monomeric complexes [M(L)₂(H₂O)₄] (M = Fe^II for 1, Co^II for 2, and Ni^II for 3) and a 1-D polymeric species {[Zn(L)₂(H₂O)] · H₂O}_n (4). The crystal structures of the ligand HL and these four complexes have been determined by using the X-ray single-crystal diffraction technique. The results suggest that complexes 1-3 are isostructural, displaying novel 3-D pillar-layered networks through multiple intermolecular hydrogen bonds, whereas in coordination polymer 4, the 1-D comb-like coordination chains are extended to generate a hydrogen-bonded layer, which is further reinforced via aromatic stacking interactions. Solid-state properties such as thermal stability and fluorescence emission of the polymeric Zn^II complex 4 have also been investigated.     

Ferrocenesuccinate-bridged lanthanide polymeric complexes: Syntheses, structures and properties

One-dimensional lanthanide-ferrocenesuccinate polymeric complexes [M(η²-FcCOC₂H₄COO)(μ₂-η²-FcCOC₂H₄COO)₂(H₂O)₂]_n (Fc = (η⁵-C₅H₄)Fe(η⁵-C₅H₄), M = Pr, 1; Ce, 2; La, 3) have been synthesized and structurally characterized by single-crystal X-ray crystallography. The three polymers are isomorphous, in which each Ln(III) ion is 10-coordinated and connects with two water molecules and eight oxygen atoms from ferrocenesuccinate units in two kinds of coordination modes: bidentate-chelating mode and tridentate-bridging mode. The variable-temperature magnetic susceptibility in the temperature range 5-300 K for 1 and 2 shows that both of them display weak antiferromagnetic interaction. In addition, the redox and fluorescent properties have been investigated. The redox properties are different from the previous results of transition metal compounds containing ferrocenyl systems. Compared with sodium ferrocenesuccinate, polymers 1 and 3, the fluorescent intensities of 2 are markedly enhanced in the solid state.     

Insect antimicrobial peptides: structures, properties and gene regulation

Antimicrobial peptides (AMPs) are part of the armament that insects have developed to fight off pathogens. Insect AMPs are typically cationic and often made of less than 100 amino acid residues. Although their structures are diverse, most of the AMPs can be assigned to a limited number of families. The most common structures are represented by peptides assuming a alpha-helical conformation in organic solutions or disulfide-stabilized beta-sheets with or without alpha-helical domains present. The diverse activity spectrum of these peptides may indicate different modes of action. Genetic analysis in the Drosophila model evidenced that multiple signal transduction pathways are activating the genes coding AMPs.     

m-Terphenylphosphines: Synthesis, structures and coordination properties

A series of m-terphenylphosphines TerphPCl₂, TerphPH₂ and TerphPMe₂ (Terph = 2,6-Mes₂C₆H₃-, 2,6-(4-t-BuC₆H₄)₂C₆H₃-, 2,6-(3,5-Me₂C₆H₃)₂C₆H₃-, 2,6-(2,6-Et₂C₆H₃)₂C₆H₃-, and 2,6-(2,6-i-Pr₂C₆H₃)₂C₆H₃-; Mes = 2,4,6-Me₃C₆H₂-) was prepared and fully characterized. The structural investigation by X-ray crystallography and density functional theory revealed significant distortions in the environment of the ipso carbon and phosphorus centers. These can be traced back to steric interactions and repulsions of the chlorine and methyl substituents on phosphorus with one of the flanking arenes of the m-terphenyl substituents. The primary phosphine 2,6-Mes₂C₆H₃PH₂, 6, and the dimethylphosphine 2,6-(3,5-Me₂C₆H₃)₂C₆H₃PMe₂, 9, readily form complexes with the Cl₂Ru(p-cymene) complex fragment, whereas the larger phosphine 2,6-Mes₂C₆H₃PMe₂, 8, does not. Heating of the complexes TerphPR₂Ru(Cl₂)(p-cymene) 11 and 12 and the mixture of 8 and {(p-cymene)RuCl₂}₂ lead to expulsion of the p-cymene ligand and intramolecular η⁶ coordination of one of the flanking arene rings to the ruthenium center to afford the complexes Cl₂RuP(H₂)C₆H₃-2-η⁶-Mes-6-Mes, 13, Cl₂RuP(Me₂)C₆H₃-2-η⁶-Mes-6-Mes, 14, and Cl₂RuP(H₂)C₆H₃-2-η⁶-(3,5-Me₂C₆H₃)-6-(3,5-Me₂C₆H₃), 15. All complexes were characterized by NMR spectroscopy and complexes 14 and 15 also by X-ray crystallography.     

Gramicidin S analogs with a D-Ala, Gly, or L-Ala residue in place of the D-Phe residue: molecular conformations and interactions with phospholipid membrane

The proton nmr and CD spectra of gramicidin S (GS) cyclic-(Val^1,1′-Orn^2,2′-Leu^3,3′-D-Phe^4,4′-Pro^5,5′)₂ and of GS analogs—namely, [D-Ala^4,4′]-GS, [Gly^4,4′]-GS, and [L-Ala^4,4′]-GS—were analyzed. The molecular conformation of [D-Ala^4,4′]-GS is similar to that of GS, with the trans form about the D-Ala-Pro peptide bond. The molecular conformation of [Gly^4,4′]-GS depends on the solvent composition of dimethylsulfoxide-d₆/trifluoroethanol (DMSO)-d₆/TFE and DMSO-d₆/H₂O as well as the solute concentration. In DMSO-d₆ solution, [Gly^4,4′]-GS forms the GS-type conformation of the monomer at lower concentration. At higher concentration, the GS-type conformer is converted to the other one that forms molecular aggregates. The cis form about the X-Pro peptide bonds is found for [Gly^4,4′]-GS and [L-Ala^4,4′]-GS in DMSO-d₆ and for [L-Ala^4,4′]-GS in TFE solution. The large temperature dependences of α-proton chemical shifts of [L-Ala^4,4′]-GS in DMSO-d₆ solution indicate that the conformer equilibrium changes with temperature. The GS-type conformation is not formed in [L-Ala^4,4′]-GS. The two active peptide analogs, [D-Ala^4,4′]-GS and [Gly^4,4′]-GS, interact with the phospholipid membrane, taking the GS-type conformation. By contrast, an inactive analog, [L-Ala^4,4′]-GS, does not interact with phospholipid membrane. The activities of GS analogs are found to correlate to the formation of the GS-type conformation upon binding with phospholipid membrane.     

Protecting the hedgerow: p53 and Hedgehog pathway interactions

A common environment for the Hedgehog (Subfamily: Erinaceinae) is a row of shrubs and trees often used on farms for enclosing or separating fields, called a hedgerow. Maintenance of a continuous shrub border is important for shielding crops from weather damage, but also provides an ideal protective habitat for the hedgehog. Similar to its mammalian counterpart, the Hedgehog (Hh) signalling pathway requires a controlled environment to regulate proper functioning of the cell. When allowed to run wild, constitutive activation of the Hh pathway results in tumorigenesis in different tissues types, including brain, skin and cartilage. With an additional loss of p53 tumour suppressor activity, an increase in tumour incidence, size and metastasis have been observed. P53 has a number of functions that can suppress tumour formation and growth in most, if not all Hh-related cancers, such as the inhibition of cell cycle progression and cell survival. Furthermore, increasing evidence of an interaction between p53 and Hedgehog signalling pathways suggests a critical role for the tumour suppressor activity of p53 in “protecting the hedgerow”.     

RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties

The secondary structures of nucleic acids form a particularly important class of contact structures. Many important RNA molecules, however, contain pseudo-knots, a structural feature that is excluded explicitly from the conventional definition of secondary structures. We propose here a generalization of secondary structures incorporating ‘non-nested’ pseudo-knots, which we call bi-secondary structures, and discuss measures for the complexity of more general contact structures based on their graph-theoretical properties. Bi-secondary structures are planar trivalent graphs that are characterized by special embedding properties. We derive exact upper bounds on their number (as a function of the chain length n) implying that there are fewer different structures than sequences. Computational results show that the number of bi-secondary structures grows approximately like 2.35ⁿ. Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. We find a large fraction of neutral mutations and, in particular, networks of sequences that fold into the same shape. These neutral networks percolate through the entire sequence space.     

Binding and spectroscopic properties of ostrich neurophysins. Probing the role of residue 35 at the monomer-monomer interface.

Binding and spectroscopic properties of ostrich neurophysins were examined with emphasis on the behavior of Tyr-35, a residue that provides a potential probe of the monomer-monomer interface and of allosteric interrelationships between this region and the binding site. Mesotocin-associated ostrich neurophysin was found to bind oxytocin and related peptides with affinities comparable to the mammalian proteins, but induced a significantly different optical activity in bound peptides than the mammalian proteins. Gel-filtration studies indicated higher dimerization constants for the ostrich neurophysins than for the bovine neurophysins. Consistent with this, Tyr-35 was found to be largely buried, as monitored by tyrosine titration and lack of reactivity towards tetranitromethane under non-denaturing conditions. Reaction of Tyr-35 of the mesotocin-associated protein with tetranitromethane under denaturing conditions, followed by refolding, allowed isolation of an active product with an altered interface region as partially evidenced by its titration properties and consistent with its markedly altered CD spectrum. Comparison of the CD spectra of the modified and native proteins and analysis of pH effects indicated the contribution of Tyr-35 to an unusual 237 nm band in the mesotocin-associated protein. Small shifts in the 350 nm CD band of nitrated Tyr-35 on binding peptide and apparent effects of nitration on the induced optical activity in bound peptide provided evidence of at least weak structural communication between Tyr-35 and the binding site. However, no significant effect of nitration on binding affinity was observed, suggesting that, in the mesotocin-associated protein, the region around residue 35 is not a stringent modulator of the thermodynamic behavior of the binding site.     

Bird interactions with utility structures: collision and electrocution, causes and mitigating measures

The causes of collision and electrocution accidents involving birds and power lines, and measures to mitigate such accidents, are reviewed. It is convenient to group the causes according to (1) biological, (2) topographical, (3) meteorological and (4) technical aspects. As regards collisions with power lines, the important biological variables are connected with the morphology, aerodynamic capability, physiology, behaviour and life-history strategies of birds. To understand the electrocution problem, the relationship between body size and electrocuting installations must be considered. Removing earth wires (and modifying earthing methods). modifying line, pole and tower design, installing underground cables and conspicuous marking of lines, poles and towers are important measures for tackling the problems. The route planning process should include careful mapping of (1) topographical features which are leading lines and flight lanes for migrating birds and/or are important for local movements of resident species, (2) topographical elements such as cliffs and rows of trees that force birds to fly over power lines, (3) primary ornithological functions or uses of the area to avoid key areas for birds and avoid separating these areas and (4) local climatic conditions (including seasonal variations) like fog frequency and prevailing wind direction. The outcome depends largely on a combination of these factors. Objective assessment of the effects of mitigating measures, in particular wire marking, is required. The mitigating efforts should be directed against species known to be potential collision victims, and their design should be the result of a careful analysis of the biology and ecology of the target species. Because of the cumulative effects of negative impacts on bird populations today and the alarming number of species with endangered or vulnerable status being killed in connection with utility structures, the problem deserves increased general awareness.     

Pacemaker synaptic interactions: Modelled locking and paradoxical features

This communication describes a model for two pacemaker (i.e., regularly firing) nerve cells, such that one elicits IPSP's in the other. The assumptions involve essentially a linear dependence (delay function) of the postsynaptic interval lengthening (or delay) produced by the IPSP's on the position (or phase) with respect to the preceding spike of the latter's arrival. When the number of IPSP's in an interval increases, both the slope and intercept of the delay function increase, the former remaining under 2 and the latter unboundedly. Assumptions are more or less close to the actual biological reality, or are made for convenience. A recurrence equation for the phase can be calculated, as well as an expression for the locking phase (see below). Plots of postsynaptic vs presynaptic firing intensity averaged over steady conditions, e.g. of mean rates or intervals, are formed by a sequence of relatively broadparadoxical segments exhibiting positive slopes 1, 2, 1/2, 3, 1/3, ..., indicating that inhibited discharges are made more intense by those increases in inhibitory arrivals. These segments are separated by narrower intercalated segments where behavior is unclear except for a large overall negative slope, indicating that inhibited discharges are weakened markedly by other increases in inhibitory arrivals. Across the successive paradoxical segments that correspond to more and more intense presynaptic discharges (i.e., to higher rates or shorter intervals), postsynaptic intensities, though overlapping in part, become weaker and weaker. At the extremes, when the presynaptic discharge is very weak, or very intense, the postsynaptic cell tends to its natural undisturbed firing, or to not firing at all, respectively. The pre- and postsynaptic discharges inevitably achieve eventually an invariant relation, i.e., will lock at a constant phase, regardless of the phase of the first IPSP arrival. The characteristics of this behavior (e.g., the rate bounds of the paradoxical segments, or the magnitude of the locked phase) depend on such givens as presynaptic and postsynaptic pacemaker rates or intervals, and as the slope or intercept of the delay function.