Enhancing the correlation between in vitro and in vivo experiments in dental implant osseointegration: investigating the role of Ca ions

This study delves into the osteogenic potential of a calcium-ion modified titanium implant surface, unicCa, employing state-of-the-art proteomics techniques both in vitro (utilizing osteoblasts and macrophage cell cultures) and in vivo (in a rabbit condyle model). When human osteoblasts (Hobs) were cultured on unicCa surfaces, they displayed a marked improvement in cell adhesion and differentiation compared to their unmodified counterparts. The proteomic analysis also revealed enrichment in functions associated with cell migration, adhesion, extracellular matrix organization, and proliferation. The analysis also underscored the involvement of key signalling pathways such as PI3K-Akt and mTOR. In the presence of macrophages, unicCa initially exhibited improvement in immune-related functions and calcium channel activities at the outset (1 day), gradually tapering off over time (3 days). Following a 5-day implantation in rabbits, unicCa demonstrated distinctive protein expression profiles compared to unmodified surfaces. The proteomic analysis highlighted shifts in adhesion, immune response, and bone healing-related proteins. unicCa appeared to influence the coagulation cascade and immune regulatory proteins within the implant site. In summary, this study provides a comprehensive proteomic analysis of the unicCa surface, drawing correlations between in vitro and in vivo results. It emphasizes the considerable potential of unicCa surfaces in enhancing osteogenic behavior and immunomodulation. These findings significantly contribute to our understanding of the intricate molecular mechanisms governing the interplay between biomaterials and bone cells, thereby facilitating the development of improved implant surfaces for applications in bone tissue engineering.

Coarse Surface Microcavities Permit Bone Ingrowth and Improve Implant Osseointegration

PURPOSE

To evaluate the effects of coarse microcavities added to micron and submicron rough implant surfaces in the implant-bone anchorage in rabbits.

MATERIALS AND METHODS

Confocal interferometry was used to quantify roughness. Electron microscopy and energy-dispersive x-rays characterized the surfaces prior to and after implantation. X-ray photoelectron spectroscopy and contact angle determined the surface chemistry and energy, respectively. Fifteen New Zealand White rabbits received, respectively, one cavity-less (C-) and one cavity-rich (C+) implant per femoral condyle and were allowed to integrate for 2 and 8 weeks. The bone-to-implant contact (BIC), bone volume density (BVD), and removal torque (RTQ) were then analyzed.

RESULTS

The cavities produced on the surfaces were 48.4 ± 16.8 μm in diameter and 37.8 ± 36.5 μm deep (5.9% ± 1.1% surface coverage). C+ did not alter the surface chemistry or energy. In vivo, C+ implants produced more BIC and RTQ at 8 weeks (P = .002 and P = .059, respectively) and more BVD at 2 and 8 weeks postimplantation (P = .031 and P = .078, respectively). Bone tissue was observed inside the cavities of C+ both histologically and by scanning electron microscopy after implant removal.

CONCLUSION

Unevenly distributed coarse cavities within a micron and submicron rough surface allow bone ingrowth and increase implant stability and bone-surface unions in rabbits. These results encourage the design of implants with multilevel surface topographies to improve implant-based regeneration.

Protein adsorption/desorption dynamics on Ca-enriched titanium surfaces: biological implications

Calcium ions are used in the development of biomaterials for the promotion of coagulation, bone regeneration, and implant osseointegration. Upon implantation, the time-dependent release of calcium ions from titanium implant surfaces modifies the physicochemical characteristics at the implant-tissue interface and thus, the biological responses. The aim of this study is to examine how the dynamics of protein adsorption on these surfaces change over time. Titanium discs with and without Ca were incubated with human serum for 2 min, 180 min, and 960 min. The layer of proteins attached to the surface was characterised using nLC-MS/MS. The adsorption kinetics was different between materials, revealing an increased adsorption of proteins associated with coagulation and immune responses prior to Ca release. Implant-blood contact experiments confirmed the strong coagulatory effect for Ca surfaces. We employed primary human alveolar osteoblasts and THP-1 monocytes to study the osteogenic and inflammatory responses. In agreement with the proteomic results, Ca-enriched surfaces showed a significant initial inflammation that disappeared once the calcium was released. The distinct protein adsorption/desorption dynamics found in this work demonstrated to be useful to explain the differential biological responses between the titanium and Ca-ion modified implant surfaces.

Influence of calcium ion-modified implant surfaces in protein adsorption and implant integration

Background

Calcium (Ca) is a well-known element in bone metabolism and blood coagulation. Here, we investigate the link between the protein adsorption pattern and the in vivo responses of surfaces modified with calcium ions (Ca-ion) as compared to standard titanium implant surfaces (control). We used LC–MS/MS to identify the proteins adhered to the surfaces after incubation with human serum and performed bilateral surgeries in the medial section of the femoral condyles of 18 New Zealand white rabbits to test osseointegration at 2 and 8 weeks post-implantation (n=9).

Results

Ca-ion surfaces adsorbed 181.42 times more FA10 and 3.85 times less FA12 (p<0.001), which are factors of the common and the intrinsic coagulation pathways respectively. We also detected differences in A1AT, PLMN, FA12, KNG1, HEP2, LYSC, PIP, SAMP, VTNC, SAA4, and CFAH (p<0.01). At 2 and 8 weeks post-implantation, the mean bone implant contact (BIC) with Ca-ion surfaces was respectively 1.52 and 1.25 times higher, and the mean bone volume density (BVD) was respectively 1.35 and 1.13 times higher. Differences were statistically significant for BIC at 2 and 8 weeks and for BVD at 2 weeks (p<0.05).

Conclusions

The strong thrombogenic protein adsorption pattern at Ca-ion surfaces correlated with significantly higher levels of implant osseointegration. More effective implant surfaces combined with smaller implants enable less invasive surgeries, shorter healing times, and overall lower intervention costs, especially in cases of low quantity or quality of bone.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40729-021-00314-1.

Relevance of Topographic Parameters on the Adhesion and Proliferation of Human Gingival Fibroblasts and Oral Bacterial Strains

Dental implantology allows replacement of failing teeth providing the patient with a general improvement of health. Unfortunately not all reconstructions succeed, as a consequence of the development of infections of bacterial origin on the implant surface. Surface topography is known to modulate a differential response to bacterial and mammalian cells but topographical measurements are often limited to vertical parameters. In this work we have extended the topographical measurements also to lateral and hybrid parameters of the five most representative implant and prosthetic component surfaces and correlated the results with bacterial and mammalian cell adhesion and proliferation outcomes. Primary human oral gingival fibroblast (gum cells) and the bacterial strains: Streptococcus mutans, Streptococcus sanguinis and Aggregatibacter actinomycetemcomitans, implicated in infectious processes in the oral/implant environment were employed in the presence or absence of human saliva. The results confirm that even though not all the measured surface is available for bacteria to adhere, the overall race for the surface between cells and bacteria is more favourable to the smoother surfaces (nitrided, as machined or lightly acid etched) than to the rougher ones (strong acid etched or sandblasted/acid etched).

Acid–base behaviour and binding to double stranded DNA/RNA of benzo[g]phthalazine-based ligands

Benzo[g]phthalazine derivatives show different binding modes and base selectivity towards canonical DNA/RNA depending on the substitution of the aromatic moiety.

Corrosion behavior of surface modifications on titanium dental implant. In situ bacteria monitoring by electrochemical techniques

The effects of surface modifications and bacteria on the corrosion behavior of titanium have been studied. Five surface modifications were analyzed: two acid etchings (op V, op N), acid etching + anodic oxidation (op NT), sandblasting + acid etching (SLA), and machined surfaces (mach). The corrosion behavior of the surface modifications was evaluated by following the standard ANSI/AAMI/ISO 10993-15:2000. Cyclic potentiodynamic and potentiostatic anodic polarization tests and ion release by ICP-OES after immersion for 7 days in 0.9% NaCl were carried out. Microbiologically induced corrosion (MIC) of low and high roughness (mach, op V) was assessed in situ by electrochemical techniques. Streptococcus mutans bacteria were resuspended in PBS at a concentration of 3 × 10⁸ bacteria mL^-1 and maintained at 37°C. MIC was measured through the open circuit potential, E_oc , and electrochemical impedance spectroscopy from 2 to 28 days. Potentiodynamic curves showed the typical passive behavior for all the surface modifications. The titanium ion release after immersion was below 3 ppb. In situ bacteria monitoring showed the decrease in E_oc from -0.065 (SD 0.067) V_{vs. Ag/AgCl} in mach and -0.115 (SD 0.084) V_{vs. Ag/AgCl} in op V, to -0.333 (SD 0.147) V_{vs. Ag/AgCl} in mach and -0.263 (SD 0.005) V_{vs. Ag/AgCl} in op V, after 2 and 28 days, respectively. A reduction of the oxide film resistance, especially in op V (54 MΩ cm² and 6 MΩ cm² , after 2 and 28 days, respectively) could be seen. Streptococcus mutans negatively affected the corrosion resistance of titanium. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 997-1009, 2018.

Balancing microbial and mammalian cell functions on calcium ion-modified implant surfaces

Implant integration is a complex process mediated by the interaction of the implant surface with the surrounding ions, proteins, bacteria, and tissue cells. Although most implants achieve long-term bone-tissue integration, preventing pervasive implant-centered infections demands further advances, particularly in surfaces design. In this work, we analyzed classical microrough implant surfaces (only acid etched, AE; sandblasted then acid etching, SB + AE) and a new calcium-ion-modified implant surface (AE + Ca) in terms of soft- and hard-tissue integration, bacterial adhesion, and biofilm formation. We cultured on the surfaces primary oral cells from gingiva and alveolar bone, and three representative bacterial strains of the oral cavity, emulating oral conditions of natural saliva and blood plasma. With respect to gingiva and bone cells and in the presence of platelets and plasma proteins, AE + Ca surfaces yielded in average 86% higher adhesion, 44% more proliferation, and triggered 246% more synthesis of extracellular matrix biomolecules than AE-unmodified controls. Concomitantly, AE + Ca surfaces regardless of conditioning with saliva and/or blood plasma showed significantly less bacterial adhesion (67% reduction in average) and biofilm formation (40% reduction in average) than unmodified surfaces. These results highlight the importance of a calcium-rich hydrated interface to favor mammalian cell functions over microbial colonization at implant surfaces. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 421-432, 2018.

Effects of calcium ions on titanium surfaces for bone regeneration

The chemistry and topography of implant surfaces are of paramount importance for the successful tissue integration of load-bearing dental and orthopedic implants. Here we evaluate in vitro and in vivo titanium implant surfaces modified with calcium ions (Ca(2+) surfaces). Calcium ions produce a durable chemical and nano-topographical modification of the titanium oxide interface. Time of flight secondary ion mass spectrometry examination of the outermost surface composition, shows that calcium ions in Ca(2+) surfaces effectively prevent adventitious hydrocarbon passivation of the oxide layer. In aqueous solutions Ca(2+) surfaces release within the first minute, 2/3 of the total measured Ca(2+), the rest is released over the following 85 days. Additionally, Ca(2+) surfaces significantly increase human fetal osteoblasts-like cell adhesion, proliferation and differentiation, as measured by the autocrine synthesis of osteopontin. Relevant for clinical application, after 12 weeks of healing in sheep tibia, microcomputer tomography and histomorphometric analysis show that Ca(2+) surfaces develop significantly more bone contacts and higher bone density in the 1mm region around the implant. Consequently, titanium implants modified with calcium ions represent a valuable tool to improve endosseous integration in the clinical practice.

Nontraumatic Implant Explantation: A Biomechanical and Biological Analysis in Sheep Tibia

Preclinical research in a sheep tibia model has been conducted to evaluate the underlying mechanisms of the nontraumatic implant explantation of failed implants, which allow placing a new one in the bone bed. Twelve dental implants were placed in sheep diaphysis tibia and once osseointegrated they were explanted using a nontraumatic implant explantation approach. Implant osseointegration and explantation were monitored by means of frequency resonance, removal torque, and angle of rotation measurement. The host bone bed and the explanted implant surface were analyzed by conventional microscopy and scanning electron microscope. Results show that osseointegration was broken with an angular displacement of less than 20°. In this situation the implant returns to implant stability quotient values in the same range of their primary stability. Moreover, the explantation technique causes minimal damage to the surrounding bone structure and cellularity. This nontraumatic approach allows the straightforward replacement of failed implants and emerges as a promising strategy to resolve clinically challenging situations.

Synthetic single and double aza-scorpiand macrocycles acting as inhibitors of the antioxidant enzymes iron superoxide dismutase and trypanothione reductase in Trypanosoma cruzi with promising results in a murine model

Synthetic scorpiand-like azamacrocycles selectively inhibit SOD and TR enzymes of Trypanosoma cruzi in mice causing death of the parasites and increasing the mouse survival rate after infection and treatment.

Time-of-flight secondary ion mass spectrometry with principal component analysis of titania-blood plasma interfaces

Treatment of osseoimplant surfaces with autologous platelet-rich plasma prepared according to the plasma rich in growth factors (PRGF-Endoret) protocol prior to implantation yields promising results in the clinic. Our objective is to understand the organization of complex interfaces between blood plasma preparations of various compositions and model titania surfaces. Here we present the results of the morphological and chemical characterization of TiO(2) surfaces incubated with four types of blood plasma preparations devoid of leukocytes and red blood cells: either enriched in platelets (PRGF-Endoret) or platelet-depleted, and either activated with CaCl(2) to induce clotting, or not. Chemical characterization was done by time-of-flight secondary ion mass spectrometry with principal component analysis (ToF-SIMS/PCA). The interface morphology was studied with scanning electron and atomic force microscopy. Immunofluorescence microscopy was used to identify platelets and infer their activation state. We observe clear differences among the four types of interfaces by ToF-SIMS/PCA. Some of these could be straightforwardly related to the differences in the sample morphology and known effects of platelet activation, but others are more subtle. Strikingly, it was possible to differentiate between these samples by ToF-SIMS/PCA of the protein species alone. This clearly indicates that the composition, orientation, and/or conformation of the proteins in these specimens depend both on the platelets' presence and on their activation. The ToF-SIMS imaging functionality furthermore provides unique insight into the distribution of phospholipid species in these samples.

Plasma rich in growth factors promotes bone tissue regeneration by stimulating proliferation, migration, and autocrine secretion in primary human osteoblasts

BACKGROUND

Alveolar bone loss can be a major clinical concern affecting both functionality and esthetics. Osteoblasts are the main cells charged with the repair and regeneration of missing bone tissue. Plasma rich in growth factors (PRGF) allows delivery of a cocktail of proteins and growth factors that promote wound healing and tissue regeneration to the site of injury. This study tests the effect of this endogenous regenerative technology to stimulate alveolar osteoblast bone-forming potential.

METHODS

Primary human osteoblasts were retrieved from alveolar bone of patients undergoing oral surgery. Cell proliferation was evaluated, and culture inserts and permeable transwell supports were used to assess cell migration and chemotaxis. The expression of differentiation markers was quantified by enzyme-linked immunosorbent assay.

RESULTS

PRGF succeeded in increasing proliferation, migration, and chemotaxis of osteoblasts. Also, PRGF significantly enhanced the autocrine expression of two relevant proangiogenic factors, vascular endothelial growth factor and hepatocyte growth factor, and three markers of osteoblastic activity, procollagen I, osteocalcin, and alkaline phosphatase.

CONCLUSION

The results indicate that PRGF can stimulate some of the biologic processes of the main cells responsible for bone regeneration and help support the positive clinical outcomes that have been reported with this technology.

[Evaluation of the variability in the susceptibility of Acinetobacter baumannii to tigecycline in the same medium with two methods of quantitative diffusion different commercial]

INTRODUCTION

Tigecycline may be a therapeutic alternative for the control of multidrug-resistant Acinetobacter baumannii, although there is no consensus on the cutoffs or susceptibility to the variability of the minimum inhibitory concentration (MIC) according to the culture medium and strips for the antibiogram against this microorganism by quantitative diffusion method. Therefore, the objective was to verify this variability and propose epsilometer test strip that more closely resemble to the standard method.

MATERIAL AND METHODS

38 strains of A. baumannii were selected and evaluated their susceptibility to tigecycline with two different commercial strips (E-TEST and Liofilchem). MICs were compared with those obtained by the standard technique of microdilution broth.

RESULTS

MICs obtained by the Liofilchem strip were more similar to standard method than those obtained by E-TEST strips.

CONCLUSION

In the two studied strips, higher MICs to those obtained by the standard method were observed leading to false-positive tigecicline resistance in many cases. However, the Liofilchem strip showed the results more closely resemble to the standard method.

Glucuronic acid and phosphoserine act as mineralization mediators of collagen I based biomimetic substrates

Glucuronic acid (GlcA) and phosphoserine (pS) carrying acidic functional groups were used as model molecules for glycosaminoglycans and phosphoproteins, respectively to mimic effects of native biomolecules and influence the mineralization behaviour of collagen I. Collagen substrates modified with GlcA showed a stable interaction between GlcA and collagen fibrils. Substrates were mineralized using the electrochemically assisted deposition (ECAD) in a Ca(2+)/H( x )PO (4) ((3-x)) electrolyte at physiological pH and temperature. During mineralization of collagen-GlcA matrices, crystalline hydroxyapatite (HA) formed earlier with increasing GlcA content of the collagen matrix, while the addition of pS to the electrolyte succeeded in inhibiting the transformation of preformed amorphous calcium phosphate (ACP) to HA. The lower density of the resulting mineralization and the coalesced aggregates formed at a certain pS concentration suggest an interaction between calcium and the phosphate groups of pS involving the formation of complexes. Combining GlcA-modified collagen and pS-modified electrolyte showed dose-dependent cooperative effects.

[Methicillin resistant Staphylococcus aureus from clinical samples in Cordoba (Spain)]

Increases in methicillin-resistant Staphylococcus aureus (MRSA) strains and in isolates with reduced susceptibility to glucopeptides have become an important problem in the epidemiology of Gram-positive microorganisms. All the consecutive S. aureus collected in our hospital from 1995 to 2001 were studied. Of the 4531 isolates 24.23% were methicillin resistant in this period. The highest number of methicillin-resistant strains were found in wound exudates. In recent years an almost 20% increase in MRSA has occurred in our hospital. As MRSA strains are an important problem in our area and their prevalence is on the rise, as is multiresistance, the monitoring and control of MRSA strains in our hospitals is necessary.

Solution NMR structure of aD,L-alternating oligonorleucine as a model of ?-helix

beta-Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of beta-helices configurations does not allow a direct conformational analysis of beta-helical oligopeptides. A synthetic alternating D,L-oligopeptide with twelve norleucines (XIIMe) has been used as a model to get insight in the conformational features of beta-helix structures. The spatial configuration of XIIMe in solution has been determined by NMR. An extensive set of distances (nuclear Overhauser effect) and dihedral (J coupling constants) constraints have been included in molecular dynamics calculations. The NMR experimental data and theoretical calculations clearly indicate that the XIIMe adopts a single beta(4.4)-helix-type conformation in nonpolar solvents.

Novel, potent calmodulin antagonists derived from an all-D hexapeptide combinatorial library that inhibit in vivo cell proliferation: activity and structural characterization

Calmodulin is known to bind to various amphipathic helical peptide sequences, and the calmodulin-peptide binding surface has been shown to be remarkably tolerant sterically. D-Amino acid peptides, therefore, represent potential nonhydrolysable intracellular antagonists of calmodulin. In the present study, synthetic combinatorial libraries have been used to develop novel D-amino acid hexapeptide antagonists to calmodulin-regulated phosphodiesterase activity. Five hexapeptides were identified from a library containing over 52 million sequences. These peptides inhibited cell proliferation both in cell culture using normal rat kidney cells and by injection via the femoral vein following partial hepatectomy of rat liver cells. These hexapeptides showed no toxic effect on the cells. Despite their short length, the identified hexapeptides appear to adopt a partial helical conformation similar to other known calmodulin-binding peptides, as shown by CD spectroscopy in the presence of calmodulin and NMR spectroscopy in DMSO. The present peptides are the shortest peptide calmodulin antagonists reported to date showing potential in vivo activity.

HYPER: a hierarchical algorithm for automatic determination of protein dihedral-angle constraints and stereospecific C beta H2 resonance assignments from NMR data

A new computer program, HYPER, has been developed for automated analysis of protein dihedral angle values and C beta H2 stereospecific assignments from NMR data. HYPER uses a hierarchical grid-search algorithm to determine allowed values of phi, psi, and chi 1 dihedral angles and C beta H2 stereospecific assignments based on a set of NMR-derived distance and/or scalar-coupling constraints. Dihedral-angle constraints are valuable for restricting conformational space and improving convergence in three-dimensional structure calculations. HYPER computes the set of phi, psi, and chi 1 dihedral angles and C beta H2 stereospecific assignments that are consistent with up to nine intraresidue and sequential distance bounds, two pairs of relative distance bounds, thirteen homo- and heteronuclear scalar coupling bounds, and two pairs of relative scalar coupling constant bounds. The program is designed to be very flexible, and provides for simple user modification of Karplus equations and standard polypeptide geometries, allowing it to accommodate recent and future improved calibrations of Karplus curves. The C code has been optimized to execute rapidly (0.3-1.5 CPU-sec residue-1 using a 5 degrees grid) on Silicon Graphics R8000, R10000 and Intel Pentium CPUs, making it useful for interactive evaluation of inconsistent experimental constraints. The HYPER program has been tested for internal consistency and reliability using both simulated and real protein NMR data sets.

Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments

We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by "homology distance constraints," while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good conformational energies and are physically reasonable. The effects of mis-alignment of the unknown and the template sequences were also explored in order to determine the feasibility of this homology modeling method for distinguishing possible sequence alignments based on considerations of the resulting conformational energies of modeled structures. Differences in the alignments of the unknown and the template sequences result in significant differences in the conformational energies of the calculated homology models. These results suggest that conformational energies and residual constraint violations in these homology-constrained simulated annealing calculations can be used as criteria to distinguish between correct and incorrect sequence alignments and chain folds.

Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site

The major cold-shock protein (CspA) from Escherichia coli is a single-stranded nucleic acid-binding protein that is produced in response to cold stress. We have previously reported its overall chain fold as determined by NMR spectroscopy [Newkirk, K., Feng, W., Jiang, W., Tejero, R., Emerson, S. D., Inouye, M., and Montelione, G. T. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 5114-5118]. Here we describe the complete analysis of 1H, 13C, and 15N resonance assignments for CspA, together with a refined solution NMR structure based on 699 conformational constraints and an analysis of backbone dynamics based on 15N relaxation rate measurements. An extensive set of triple-resonance NMR experiments for obtaining the backbone and side chain resonance assignments were carried out on uniformly 13C- and 15N-enriched CspA. Using a subset of these triple-resonance experiments, the computer program AUTOASSIGN provided automatic analysis of sequence-specific backbone N, Calpha, C', HN, Halpha, and side chain Cbeta resonance assignments. The remaining 1H, 13C, and 15N resonance assignments for CspA were then obtained by manual analysis of additional NMR spectra. Dihedral angle constraints and stereospecific methylene Hbeta resonance assignments were determined using a new conformational grid search program, HYPER, and used together with longer-range constraints as input for three-dimensional structure calculations. The resulting solution NMR structure of CspA is a well-defined five-stranded beta-barrel with surface-exposed aromatic groups that form a single-stranded nucleic acid-binding site. Backbone dynamics of CspA have also been characterized by 15N T1, T2, and heteronuclear 15N-1H NOE measurements and analyzed using the extended Lipari-Szabo formalism. These dynamic measurements indicate a molecular rotational correlation time taum of 4.88 +/- 0.04 ns and provide evidence for fast time scale (taue < 500 ps) dynamics in surface loops and motions on the microsecond to millisecond time scale within the proposed nucleic acid-binding epitope.

A novel RNA-binding motif in influenza A virus non-structural protein 1

The solution NMR structure of the RNA-binding domain from influenza virus non-structural protein 1 exhibits a novel dimeric six-helical protein fold. Distributions of basic residues and conserved salt bridges of dimeric NS1(1-73) suggest that the face containing antiparallel helices 2 and 2' forms a novel arginine-rich nucleic acid binding motif.

High-resolution solution NMR structure of the Z domain of staphylococcal protein A

Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor from the bacterium Staphylococcus aureus. Because of their small size and immunoglobulin (IgG)-binding activities, domains of protein A are targets for protein engineering efforts and for the development of computational approaches for de novo protein folding. The NMR solution structure of an engineered IgG-binding domain of SpA, the Z domain (an analog of the B domain of SpA), has been determined by simulated annealing with restrained molecular dynamics on the basis of 671 conformational constraints. The Z domain contains three well-defined alpha-helices corresponding to polypeptide segments Lys7 to Leu17 (helix 1), Glu24 to Asp36 (helix 2), and Ser41 to Ala54 (helix 3). A family of ten conformers representing the solution structure of the Z domain was computed by simulated annealing of restrained molecular dynamics using the program CONGEN. The average of the root-mean-square deviations (r.m. s.d.) of the individual NMR conformers, relative to the mean coordinates, for the backbone atoms N, Calpha and C' of residues Phe5 through Ala56 is 0.69 A; the corresponding backbone r.m.s.d. for the three-helical core is 0.44 A. Helices 1, 2 and 3 are antiparallel in orientation (Omega12=-170(+/-4) degrees , Omega13=+16(+/-3) degrees , Omega23=+173(+/-7) degrees ). A comparison of backbone amide hydrogen/deuterium exchange rates in free and IgG-bound Z domains demonstrates that the amide protons of helices 1, 2 and 3 are protected from rapid exchange in both states, indicating that all three helices are also intact in the IgG-bound state. These solution NMR results differ from the previously determined X-ray structure of the similar SpA B domain in complex with the Fc fragment of a human IgG antibody, where helix 3 is not observed in the electron density map and from the solution NMR structure of the B domain, where helix 3 is observed but helix 1 is tilted by approximately 30 degrees with respect to helices 2 and 3. Hydrogen-bonded N-cap and C-cap formation is observed for all three helices of the Z domain; these capping interactions appear to be highly conserved in the five homologous domains of SpA.

Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1

We have developed an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures, together with conformational search algorithms available in the molecular mechanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168). The accuracy of the method is validated by "predicting" structures of two homeodomain proteins with known three-dimensional structures, and then applied to predict the three-dimensional structure of the homeodomain of the murine Msx-1 transcription factor. Regions of the unknown protein structure that are highly homologous to the known template structure are constrained by "homology distance constraints," whereas the conformations of nonhomologous regions of the unknown protein are defined only by the potential energy function. A full energy function (excluding explicit solvent) is employed to ensure that the calculated structures have good conformational energies and are physically reasonable. As in NMR structure determinations, information on the consistency of the structure prediction is obtained by superposition of the resulting family of protein structures. In this paper, our homology modeling algorithm is described and compared with related homology modeling methods using spatial constraints derived from the structures of homologous proteins. The software is then used to predict the DNA-bound structures of three homeodomain proteins from the X-ray crystal structure of the engrailed homeodomain protein (Kissinger CR et al., 1990, Cell 63:579-590). The resulting backbone and side-chain conformations of the modeled yeast Mat alpha 2 and D. melanogaster Antennapedia homeodomains are excellent matches to the corresponding published X-ray crystal (Wolberger C et al., 1991, Cell 67:517-528) and NMR (Billeter M et al., 1993, J Mol Biol 234:1084-1097) structures, respectively. Examination of these structures of Msx-1 reveals a network of highly conserved surface salt bridges that are proposed to play a role in regulating protein-protein interactions of homeodomains in transcription complexes.

Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints

A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented in CONGEN. In this benchmark study, internuclear distance, dihedral angle, and vicinal coupling constant constraints were calculated from the energy-minimized X-ray crystal structure of the 46-amino acid polypeptide crambin (ICRN). Three-dimensional structures of crambin that satisfy these simulated NMR constraints were generated using restrained MD and SA. Polypeptide structures with extended backbone and side-chain conformations were used as starting conformations. Dynamical annealing calculations using extended starting conformations and assignments of initial velocities taken randomly from a Maxwellian distribution were found to adequately sample the conformational space consistent with the constraints. These calculations also show that loosened internuclear constraints can allow molecules to overcome local minima in the search for a global minimum with respect to both the NMR-derived constraints and conformational energy. This protocol and the modified version of the CONGEN program described here are shown to be reliable and robust, and are applicable generally for protein structure determination by dynamical simulated annealing using NMR data.

Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors

The new functionality of the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168; Bassolino-Klimas D et al., 1996, Protein Sci 5:593-603) has been applied for energy refinement of two previously determined solution NMR structures, murine epidermal growth factor (mEGF) and human type-alpha transforming growth factor (hTGF alpha). A summary of considerations used in converting experimental NMR data into distance constraints for CONGEN is presented. A general protocol for simulated annealing with restrained molecular dynamics is applied to generate NMR solution structures using CONGEN together with real experimental NMR data. A total of 730 NMR-derived constraints for mEGF and 424 NMR-derived constraints for hTGF alpha were used in these energy-refinement calculations. Different weighting schemes and starting conformations were studied to check and/or improve the sampling of the low-energy conformational space that is consistent with all constraints. The results demonstrate that loosened (i.e., "relaxed") sets of the EGF and hTGF alpha internuclear distance constraints allow molecules to overcome local minima in the search for a global minimum with respect to both distance restraints and conformational energy. The resulting energy-refined structures of mEGF and hTGF alpha are compared with structures determined previously and with structures of homologous proteins determined by NMR and X-ray crystallography.

The mechanism of binding staphylococcal protein A to immunoglobin G does not involve helix unwinding

Structural changes in staphylococcal protein A (SpA) upon its binding to the constant region (Fc) of immunoglobulin G (IgG) have been studied by nuclear magnetic resonance and circular dichroism (CD) spectroscopy. The NMR solution structure of the engineered IgG-binding domain of SpA, the Z domain (an analogue of the B domain of SpA), has been determined by simulated annealing with molecular dynamics, using 599 distance and dihedral angle constraints. Domain Z contains three alpha-helices in the polypeptide segments Lys7 to His18 (helix 1), Glu25 to Asp36 (helix 2), and Ser41 to Ala54 (helix 3). The overall chain fold is an antiparallel three-helical bundle. This is in contrast to the previously determined X-ray structure of the similar SpA domain B in complex with Fc, where helix 3 is not observed in the electron density map [Deisenhofer, J. (1981) Biochemistry 20, 2361-2370], but similar to the solution NMR structure of domain B, which is also a three-helical bundle structure [Gouda, H., et al. (1992) Biochemistry 31, 9665-9672]. In order to characterize possible secondary structural changes associated with IgG binding, far-UV CD spectra were collected for the Z domain, an engineered repeat of this molecule (ZZ), recombinant Fc from IgG subclass 1 (Fc1), recombinant Fc from IgG subclass 3 (Fc3), and mixtures of Z/Fc1, Z/Fc3, ZZ/Fc1, and ZZ/Fc3. Fc3 was included as a control for possible changes of the CD spectrum in the mixture of noncomplexed molecules, since SpA is known not to bind Fc3. From these CD spectra, it was concluded that the third alpha-helix in Z is not disrupted in its complexes with Fc1. Similar results were obtained for the ZZ molecule. However, in both Z and ZZ there are some perturbations in CD spectra at high energy wavelengths (i.e., lambda < 215 nm) accompanying complex formation. On the basis of the combined CD and NMR results, as well as previously described binding studies of Z mutant proteins to Fc1, we conclude that the Z domain maintains its three-helical bundle structure in the Z-Fc complex, though there may be a small structural change involved in the binding mechanism.

Combined use of 13C chemical shift and 1H alpha-13C alpha heteronuclear NOE data in monitoring a protein NMR structure refinement

A large portion of the 13C resonance assignments for murine epidermal growth factor (mEGF) at pH 3.1 and 28 degrees C has been determined at natural isotope abundance. Sequence-specific 13C assignments are reported for 100% of the assignable C alpha, 96% of the C beta, 86% of the aromatic and 70% of the remaining peripheral aliphatic resonances of mEGF. A good correlation was observed between experimental and back-calculated C alpha chemical shifts for regions of regular beta-sheet structure. These assignments also provide the basis for interpreting 1H alpha-13C alpha heteronuclear NOE (HNOE) values in mEGF at natural isotope abundance. Some of the backbone polypeptide segments with high internal mobility, indicated by these 1H alpha-13C alpha HNOE measurements, correlate with locations of residues involved in the putative mEGF-receptor binding site. Using four families of mEGF structures obtained over the last few years, we demonstrate that standard deviations between experimental and back-calculated delta delta C alpha values can be used to monitor the refinement of this protein's structure, particularly for beta-sheet regions. Improved agreement between calculated and observed values of delta delta C alpha is correlated with other measures of structure quality, including lowered values of residual constraint violations and more negative values of conformational energy. These results support the view that experimental conformation-dependent chemical shifts, delta delta C alpha, can provide a reliable source of information for monitoring the process of protein structure refinement and are potentially useful restraints for driving the refinement.

Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA

Sequence-specific 1H and 15N resonance assignments have been determined for the major cold shock protein (CspA) from Escherichia coli with recently developed three-dimensional triple-resonance NMR experiments. By use of these assignments, five antiparallel beta-strands were identified from analysis of NMR data. Strands 1-4 have a classical 3-2-1-4 Greek key beta-sheet topology and there are two beta-bulges, at positions Lys10-Trp11 and Gly65-Asn66. Three-dimensional structures of CspA were generated from NMR data by using simulated annealing with molecular dynamics. The overall chain fold of CspA is a beta-barrel structure, with a tightly packed hydrophobic core. Two-dimensional isotope-edited pulsed-field gradient 15N-1H heteronuclear single-quantum coherence spectroscopy was used to characterize the 15N-1H fingerprint spectrum with and without a 24-base oligodeoxyribonucleotide, 5'-AACGGTTTGACGTACAGACCATTA-3'. Protein-DNA complex formation perturbs a subset of the amide resonances that are located mostly on one face of the CspA molecule. This portion of the CspA molecular surface includes two putative RNA-binding sequence motifs which contribute to an unusual cluster of eight surface aromatic side chains: Trp11, Phe12, Phe18, Phe20, Phe31, His33, Phe34, and Tyr42. These surface aromatic groups, and also residues Lys16, Ser44, and Lys60 located on this same face of CspA, are highly conserved in the family of CspA homologues. These isotope-edited pulsed-field gradient NMR data provide a low-resolution mapping of a DNA-binding epitope on CspA.