Interleukin-10 contributes to reservoir establishment and persistence in SIV-infected macaques treated with antiretroviral therapy

Interleukin-10 (IL-10) is an immunosuppressive cytokine that signals through STAT3 to regulate T follicular helper (Tfh) cell differentiation and germinal center formation. In SIV-infected macaques, levels of IL-10 in plasma and lymph nodes (LNs) were induced by infection and not normalized with antiretroviral therapy (ART). During chronic infection, plasma IL-10 and transcriptomic signatures of IL-10 signaling were correlated with the cell-associated SIV-DNA content within LN CD4+ memory subsets, including Tfh cells, and predicted the frequency of CD4+ Tfh cells and their cell-associated SIV-DNA content during ART, respectively. In ART-treated rhesus macaques, cells harboring SIV-DNA by DNAscope were preferentially found in the LN B cell follicle in proximity to IL-10. Finally, we demonstrated that the in vivo neutralization of soluble IL-10 in ART-treated, SIV-infected macaques reduced B cell follicle maintenance and, by extension, LN memory CD4+ T cells, including Tfh cells and those expressing PD-1 and CTLA-4. Thus, these data support a role for IL-10 in maintaining a pool of target cells in lymphoid tissue that serve as a niche for viral persistence. Targeting IL-10 signaling to impair CD4+ T cell survival and improve antiviral immune responses may represent a novel approach to limit viral persistence in ART-suppressed people living with HIV.

Characterization and Modeling of Reversible Antibody Self-Association Provide Insights into Behavior, Prediction, and Correction

Reversible antibody self-association, while having major developability and therapeutic implications, is not fully understood or readily predictable and correctable. For a strongly self-associating humanized mAb variant, resulting in unacceptable viscosity, the monovalent affinity of self-interaction was measured in the low μM range, typical of many specific and biologically relevant protein-protein interactions. A face-to-face interaction model extending across both the heavy-chain (HC) and light-chain (LC) Complementary Determining Regions (CDRs) was apparent from biochemical and mutagenesis approaches as well as computational modeling. Light scattering experiments involving individual mAb, Fc, Fab, and Fab'2 domains revealed that Fabs self-interact to form dimers, while bivalent mAb/Fab'2 forms lead to significant oligomerization. Site-directed mutagenesis of aromatic residues identified by homology model patch analysis and self-docking dramatically affected self-association, demonstrating the utility of these predictive approaches, while revealing a highly specific and tunable nature of self-binding modulated by single point mutations. Mutagenesis at these same key HC/LC CDR positions that affect self-interaction also typically abolished target binding with notable exceptions, clearly demonstrating the difficulties yet possibility of correcting self-association through engineering. Clear correlations were also observed between different methods used to assess self-interaction, such as Dynamic Light Scattering (DLS) and Affinity-Capture Self-Interaction Nanoparticle Spectroscopy (AC-SINS). Our findings advance our understanding of therapeutic protein and antibody self-association and offer insights into its prediction, evaluation and corrective mitigation to aid therapeutic development.

Predicting Antibody Developability Profiles Through Early Stage Discovery Screening

Monoclonal antibodies play an increasingly important role for the development of new drugs across multiple therapy areas. The term 'developability' encompasses the feasibility of molecules to successfully progress from discovery to development via evaluation of their physicochemical properties. These properties include the tendency for self-interaction and aggregation, thermal stability, colloidal stability, and optimization of their properties through sequence engineering. Selection of the best antibody molecule based on biological function, efficacy, safety, and developability allows for a streamlined and successful CMC phase. An efficient and practical high-throughput developability workflow (100 s-1,000 s of molecules) implemented during early antibody generation and screening is crucial to select the best lead candidates. This involves careful assessment of critical developability parameters, combined with binding affinity and biological properties evaluation using small amounts of purified material (<1 mg), as well as an efficient data management and database system. Herein, a panel of 152 various human or humanized monoclonal antibodies was analyzed in biophysical property assays. Correlations between assays for different sets of properties were established. We demonstrated in two case studies that physicochemical properties and key assay endpoints correlate with key downstream process parameters. The workflow allows the elimination of antibodies with suboptimal properties and a rank ordering of molecules for further evaluation early in the candidate selection process. This enables any further engineering for problematic sequence attributes without affecting program timelines.

Crystal Structure and Characterization of Human Heavy-Chain Only Antibodies Reveals a Novel, Stable Dimeric Structure Similar to Monoclonal Antibodies

We report the novel crystal structure and characterization of symmetrical, homodimeric humanized heavy-chain-only antibodies or dimers (HC2s). HC2s were found to be significantly coexpressed and secreted along with mAbs from transient CHO HC/LC cotransfection, resulting in an unacceptable mAb developability attribute. Expression of full-length HC2s in the absence of LC followed by purification resulted in HC2s with high purity and thermal stability similar to conventional mAbs. The V_H and C_H1 portion of the heavy chain (or Fd) was also efficiently expressed and yielded a stable, covalent, and reducible dimer (Fd2). Mutagenesis of all heavy chain cysteines involved in disulfide bond formation revealed that Fd2 intermolecular disulfide formation was similar to Fabs and elucidated requirements for Fd2 folding and expression. For one HC2, we solved the crystal structure of the Fd2 domain to 2.9 Å, revealing a highly symmetrical homodimer that is structurally similar to Fabs and is mediated by conserved (C_H1) and variable (V_H) contacts with all CDRs positioned outward for target binding. Interfacial dimer contacts revealed by the crystal structure were mutated for two HC2s and were found to dramatically affect HC2 formation while maintaining mAb bioactivity, offering a potential means to modulate novel HC2 formation through engineering. These findings indicate that human heavy-chain dimers can be secreted efficiently in the absence of light chains, may show good physicochemical properties and stability, are structurally similar to Fabs, offer insights into their mechanism of formation, and may be amenable as a novel therapeutic modality.

Structural insights into humanization of anti-tissue factor antibody 10H10

Murine antibody 10H10 raised against human tissue factor is unique in that it blocks the signaling pathway, and thus inhibits angiogenesis and tumor growth without interfering with coagulation. As a potential therapeutic, the antibody was humanized in a two-step procedure. Antigen-binding loops were grafted onto selected human frameworks and the resulting chimeric antibody was subjected to affinity maturation by using phage display libraries. The results of humanization were analyzed from the structural perspective through comparison of the structure of a humanized variant with the parental mouse antibody. This analysis revealed several hot spots in the framework region that appear to affect antigen binding, and therefore should be considered in human germline selection. In addition, some positions in the Vernier zone, e.g., residue 71 in the heavy chain, that are traditionally thought to be crucial appear to tolerate amino acid substitutions without any effect on binding. Several humanized variants were produced using both short and long forms of complementarity-determining region (CDR) H2 following the difference in the Kabat and Martin definitions. Comparison of such pairs indicated consistently higher thermostability of the variants with short CDR H2. Analysis of the binding data in relation to the structures singled out the ImMunoGeneTics information system® germline IGHV1-2*01 as dubious owing to two potentially destabilizing mutations as compared to the other alleles of the same germline and to other human germlines.

Antigen-binding site anatomy and somatic mutations in antibodies that recognize different types of antigens

The number of antibody structures co-crystallized with their respective antigens has increased rapidly in the last few years, thus offering a formidable source of information to gain insight into the structure-function relationships of this family of proteins. We have analyzed here 140 unique middle-resolution to high-resolution (<3 Å) antibody structures, including 55 in complex with proteins, 39 with peptides, and 46 with haptens. We determined (i) length variations of the hypervariable loops, (ii) number of contacts with antigen, (iii) solvent accessible area buried upon binding, (iv) location and frequency of antigen contacting residues, (v) type of residues interacting with antigens, and (vi) putative somatic mutations. Except for somatic mutations, distinctive profiles were identified for all the variables analyzed. Compared with contacts, somatic mutations occurred with less abundance at any given position and extended beyond the regions in contact, with no clear difference among antibodies that recognize different types of antigens. This observation is consistent with the fact that although antigen recognition accomplished by shape and physicochemical complementarity is selective in nature, the somatic mutation process is stochastic and selection for mutations leading to improved affinity is not directly related to contact residues. Thus, the knowledge emerging from this study enhances our understanding of the structure-function relationship in antibodies while providing valuable guidance to design libraries for antibody discovery and optimization.

Characterization of a high-affinity human antibody with a disulfide bridge in the third complementarity-determining region of the heavy chain

Disulfide bridges are common in the antigen-binding site from sharks (new antigen receptor) and camels (single variable heavy-chain domain, VHH), in which they confer both structural diversity and domain stability. In human antibodies, cysteine residues in the third complementarity-determining region of the heavy chain (CDR-H3) are rare but naturally encoded in the IGHD germline genes. Here, by panning a phage display library designed based on human germline genes and synthetic CDR-H3 regions against a human cytokine, we identified an antibody (M3) containing two cysteine residues in the CDR-H3. It binds the cytokine with high affinity (0.4 nM), recognizes a unique epitope on the antigen, and has a distinct neutralization profile as compared with all other antibodies selected from the library. The two cysteine residues form a disulfide bridge as determined by mass spectrometric peptide mapping. Replacing the cysteines with alanines did not change the solubility and stability of the monoclonal antibody, but binding to the antigen was significantly impaired. Three-dimensional modeling and dynamic simulations were employed to explore how the disulfide bridge influences the conformation of CDR-H3 and binding to the antigen. On the basis of these results, we envision that designing human combinatorial antibody libraries to contain intra-CDR or inter-CDR disulfide bridges could lead to identification of human antibodies with unique binding profiles.

Human framework adaptation of a mouse anti-human IL-13 antibody

Humanization of a potent neutralizing mouse anti-human IL-13 antibody (m836) using a method called human framework adaptation (HFA) is reported. HFA consists of two steps: human framework selection (HFS) and specificity-determining residue optimization (SDRO). The HFS step involved generation of a library of m836 antigen binding sites combined with diverse human germline framework regions (FRs), which were selected based on structural and sequence similarities between mouse variable domains and a repertoire of human antibody germline genes. SDRO consisted of diversifying specificity-determining residues and selecting variants with improved affinity using phage display. HFS of m836 resulted in a 5-fold loss of affinity, whereas SDRO increased the affinity up to 100-fold compared to the HFS antibody. Crystal structures of Fabs in complex with IL-13 were obtained for m836, the HFS variant chosen for SDRO, and one of the highest-affinity SDRO variants. Analysis of the structures revealed that major conformational changes in FR-H1 and FR-H3 occurred after FR replacement, but none of them had an evident direct impact on residues in contact with IL-13. Instead, subtle changes affected the V(L)/V(H) (variable-light domain/variable-heavy domain) interface and were likely responsible for the 5-fold decreased affinity. After SDRO, increased affinity resulted mainly from rearrangements in hydrogen-bonding pattern at the antibody/antigen interface. Comparison with m836 putative germline genes suggested interesting analogies between natural affinity maturation and the engineering process that led to the potent HFA anti-human IL-13 antibody.

Unenhanced multidetector CT (CT KUB) in the initial imaging of suspected acute renal colic: evaluating a new service

AIM

To evaluate a new imaging pathway for the investigation of patients presenting with suspected acute renal colic.

MATERIALS AND METHODS

A retrospective review of 500 consecutive cases of suspected acute renal colic was undertaken to evaluate the initial results of a new imaging pathway introduced at our institution, which completely replaced the intravenous urogram (IVU) with unenhanced multidetector CT (CT KUB).

RESULTS

The positive rate for urolithiasis was 44% (221/500), the negative rate 46% (229/500) and the rate of other significant findings was 12% (59/500). Female patients had a low positive rate compared with male patients (27.5 versus 57.5%; p<0.001). Urological intervention was required in 28% (61/221) and these patients had a larger average stone size (6.6 versus 3.7 mm; p<0.001) and the stone was located more proximally. Out-of-hours imaging was performed in 37% (186/500), and these patients had a higher positive rate (52 versus 40%; p<0.001). Other findings included a wide range of acute non-urological conditions.

CONCLUSION

The feasibility of replacing the acute IVU with CT KUB in the initial assessment of suspected acute renal colic was demonstrated in the present study. The technique enables rapid diagnosis of urolithiasis, stratification of patients likely to proceed to urological intervention, and prompt diagnosis of a variety of other acute pathological conditions.

Sequencing and model structure of a Naja naja atra protein fragment

We report the amino acid sequence of a basic protein isolated from the snake venom of Naja naja atra. An automated Edman sequencer was used to determine the 65-residue sequence, aided by electrospray ionization/mass spectrometry. Online reduction and pyridylethylation of the peptide was performed to identify the cysteine residues. Trypsin, chymotrypsin and aspartic digestions were carried out to derive peptide fragments for further sequencing. Fragmented peptides were overlapped to obtain the complete sequence. Molecular mass measurements of the whole protein and its fragments were used as a countercheck for sequence assignment. Further confirmation of the sequence was indicated by sequence homology to other snake venom neurotoxins. A molecular model of the tertiary structure was constructed based on sequence homology, and was refined by global minimization and extensive quality control algorithms. Electrostatic and hydrophobic surface calculations and molecular dynamics simulations were carried out to determine the functional properties of the molecule.

Ideal architecture of residue packing and its observation in protein structures

A simple model of sphere packing has been investigated as an ideal model for long-range interactions for the packing of non-bonded residues in protein structures. By superposing all residues, the geometry of packing around a central residue is investigated. It is found that all residues conform almost perfectly to this lattice model for sphere packing when a radius of 6.5 A is used to define non-bonded (virtual) interacting residues. Side-chain positions with respect to sequential backbone segments are relatively regular as well. This lattice can readily be used in conformation simulations to reduce the conformational space.

Structure of Py.Pu.Py DNA triple helices. Fourier transforms of fiber-type x-ray diffraction of single crystals

Well-formed hexagonal crystals of oligomeric DNA triple helices exhibit fiber-type x-ray diffraction patterns [cf., Liu et al. (1994) Nature Struct. Biol. 1, 11], which can be interpreted in terms of Fourier transforms of these helices. Precession photographs of a triplex formed of dA and dT chains show that it has 13 residues per turn. In contrast, a sequence containing the four natural bases A, G, C, and T has 12 residues per turn. In this sense the triple helices exhibit a sequence-dependent polymorphism, though both have C2'-endo sugar pucker and B rather than A conformation. New models are constructed, using constraints from x-ray diffraction, and Fourier transforms of the models are calculated. Good agreement in the amplitudes and positions of the calculated and observed diffraction intensities confirms the structures for both triple helices. These are the first stereochemically satisfactory DNA triple helices for which coordinates based on adequate experimental data were provided. Sequences for crystallization are designed to achieve unique base alignments and are screened for the presence of sharp bands on gel electrophoresis to assure the absence of multiple species caused by strand slippage. Despite intensive efforts to observe normal crystal diffraction by varying sequences and conditions, all crystals exhibited only fiber-type diffraction. We suggest that this behavior may be an intrinsic property of triple helices and discuss possible reasons for the results. Spectroscopic and chemical experiments establish that the oligonucleotides exist in solution as triple helices under the conditions of crystallization.

Symmetry and structure of RNA and DNA triple helices

Despite wide interest in nucleic acid triple helices, there has been no stereochemically satisfactory structure of an RNA triple helix in atomic detail. AN RNA triplex structure has previously been proposed based on fiber diffraction and molecular modeling [S. Arnott and P. J. Bond (1973) Nature New Biology, Vol. 244, pp. 99-101; S. Arnott, P. J. Bond, E. Selsing, and P. J. C. Smith (1976) Nucleic Acids Research, Vol. 3, pp. 2459-2470], but it has nonallowed close contacts at every triplet and is therefore not stereochemically acceptable. We propose here a new model for an RNA triple helix in which the three chains have identical backbone conformations and are symmetry related. There are no short contacts. The modeling employs a novel geometrical approach using the linked atom least squares [P. J. C. Smith and S. Arnott (1978) Acta Crystallographica, Vol. A34, pp. 3-11] program and is not based on energy minimization. In general, the method leads to a range of possible structures rather than a unique structure. In the present case, however, the constraints resulting from the introduction of a third strand limit the possible structures to a very small range of conformation space. This method was used previously to obtain a model for DNA triple helices [G. Raghunathan, H. T. Miles, and V. Sasisekharan (1993) Biochemistry, Vol. 32, pp. 455-462], subsequently confirmed by fiber-type x-ray diffraction of oligomeric crystals [K. Liu, H. T. Miles, K. D. Parris, and V. Sasisekharan (1994) Nature Structural Biology, Vol. 1, pp. 11-12]. The above triple helices have Watson-Crick-Hoogsteen [K. Hoogsteen (1963) Acta Crystallographica, Vol. 16, pp. 907-916] pairing of the three bases. The same modeling method was used to investigate the feasibility of three-dimensional structures based on the three possible alternative hydrogen-bonding schemes: Watson-Crick-reverse Hoogsteen, Donohue [J. Donohue (1953) Proceedings of the National Academy of Science USA, Vol. 39, pp. 470-475] (reverse Watson-Crick)-Hoogsteen, and Donohue-reverse Hoogsteen. We found that none of these can occur in either RNA or DNA helices because they give rise only to structures with prohibitively short contacts between backbone and base atoms in the same chain.

Parallel nucleic acid helices with Hoogsteen base pairing: symmetry and structure

Molecular structures for parallel DNA and RNA double helices with Hoogsteen pairing are proposed for the first time. The DNA helices have sugars in the C2'-endo region and the phosphodiester conformations are (trans, gauche-), and the RNA helices have sugars in the C3'-endo region and the phosphodiester conformations are (gauche-, gauche-). A pseudorotational symmetry relates the two parallel strands of DNA helices and a screw symmetry relates the two strands of RNA helices, which have an associated tilt of the bases. The conformational space of parallel helices with Hoogsteen base pairing, unlike the Watson-Crick duplex, is highly restricted due to the unique positioning of the symmetry axis in the former case. The features of the parallel double helix with Hoogsteen pairing are compared with the Watson-Crick duplex and the corresponding triple helix.

Geometries, charges, dipole moments and interaction energies of normal, tautomeric and novel bases

Ab initio molecular orbital calculations with the STO-3G and 4-31G basis sets are performed to study the geometries and interactions of natural and "novel" Watson-Crick base pairs, as well as some non-Watson-Crick base pairs. First the optimized geometries of bases are determined using the STO-3G basis set, and then for the base pairs with the STO-3G and 4-31G basis sets. Interaction energies of these base pairs are evaluated, and their relative stabilities are discussed. Hydrogen bond features, partial charges and dipole moments of the base pairs are described. The calculated stabilities are in reasonable agreement with the limited available experimental data from thermal melting studies. Hydrogen bond geometries at the 4-31G level are in good agreement with the crystal structure data. The order of relative stabilities is found to be: iG:iC > G:C > G:T* > rG:rC > A*:C > Am:U > tau:kappa > chi:kappa > G*:T > A:C* > A:U = A:T where, A*, T*, G* and C* are tautomers, iG and iC are iso-G and iso-C, Am is 2-amino adenine, chi is xanthosine, kappa is 2,4-diaminopyrimidine, tau is 7-methyl oxoformycin B, rG is modified guanine with substitutions at positions 5 and 7, and rC is modified cytosine with a substitution at position 6. Pairing strengths with modified bases may affect the efficiency of protein production.

Stability and cooperativity of nucleic acid base triplets

Geometries and stabilities of various base triplets have been studied using ab initio quantum chemical methods. Their optimized geometries are determined using the STO-3G basis set, and those of Hoogsteen and reverse Hoogsteen base pairs are evaluated with the 4-31G basis set. Moreover, the preferred hydrogen bond patterns of the bases in triple helices are discussed. A cooperative effect for base pairing in triplets is presented, and it can be either positive or negative. Almost all base triplets that contain Watson-Crick G:C base pairs show a positive cooperativity. Conversely, the base triplets with Watson-Crick A:T base pairs mostly display a negative cooperativity. The interaction energies of base triplets are reported and the relative stabilities of base triplets are found as follows: A+.GC > C+.GC(H) > C+.GC(rH) > G.GC(H) > G.GC(rH) > A.GC > T.AT(rH) > U.AU(H) > U.AT(H) > A.AT > G.AT > T.AT(m) > G.TA(2) > G.TA(1) H and rH denote the Hoogsteen and reverse Hoogsteen positions of the third base that would lead to parallel and antiparallel orientations respectively of the third chain with respect to the Watson-Crick paired purine chain. 'm' denotes the middle pairing scheme, in which the third base hydrogen bonds to both bases of Watson-Crick pair.

A parallel DNA triplex as a model for the intermediate in homologous recombination

Parallel DNA triplexes considered to be putative intermediates in homologous recombination, are studied by means of theoretical conformational analysis. These triplexes are denoted as the R-form DNA. Two types of triplexes are analyzed: extended R-form DNA, modeling the triple standard structure, created transiently in the presence of recombination proteins (e.g. RecA); and collapsed R-form, obtained after deproteinization. These structures are stereochemically possible for any arbitrary sequence and have the following properties: (1) the third, R-strand, is parallel to the identical duplex strand and is located in the major groove of the duplex; (2) positions of all four bases in the R-strand are nearly isomorphic; (3) the proposed triplets are consistent with the chemical modification data for deproteinized DNA; we suggest, however, that they are the same in the RecA-DNA complex as well. Since the patterns of charges on each base of the R-strand are strictly complementary to the charges of the homologous Watson-Crick (WC) pair in the major groove, we propose that the selection of the homologous sequence may occur through these complementary electrostatic interactions (electrostatic recognition code). We demonstrate that in the collapsed triplex with a rise of about 3.4 A, the bases from the third R-strand can be inclined and interact with two WC base-pairs simultaneously, which could lead to recognition errors. These mispairings are unlikely in the extended triplex. Therefore, we speculate that a functional role of the extended and underwound DNA structure, transiently formed in the complex with RecA protein, is to obviate such errors and increase the stringency of recognition. In other words, RecA plays the role of a DNA chaperone facilitating the recognition of the single stranded DNA and the duplex. Finally, we show that the proposed isomorphic triplets are conformationally advantageous for strand exchange.

Symmetry and molecular structure of a DNA triple helix: d(T)n.d(A)n.d(T)n

A structure for the triple helix d(T)n.d(A)n.d(T)n consistent with recent infrared spectral data is proposed, and its salient features are discussed. The present structure preserves the pseudodyad between the Watson-Crick base-paired adenine and thymine strands and in addition has a pseudorotational symmetry relating the Hoogsteen-paired adenine and thymine strands. The simultaneous presence of these two symmetries gives rise to a dyad between the two thymine polynucleotides. These symmetries result in identical backbone conformations for all three strands, unlike any previously proposed model for a triple helix. The proposed structure has an axial rise per residue of 3.26 A and 12 residues per turn obtained from X-ray fiber diffraction [Arnott S., & Selsing, E. (1974) J. Mol. Biol. 88, 509-521]. The present structure is structurally and conformationally similar to double helical B-form DNA and has sugar pucker in the C2'-endo region. This structure is fundamentally different from the one proposed by Arnott and co-workers, which was based on structural and conformational features similar to double helical A-form DNA with C3'-endo sugar pucker. It is stereochemically satisfactory, and it does not have the disallowed nonbonded distances present in the earlier model of Arnott and co-workers. It is energetically much more favorable than their structure. Coordinates of the present structure are given.

Modeling the ion channel structure of cecropin

Atomic-scale computer models were developed for how cecropin peptides may assemble in membranes to form two types of ion channels. The models are based on experimental data and physiochemical principles. Initially, cecropin peptides, in a helix-bend-helix motif, were arranged as antiparallel dimers to position conserved residues of adjacent monomers in contact. The dimers were postulated to bind to the membrane with the NH2-terminal helices sunken into the head-group layer and the COOH-terminal helices spanning the hydrophobic core. This causes a thinning of the top lipid layer of the membrane. A collection of the membrane bound dimers were then used to form the type I channel structure, with the pore formed by the transmembrane COOH-terminal helices. Type I channels were then assembled into a hexagonal lattice to explain the large number of peptides that bind to the bacterium. A concerted conformational change of a type I channel leads to the larger type II channel, in which the pore is formed by the NH2-terminal helices. By having the dimers move together, the NH2-terminal helices are inserted into the hydrophobic core without having to desolvate the charged residues. It is also shown how this could bring lipid head-groups into the pore lining.

Structure of d(T)n.d(A)n.d(T)n: the DNA triple helix has B-form geometry with C2'-endo sugar pucker

The polynucleotide helix d(T)n.d(A)n.d(T)n is the only deoxypolynucleotide triple helix for which a structure has been published, and it is generally assumed as the structural basis for studies of DNA triplexes. The helix has been assigned to an A-form conformation with C3'-endo sugar pucker by Arnott and Selsing [1974; cf. Arnott et al. (1976)]. We show here by infrared spectroscopy in D2O solution that the helix is instead B-form and that the sugar pucker is in the C2'-endo region. Distamycin A, which binds only to B-form and not to A-form helices, binds to the triple helix without displacement of the third strand, as demonstrated by CD spectroscopy and gel electrophoresis. Molecular modeling shows that a stereochemically satisfactory structure can be build using C2'-endo sugars and a displacement of the Watson-Crick base-pair center from the helix axis of 2.5 A. Helical constraints of rise per residue (h = 3.26 A) and residues per turn (n = 12) were taken from fiber diffraction experiments of Arnott and Selsing (1974). The conformational torsion angles are in the standard B-form range, and there are no short contacts. In contrast, we were unable to construct a stereochemically allowed model with A-form geometry and C3'-endo sugars. Arnott et al. (1976) observed that their model had short contacts (e.g., 2.3 A between the phosphate-dependent oxygen on the A strand and O2 in the Hoogsteen-paired thymine strand) which are generally known to be outside the allowed range.(ABSTRACT TRUNCATED AT 250 WORDS)

Magainin 2, a natural antibiotic from frog skin, forms ion channels in lipid bilayer membranes

We have examined the ion channel forming properties of magainin 2 by incorporating the peptide into artificial lipid bilayers held under voltage clamp. Magainin 2 increased lipid bilayer conductance in a concentration dependent manner with a Hill coefficient of 1.7. The magainin 2 conductance was selective for monovalent cations over anions with a ratio of 5:1 and had both voltage-sensitive and -insensitive components. Two structurally related but antibiotically less potent analogues, magainin 1 and Z-12, also increased lipid bilayer conductance with a similar ion selectivity but these peptides were less potent than magainin 2. We propose that the weak cation selectivity of the magainin channels can be accounted for by the inclusion of negatively charged lipids in the channel complex and suggest two possible structures for such a channel. The ionophoric properties of these peptides are likely to be proximal to their antibiotic activities.

Structural and functional studies of full-length vascular cell adhesion molecule-1: internal duplication and homology to several adhesion proteins

Full-length vascular cell adhesion molecule-1 (VCAM-1) cDNA cloned by polymerase chain reaction (PCR) of poly(A)+RNA from interleukin-1 (IL-1)-activated human umbilical vein endothelial cells (HUVEC) contained an insert of 276 nucleotides after position 1,034 of the previously published sequence. Synthetic oligomer probes, specific for each of the two possible species of VCAM-1 mRNA, detected only the longer form of VCAM-1 by Northern analysis of activated endothelial cell mRNA. This full-length VCAM-1 contains two internally repeated domains of approximately 273 amino acids with a high degree of homology. This new sequence information reveals homologies with additional members of the immunoglobulin superfamily and improves ALIGN scores for previously cited adhesion proteins. Removal of the transmembrane domain and the carboxy-terminal end of the full-length VCAM-1 molecule allows the molecule to be secreted into the culture medium from cells transfected with an expression vector containing the corresponding VCAM-1 cDNA.

Conformational feasibility of a hairpin with two purines in the loop. 5'-d-GGTACIAGTACC-3'

Structural feasibility and conformational requirements for the sequence 5'-d-GGTACIAGTACC-3' to adopt a hairpin loop with I6 and A7 in the loop are studied. It is shown that a hairpin loop containing only two nucleotides can readily be formed without any unusual torsional angles. Stacking is continued on the 5'-side of the loop, with the I6 stacked upon C5. The base A7, on the 3'-side of the loop, can either be partially stacked with I6 or stick outside without stacking. Loop closure can be achieved for both syn and anti conformations of the glycosidic torsions for G8 while maintaining the normal Watson-Crick base pairing with the opposite C5. All torsional angles in the stem fall within the standard B-family of DNA helical structures. The phosphodiesters of the loop have trans,trans conformations. Loop formation might require the torsion about the C4'-C5' bond of G8 to be trans as opposed to the gauche+ observed in B-DNA. These results are discussed in relation to melting temperature studies [Howard et al. (1991) Biochemistry (preceding paper in this issue)] that suggest the formation of very stable hairpin structures for this sequence.

Solvation effects on the sequence variability of DNA double helical conformations

The role of solvation on the sequence dependent conformational variabilities in DNA has been studied by calculating hydration free energies from solvent accessible surface areas for several base steps, as a function of various helical parameters, roll, twist and propeller twist. The results of roll calculations suggest opposite trends for AA and GG steps, with the former tending to have a compressed minor groove and the latter a compressed major groove. These trends are consistent with the experimental findings on sequence preferences and the nature of anisotropic bending of DNA observed in nucleosomes (Drew, H.R. and Travers, A.A., J. Mol. Biol. 186, 773-790 (1985); Satchwell, S.C., Drew, H.R. and Travers, A.A., J. Mol. Biol. 191, 659-675 (1986)) and CAP-DNA interactions (Gartenberg, M.R. and Crothers, D.M., Nature 333, 824-829, (1988)). Solvation energy profiles also indicate preferences for the base pairs in GG and AA steps to adopt low and high propeller twists, respectively. Such agreements may either reflect a coincidence of solvation effects with other energy terms or a dominance of solvent effects. The results are discussed in the context of the crystallographic observations of structural tendencies.

Conformational features of DNA containing a cis-syn photodimer

In an effort to understand the conformational and structural changes in DNA brought about by thymine photodimer, computer modeling and molecular mechanics energy calculations were performed on DNA hexamer and dodecamer duplexes containing a cis-syn photodimer. The conformation of the crystal structure of the cyanoethyl phosphate ester of the thymine dimer (Hruska et al., Biopolymers 25, 1399-1417 (1986)) was used in modeling the photodimer portion. Various starting conformations were used in the modeling procedure and the structures were minimized both retaining and later relaxing the crystallographic geometry of the cyclobutane ring. The results indicate that most of the deformation is restricted to the thymine dimer region, and that the conformational changes decrease rapidly on either side of the region containing the photodimer. The structural changes brought about by the introduction of the photodimer can be accommodated within six base paired duplex without significant bend in the DNA. More conformational changes are observed on the 5'-side of the photodimer than on the 3'-side. The conformational features, such as backbone torsion angles and sugar puckers, of the energy minimized structures are discussed in the context of the solution structures determined by NMR on a series of oligomers containing photodimers (Rycyna et al., Biochemistry 27, 3152-3163 (1988)).

Models of delta-hemolysin membrane channels and crystal structures

Molecular modeling and energy calculations have been used to study how delta-hemolysin and melittin helices may aggregate on membrane surfaces and insert through membranes to form channels. In these models adjacent antiparallel amphipathic helices form planar "raft" structures, in which one surface is hydrophobic and the other hydrophilic. Models of delta-hemolysin crystal structure were developed using these "rafts." These models are based on the unit cell constants and the crystal symmetry obtained from the preliminary crystal data. Energy calculations favor channel models of delta-hemolysin with six or eight monomers per channel.

Structural elements and organization of the ancestral translational machinery

The molecular mechanisms underlying the primitive translational apparatus have been studied in light of present day protein biosynthesis. Using the structural information available from the contemporary system as a key to its function, both the structural necessities for an early adaptor and the multipoint recognition properties of such adaptors have been investigated. This was done by first critically examining the potential feasibility of right- and left-handed hairpin adaptor models. Second, a molecular model of the contemporary transpeptidation complex has been constructed in order to ascertain the structural requirements of the adaptor molecule needed for peptidyl transfer. Third, a model of the tRNATyr-tyrosyl tRNA synthetase complex including the positioning of the disordered region is proposed. This model is used to illustrate those required recognition properties of aminoacyl synthetase which lead to a perspective on the structure of the ancestor synthetase.

Structural requirements for a primitive adaptor molecule

Adaptor properties of linear hairpin helices have been examined. The analysis suggests that neither right nor left handed hairpin helices can simultaneously read a comma free messenger and align aminoacyl residues for peptide condensation. Comparison of these studies with the model of the present day peptidyl transfer intermediate suggests that the "L" shaped folding of the present day tRNAs may be a prerequisite for adaptor function. Therefore, the three-dimensional organization of the ancestral adaptor molecule must have had structural features similar to its present day counterpart.

Multistep modeling (MSM) of biomolecular structure application to the A-G mispair in the B-DNA environment

A multistep modeling procedure has been evolved to study the structural changes introduced by lesions in DNA. We report here the change in the structure of regular B-DNA geometry due to the incorporation of Ganti-Aanti mispair in place of a regular G-C pair, preserving the helix continuity. The energetics of the structure so obtained is compared with the Ganti-Asyn configuration under similar constrained conditions. We present the methodology adopted and discuss the results.

Conformational relationships between amino acids and their anticodons in the primitive decoding system

Detailed calculations of the conformational characteristics of a primitive decoding system are presented. A penta-nucleotide serves as the primitive tRNA (PIT) with a triplet of primitive anticodon (PAC) in a helical conformation. This molecular moiety has a cleft in the middle. An amino acid can comfortably nestle into the cleft. The conformation of this molecular association is stabilised by a few hydrogen bonds. The stereochemistry of the moiety restricts the conformational possibilities and the sidechain of the amino acid gets oriented at a proper position and in the correct direction to interact intimately with the PAC in the middle of the PIT. The model favours L-amino acids for beta-D-ribonucleotides. The location of the sidechain of the amino acid in the PIT gives a raison d'être for the important features of the organisation of nucleotide triplets for amino acids in the Genetic Code. The interaction of a few key amino acids with the different combinations of bases as PAC sequences has been studied and the stereochemical basis for the selection of the anticodons for amino acids is elucidated.

A conformational rationale for the origin of the mechanism of nucleicacid-directed protein synthesis of 'living' organisms

The physical basis for the natural evolution of a primitive decoding system is presented using the concepts of molecular interactions. Oligoribonucleotides of five residues having U at the 5'-end, a purine at the 3'-end and any combination of three bases in the middle is taken as a primitive tRNA (PIT). From conformational considerations PIT is expected to have U-turn conformation wherein, N3-H3 of base U hydrogen-bonds with phosphate, three residues ahead leaving triplet bases called primitive anticodons (PAC) into a helical conformation, and this creates a cleft between U and PAC. An amino acid can be comfortably nestled into the cleft with the amide hydrogens and carboxyl oxygen hydrogen-bonded to the last purine and the first uridine, while the side-chain can interact with the cleft side of PAC. The other side of PAC is free to base-pair with triplet codons on a longer RNA. Also two PACs can 'recognize' consecutive triplet codons, and this leads to a dynamic interaction in which the amino and carboxyl ends are brought into proximity, making the formation of peptide bond feasible. The cleft formed by different anticodon triplets, broadly speaking, shows preferences for the corresponding amino acids of the presently known codon assignment. Thus the nucleicacid-directed protein synthesis, which is a unique feature of all 'living' organisms is shown to be a natural consequence of a particular way of favourable interaction between nucleic acids and amino acids, and our model provides the missing link between the chemical evolution of small organic molecules and biological evolution through the process of mutations in nucleicacids and nucleicacid-directed protein synthesis.