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Biomedical subjects

J T Pedersen

Publications and source records attributed to J T Pedersen.

At least 19 recordsLinked to original sources
PubMed1999

[Tuberculosis and migration].

The decline of tuberculosis in many western countries has faded off in many countries in recent years because of migration of people from high-prevalence to low-prevalence areas. Tuberculosis in immigrants mirrors tuberculosis in the country of origin with a predominance of young people with a high incidence of extrapulmonary tuberculosis. Typically, the tuberculosis appears in the first five years after arrival. The impact of immigrant tuberculosis has been discussed in a number of recent publications. In Denmark the incidence of tuberculosis in immigrants now outnumbers the incidence in Danes. Screening for tuberculosis in immigrants is not obligatory and is only offered to asylum seekers under the care of the Danish Red Cross but could be considered in all immigrants from high-prevalence countries.

Communicable Disease Control↗
PubMed1997

Protein folding simulations with genetic algorithms and a detailed molecular description.

We have explored the application of genetic algorithms (GA) to the determination of protein structure from sequence, using a full atom representation. A free energy function with point charge electrostatics and an area based solvation model is used. The method is found to be superior to previously investigated Monte Carlo algorithms. For selected fragments, up to 14 residues long, the lowest free energy structures produced by the GA are similar in conformation to the corresponding experimental structures in most cases. There are three main conclusions from these results. First, the genetic algorithm is an effective method for searching amongst the compact conformations of a polypeptide chain. Second, the free energy function is generally able to select native-like conformations. However, some deficiencies are identified, and further development is proposed. Third, the selection of native-like conformations for some protein fragments establishes that in these cases the conformation observed in the full protein structure is largely context independent. The implications for the nature of protein folding pathways are discussed.

Algorithms↗
PubMed1997

Ab initio protein folding simulations with genetic algorithms: simulations on the complete sequence of small proteins.

Ab-initio folding simulations have been performed on three small proteins using a genetic algorithm- (GA-) based search method which operates on an all atom representation. Simulations were also performed on a number of small peptides expected to be independent folding units. The present genetic algorithm incorporates the results of developments made to the method first tested in CASP1. Additional operators have been introduced into the search in order to allow the simulation of longer sequences and to avoid the simulation of longer sequences and to avoid premature free energy convergence. Secondary structure information derived from a consensus of eight methods and Monte Carlo simulations on sets of homologous sequences has been used to bias the starting populations used in the GA simulations. For the fragment simulations, the results generally have approximately correct local structure, but tend to be too compact, leading to poor RMS error values. One of the three small protein structures has the topology and most of the general organization correct, although many of the details are incorrect.

Algorithms↗
PubMed1996

Genetic algorithms for protein structure prediction.

Genetic algorithms are a general class of search methods that mimic natural gene-based optimization mechanisms. Mutation, cross-over and replication operations are performed on strings. When applied to structure prediction, each string describes a particular conformation of a protein molecule. There are many ways in which such search methods may be implemented. Recent results show potential for helping with protein structure prediction, but more data are needed before a complete assessment can be made.

Algorithms↗
PubMed1996

A comparison of two murine monoclonal antibodies humanized by CDR-grafting and variable domain resurfacing.

The variable domain resurfacing and CDR-grafting approaches to antibody humanization were compared directly on the two murine monoclonal antibodies N901 (anti-CD56) and anti-B4 (anti-CD19). Resurfacing replaces the set of surface residues of a rodent variable region with a human set of surface residues. The method of CDR-grafting conceptually consists of transferring the CDRs from a rodent antibody onto the Fv framework of a human antibody. Computer-aided molecular modeling was used to design the initial CDR-grafted and resurfaced versions of these two antibodies. The initial versions of resurfaced N901 and resurfaced anti-B4 maintained the full binding affinity of the original murine parent antibodies and further refinements to these versions described herein generated five new resurfaced antibodies that contain fewer murine residues at surface positions, four of which also have the full parental binding affinity. A mutational study of three surface positions within 5 A of the CDRs of resurfaced anti-B4 revealed a remarkable ability of the resurfaced antibodies to maintain binding affinity despite dramatic changes of charges near their antigen recognition surfaces, suggesting that the resurfacing approach can be used with a high degree of confidence to design humanized antibodies that maintain the full parental binding affinity. By comparison CDR-grafted anti-B4 antibodies with parental affinity were produced only after seventeen versions were attempted using two different strategies for selecting the human acceptor frameworks. For both the CDR-grafted anti-B4 and N901 antibodies, full restoration of antigen binding affinity was achieved when the most identical human acceptor frameworks were selected. The CDR-grafted anti-B4 antibodies that maintained high affinity binding for CD19 had more murine residues at surface positions than any of the three versions of the resurfaced anti-B4 antibody. This observation suggests that the resurfacing approach can be used to produce humanized antibodies with reduced antigenic potential relative to their corresponding CDR-grafted versions.

Amino Acid Sequence↗
PubMed1995

[Tuberculosis in low prevalence countries. Back to the future?].

The incidence of tuberculosis has declined in all European countries in this century but in several countries the decline has come to a stop. Microscopy a.m. Ziehl-Neelsen and culture are still the mainstays in the diagnosis of tuberculosis but new DNA-technics such as PCR and RFLP are increasingly used. The tuberculin test is hitherto the only practically feasible test for identification of subjects infected with M. tuberculosis. BCG is the most used vaccine in the world but the protective mechanisms are not fully understood and the efficacy controversial. Immunotherapy with M. vaccae may be used as an adjuvant to chemotherapy. Few cases of tuberculosis are observed in AIDS-patients in Denmark. Modern standard treatment of tuberculosis comprises a six-month regimen with isoniazid, rifampicin, pyrazinamide and possibly ethambutol. Multidrug resistance in tuberculosis is rare in Western Europe. Chemoprophylaxis with isoniazid is debatable. Patients with smear-positive sputum may be infectious whereas patients with extrapulmonary tuberculosis normally pose no risk.

Disease Outbreaks↗
PubMed1995

Confronting the problem of interconnected structural changes in the comparative modeling of proteins.

Comparative models of three proteins have been built using a variety of computational methods, heavily supplemented by visual inspection. We consider the accuracy obtained to be worse than expected. A careful analysis of the models shows that a major reason for the poor results is the interconnectedness of the structural differences between the target proteins and the template structures they were modeled from. Side chain conformations are often determined by details of the structure remote in the sequence, and can be influenced by relatively small main chain changes. Almost all of the regions of substantial main chain conformational change interact with at least one other such region, so that they often cannot be modeled independently. Visual inspection is sometimes effective in correcting errors in sequence alignment and in spotting when an alternative template structure is more appropriate. We expect some improvements in the near future through the development of structure-based sequence alignment tools, side chain interconnectedness rotamer choice algorithms, and a better understanding of the context sensitivity of conformational features.

Amino Acid Sequence↗
PubMed1995

Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms.

Ab initio folding simulations have been performed on three peptides, using a genetic algorithm-based search method which operates on a full atom representation. Conformations are evaluated with an empirical force field parameterized by a potential of mean force analysis of experimental structures. The dominant terms in the force field are local and nonlocal main chain electrostatics and the hydrophobic effect. Two of the simulated structures were for fragments of complete proteins (eosinophil-derived neurotoxin (EDN) and the subtilisin propeptide) that were identified as being likely initiation sites for folding. The experimental structure of one of these (EDN) was subsequently found to be consistent with that prediction (using local hydrophobic burial as the determinant for independent folding). The simulations of the structures of these two peptides were only partly successful. The most successful folding simulation was that of a 22-residue peptide corresponding to the membrane binding domain of blood coagulation factor VIII (Membind). Three simulations were performed on this peptide and the lowest energy conformation was found to be the most similar to the experimental structure. The conformation of this peptide was determined with a C alpha rms deviation of 4.4 A. Although these simulations were partly successful there are still many unresolved problems, which we expect to be able to address in the next structure prediction experiment.

Algorithms↗
PubMed1994

Cavity mutants of Savinase. Crystal structures and differential scanning calorimetry experiments give hints of the function of the buried water molecules in subtilisins.

The subtilisin molecule possesses several internal water molecules, which may be characterised as an integral part of the protein structure. We have introduced specific mutations (T71I, T71S, T71V, T71A and T71G) at position 71 in the subtilisin variant Savinase from Bacillus lentus. This position is involved in a hydrogen bonded network with several internal water molecules, forming a water channel. The water channel and most of the other internal water molecules are positioned in the interface between two half-domains of the subtilisin molecule. The data presented here indicate that the internal water molecules are structural, and may be the result of trapping during the folding process.

Amino Acids↗
PubMed1994

Humanization of murine monoclonal antibodies through variable domain resurfacing.

Two murine monoclonal antibodies, N901 (anti-CD56) and anti-B4 (anti-CD19), were humanized by a process we call "resurfacing." A systematic analysis of known antibody structures has been used to determine the relative solvent accessibility distributions of amino acid residues in murine and human antibody variable (Fv) regions and has shown that the sequence alignment positions of surface amino acids for human and murine variable region heavy (VH) and light (VL) chains are conserved with 98% fidelity across species. While the amino acid usage at these surface positions creates surface residue patterns that are conserved within species, there are no identical patterns across species. However, surprisingly few amino acid changes need to be made to convert a murine Fv surface pattern to that characteristic of a human surface. Resurfacing was used to change the patterns of surface accessible residues in the Fv regions of the N901 and anti-B4 antibodies to resemble those found on the Fv regions of human antibody sequences. Two different procedures for selecting a human sequence were compared. For anti-B4, a data base of clonally derived human VL-VH sequence pairs was used, while for N901, sequences for VL and VH were independently selected from the Kabat et al. data base [Kabat, E. A., Wu, T. T., Reid-Miller, M., Perry, H. M. & Gottesman, K. S. (1991) Sequences of Proteins of Immunological Interest (DHHS, Washington, DC), 5th Ed.]. Resurfaced N901 and anti-B4 antibodies had apparent affinities for their cell surface ligands that were identical to those of their respective parent murine antibodies. These data provide evidence that, despite the differences in the surfaces of mouse and human Fv regions, it is possible to substitute one for the other while retaining full antigen binding affinity.

Amino Acid Sequence↗
PubMed1994

Comparison of surface accessible residues in human and murine immunoglobulin Fv domains. Implication for humanization of murine antibodies.

Statistical analysis of a database of unique human and murine immunoglobulin heavy chain and light chain variable regions reveals that the precise patterns of exposed residues are different in human and murine antibodies, while most individual surface positions have strong preferences for a small number of residue types. Consideration of these surface patterns alone generates almost identical family groupings for light and heavy chain variable domain sequences to those produced by methods such as those of Kabat et al., where N-terminal framework sequences only are compared, or Tomlinson et al., in which entire variable region nucleotide sequences are used. This unexpected result suggests that the surfaces of V-regions are at least as well conserved as the core framework sequences. Furthermore, using these patterns of human and murine surface residues a novel method for the "humanization" of murine antibodies has been developed and tested.

Algorithms↗
PubMed1994

Antibody design: beyond the natural limits.

Dissection of antibody-antigen interactions requires a knowledge of antibody structure, the ability to model accurately the conformation of antibody-combining sites, and an understanding of the energetic factors governing the interactions. When this understanding has reached the point where the molecular shape and chemical character of a combining site necessary to define a particular specificity and binding requirement can be designed, the antibody repertoire will have been extended 'beyond the natural limits'.

Animals↗