Biomedical subjects

B I Dahiyat

Publications and source records attributed to B I Dahiyat.

8 recordsLinked to original sources

PubMed1999

In silico design for protein stabilization.

Newly developed in silico protein design methods have recently been applied to problems in protein stabilization. Stabilized protein sequences can be designed by combining potential functions that model a protein sequence's compatibility with a structure and fast optimization tools that can search the enormous number of sequence possibilities. The experimental testing of several sequence-design strategies has demonstrated that a wide range of protein structures can be stabilized. The primary advantage of in silico design is the vast number of sequences that can be rapidly screened in the search for an optimal design, far exceeding non-computational methods. This feature allows very large changes in protein properties to be discovered.

Biotechnology↗

PubMed1997

De novo protein design: towards fully automated sequence selection.

Several groups have applied and experimentally tested systematic, quantitative methods to protein design with the goal of developing general design algorithms. We have sought to expand the range of computational protein design by developing quantitative design methods for residues of all parts of a protein: the buried core, the solvent exposed surface, and the boundary between core and surface. Our goal is an objective, quantitative design algorithm that is based on the physical properties that determine protein structure and stability and which is not limited to specific folds or motifs. We chose the betabetaalpha motif typified by the zinc finger DNA binding module to test our design methodology. Using previously published sequence scoring functions developed with a combined experimental and computational approach and the Dead-End Elimination theorem to search for the optimal sequence, we designed 20 out of 28 positions in the test motif. The resulting sequence has less than 40% homology to any known sequence and does not contain any metal binding sites or cysteine residues. The resulting peptide, pda8d, is highly soluble and monomeric and circular dichroism measurements showed it to be folded with a weakly cooperative thermal unfolding transition. The NMR solution structure of pda8d was solved and shows that it is well-defined with a backbone ensemble rms deviation of 0. 55 A. Pda8d folds into the desired betabetaalpha motif with well-defined elements of secondary structure and tertiary organization. Superposition of the pda8d backbone to the design target is excellent, with an atomic rms deviation of 1.04 A.

Algorithms↗

PubMed1997

De novo protein design: fully automated sequence selection.

The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 x 10(27) possible amino acid sequences for compatibility with the design target, a betabetaalpha protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.

Algorithms↗

PubMed1997

Probing the role of packing specificity in protein design.

By using a protein-design algorithm that quantitatively considers side-chain packing, the effect of specific steric constraints on protein design was assessed in the core of the streptococcal protein G beta1 domain. The strength of packing constraints used in the design was varied, resulting in core sequences that reflected differing amounts of packing specificity. The structural flexibility and stability of several of the designed proteins were experimentally determined and showed a trend from well-ordered to highly mobile structures as the degree of packing specificity in the design decreased. This trend both demonstrates that the inclusion of specific packing interactions is necessary for the design of native-like proteins and defines a useful range of packing specificity for the design algorithm. In addition, an analysis of the modeled protein structures suggested that penalizing for exposed hydrophobic surface area can improve design performance.

Algorithms↗

PubMed1997

Automated design of the surface positions of protein helices.

Using a protein design algorithm that quantitatively considers side-chain interactions, the design of surface residues of alpha helices was examined. Three scoring functions were tested: a hydrogen-bond potential, a hydrogen-bond potential in conjunction with a penalty for uncompensated burial of polar hydrogens, and a hydrogen-bond potential in combination with helix propensity. The solvent exposed residues of a homodimeric coiled coil based on GCN4-p1 were designed by using the Dead-End Elimination Theorem to find the optimal amino acid sequence for each scoring function. The corresponding peptides were synthesized and characterized by circular dichroism spectroscopy and size exclusion chromatography. The designed peptides were dimeric and nearly 100% helical at 1 degree C, with melting temperatures from 69-72 degrees C, over 12 degrees C higher than GCN4-p1, whereas a random hydrophilic sequence at the surface positions produced a peptide that melted at 15 degrees C. Analysis of the designed sequences suggests that helix propensity is the key factor in sequence design for surface helical positions.

Algorithms↗

PubMed1996

Protein design automation.

We have conceived and implemented a cyclical protein design strategy that couples theory, computation, and experimental testing. The combinatorially large number of possible sequences and the incomplete understanding of the factors that control protein structure are the primary obstacles in protein design. Our protein design automation algorithm objectively predicts protein sequences likely to achieve a desired fold. Using a rotamer description of the side chains, we implemented a fast discrete search algorithm based on the Dead-End Elimination Theorem to rapidly find the globally optimal sequence in its optimal geometry from the vast number of possible solutions. Rotamer sequences were scored for steric complementarity using a van der Waals potential. A Monte Carlo search was then executed, starting at the optimal sequence, in order to find other high-scoring sequences. As a test of the design methodology, high-scoring sequences were found for the buried hydrophobic residues of a homodimeric coiled coil based on GCN4-p1. The corresponding peptides were synthesized and characterized by CD spectroscopy and size-exclusion chromatography. All peptides were dimeric and nearly 100% helical at 1 degree C, with melting temperatures ranging from 24 degrees C to 57 degrees C. A quantitative structure activity relation analysis was performed on the designed peptides, and a significant correlation was found with surface area burial. Incorporation of a buried surface area potential in the scoring of sequences greatly improved the correlation between predicted and measured stabilities and demonstrated experimental feedback in a complete design cycle.

Algorithms↗

PubMed1993

Synthesis and characterization of putrescine-based poly(phosphoester-urethanes).

A novel set of putrescine-based segmented polyurethanes was synthesized using 1,4-butane-diisocyanate and phosphoester diols, and was characterized for its potential as a degradable biomaterial. These poly(phosphoester-urethanes) (PPU) were flexible polymers with ultimate tensile strength (UTS) from 2 to 3 MPa, elongations up to 80% and tan delta near 0.15. The incorporation of phosphoester bonds in the backbone of the polymer by using bis(2-hydroxyethyl)phosphite (BGP) and bis(6-hydroxyhexyl)phosphite (BHP) as chain extenders resulted in hydrolytic degradation which was evaluated in vitro. By varying the content of the phosphoester diol BGP, degradation rate, as followed by mass loss and GPC, could be modulated. Polymers based on the more hydrophobic monomer, BHP, showed slower degradation than corresponding BGP based polymers. Tensile properties of PPU-B2 after 22 days in vitro degradation show more than a 50% drop in UTS and ultimate elongation, likely caused by void spaces left behind in the polymer after mass loss and swelling. The attachment of a drug, PAS, pendant to the phosphoester group of the PPU was demonstrated. PAS was linked via the spacer 4-hydroxybenzaldehyde, and free, intact drug was released in about 5 h from a thin film.

Aminosalicylic Acid↗

PubMed1991

Evaluation of polyphosphates and polyphosphonates as degradable biomaterials.

A series of polymers, bisphenol A-based poly(phosphoesters), were evaluated as degradable biomaterials. Degradation was observed for the four polymers studied under both in vitro and in vivo conditions. The rate of degradation was affected by polymer side-chain structure and correlated with the swelling behavior. The ethyl side-chain polymers absorbed more water than their phenyl counterparts. Among the sterilization methods, UV irradiation followed by antibiotic treatment was the most suitable, as steam autoclave and ethylene oxide treatments altered the properties of several of the poly (phosphoesters). Tissue response to the poly(phosphoesters) in rabbits was characterized by minor encapsulation and slight or no lymphocyte, giant cell, or macrophage activity. No evidence of edema or necrosis was found. The elastic moduli of these materials varied from 488 MPa for poly(bisphenol A-ethylphosphate) (BPA/EOP) to 627 MPa for the more rigid poly(bisphenol A-phenylphosphonate) (BPA/PP). The ultimate strength, modulus, and energy to failure of BPA/PP were lower than those of similarly compression molded high-molecular-weight poly(L-lactic acid) (PLLA).

Animals↗