201
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Zhang Y, Weber JK, Zhou R. Folding and Stabilization of Native-Sequence-Reversed Proteins. Sci Rep 2016; 6:25138. [PMID: 27113844 PMCID: PMC4844985 DOI: 10.1038/srep25138] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/06/2016] [Indexed: 11/29/2022] Open
Abstract
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle, and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols.
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Affiliation(s)
- Yuanzhao Zhang
- Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China.,Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Jeffrey K Weber
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Ruhong Zhou
- Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China.,Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA.,Department of Chemistry, Columbia University, New York, NY 10027, USA
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202
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Gaillard T, Panel N, Simonson T. Protein side chain conformation predictions with an MMGBSA energy function. Proteins 2016; 84:803-19. [PMID: 26948696 DOI: 10.1002/prot.25030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 02/22/2016] [Accepted: 02/27/2016] [Indexed: 12/17/2022]
Abstract
The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Thomas Gaillard
- Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Nicolas Panel
- Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Thomas Simonson
- Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
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203
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Long antibody HCDR3s from HIV-naïve donors presented on a PG9 neutralizing antibody background mediate HIV neutralization. Proc Natl Acad Sci U S A 2016; 113:4446-51. [PMID: 27044078 DOI: 10.1073/pnas.1518405113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Development of broadly neutralizing antibodies (bnAbs) against HIV-1 usually requires prolonged infection and induction of Abs with unusual features, such as long heavy-chain complementarity-determining region 3 (HCDR3) loops. Here we sought to determine whether the repertoires of HIV-1-naïve individuals contain Abs with long HCDR3 loops that could mediate HIV-1 neutralization. We interrogated at massive scale the structural properties of long Ab HCDR3 loops in HIV-1-naïve donors, searching for structured HCDR3s similar to those of the HIV-1 bnAb PG9. We determined the nucleotide sequences encoding 2.3 × 10(7)unique HCDR3 amino acid regions from 70 different HIV-1-naïve donors. Of the 26,917 HCDR3 loops with 30-amino acid length identified, we tested 30 for further study that were predicted to have PG9-like structure when chimerized onto PG9. Three of these 30 PG9 chimeras bound to the HIV-1 gp120 monomer, and two were neutralizing. In addition, we found 14 naturally occurring HCDR3 sequences that acquired the ability to bind to the HIV-1 gp120 monomer when adding 2- to 7-amino acid mutations via computational design. Of those 14 designed Abs, 8 neutralized HIV-1, with IC50values ranging from 0.7 to 98 µg/mL. These data suggest that the repertoire of HIV-1-naïve individuals contains rare B cells that encode HCDR3 loops that bind or neutralize HIV-1 when presented on a PG9 background with relatively few or no additional mutations. Long HCDR3 sequences are present in the HIV-naïve B-cell repertoire, suggesting that this class of bnAbs is a favorable target for rationally designed preventative vaccine efforts.
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204
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016; 12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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Affiliation(s)
- Tatiana Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Ryan Moffatt
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
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205
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Khan FI, Wei DQ, Gu KR, Hassan MI, Tabrez S. Current updates on computer aided protein modeling and designing. Int J Biol Macromol 2016; 85:48-62. [DOI: 10.1016/j.ijbiomac.2015.12.072] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022]
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206
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Xiao X, Agris PF, Hall CK. Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success. Proteins 2016; 84:700-11. [PMID: 26914059 DOI: 10.1002/prot.25021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/26/2016] [Accepted: 02/10/2016] [Indexed: 12/30/2022]
Abstract
A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL(Lys3)) of human tRNAUUULys3 for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL(Lys3). Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL(Lys3). Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search.
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Affiliation(s)
- Xingqing Xiao
- Chemical and Biomolecular Engineering Department, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Paul F Agris
- The RNA Institute, University at Albany, State University of New York, Albany, New York, 12222
| | - Carol K Hall
- Chemical and Biomolecular Engineering Department, North Carolina State University, Raleigh, North Carolina, 27695-7905
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207
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Kim DN, Jacobs TM, Kuhlman B. Boosting protein stability with the computational design of β-sheet surfaces. Protein Sci 2016; 25:702-10. [PMID: 26701383 PMCID: PMC4815415 DOI: 10.1002/pro.2869] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 11/09/2022]
Abstract
β-sheets often have one face packed against the core of the protein and the other facing solvent. Mutational studies have indicated that the solvent-facing residues can contribute significantly to protein stability, and that the preferred amino acid at each sequence position is dependent on the precise structure of the protein backbone and the identity of the neighboring amino acids. This suggests that the most advantageous methods for designing β-sheet surfaces will be approaches that take into account the multiple energetic factors at play including side chain rotamer preferences, van der Waals forces, electrostatics, and desolvation effects. Here, we show that the protein design software Rosetta, which models these energetic factors, can be used to dramatically increase protein stability by optimizing interactions on the surfaces of small β-sheet proteins. Two design variants of the β-sandwich protein from tenascin were made with 7 and 14 mutations respectively on its β-sheet surfaces. These changes raised the thermal midpoint for unfolding from 45°C to 64°C and 74°C. Additionally, we tested an empirical approach based on increasing the number of potential salt bridges on the surfaces of the β-sheets. This was not a robust strategy for increasing stability, as three of the four variants tested were unfolded.
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Affiliation(s)
- Doo Nam Kim
- Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Timothy M. Jacobs
- Program in Bioinformatics and Computational BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Brian Kuhlman
- Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
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208
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Louros NN, Chrysina ED, Baltatzis GE, Patsouris ES, Hamodrakas SJ, Iconomidou VA. A common 'aggregation-prone' interface possibly participates in the self-assembly of human zona pellucida proteins. FEBS Lett 2016; 590:619-30. [PMID: 26879157 DOI: 10.1002/1873-3468.12099] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 02/03/2023]
Abstract
Human zona pellucida (ZP) is composed of four glycoproteins, namely ZP1, ZP2, ZP3 and ZP4. ZP proteins form heterodimers, which are incorporated into filaments through a common bipartite polymerizing component, designated as the ZP domain. The latter is composed of two individually folded subdomains, named ZP-N and ZP-C. Here, we have synthesized six 'aggregation-prone' peptides, corresponding to a common interface of human ZP2, ZP3 and ZP4. Experimental results utilizing electron microscopy, X-ray diffraction, ATR FT-IR spectroscopy and polarizing microscopy indicate that these peptides self-assemble forming fibrils with distinct amyloid-like features. Finally, by performing detailed modeling and docking, we attempt to shed some light in the self-assembly mechanism of human ZP proteins.
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Affiliation(s)
- Nikolaos N Louros
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | | | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
| | - Vassiliki A Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
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209
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Abstract
Allosteric transition, defined as conformational changes induced by ligand binding, is one of the fundamental properties of proteins. Allostery has been observed and characterized in many proteins, and has been recently utilized to control protein function via regulation of protein activity. Here, we review the physical and evolutionary origin of protein allostery, as well as its importance to protein regulation, drug discovery, and biological processes in living systems. We describe recently developed approaches to identify allosteric pathways, connected sets of pairwise interactions that are responsible for propagation of conformational change from the ligand-binding site to a distal functional site. We then present experimental and computational protein engineering approaches for control of protein function by modulation of allosteric sites. As an example of application of these approaches, we describe a synergistic computational and experimental approach to rescue the cystic-fibrosis-associated protein cystic fibrosis transmembrane conductance regulator, which upon deletion of a single residue misfolds and causes disease. This example demonstrates the power of allosteric manipulation in proteins to both elucidate mechanisms of molecular function and to develop therapeutic strategies that rescue those functions. Allosteric control of proteins provides a tool to shine a light on the complex cascades of cellular processes and facilitate unprecedented interrogation of biological systems.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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210
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Li J, Csakai A, Jin J, Zhang F, Yin H. Therapeutic Developments Targeting Toll-like Receptor-4-Mediated Neuroinflammation. ChemMedChem 2016; 11:154-65. [PMID: 26136385 PMCID: PMC4983275 DOI: 10.1002/cmdc.201500188] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 02/06/2023]
Abstract
Toll-like receptors (TLRs) have been shown to play an important role in the immune system, which warrants study of their remarkable potential as pharmacological targets. Activation of TLRs requires participation from specific pathogen-associated molecular patterns (PAMPs) and accessory proteins such as myeloid differentiation protein 2 (MD2), lipopolysaccharide binding protein (LBP), and cluster differentiation antigen 14 (CD14). Assembly of the TLR4-MD2-LPS complex is essential in TLR4 activation. Recent studies have revealed that TLR4 activation is a significant trigger of signal transmission pathways in the nervous system, which could result in chronic pain as well as opioid tolerance and dependence. Researchers of the molecular structure of TLRs and their accessory proteins have opened a door to syntheses of TLRs agonists and antagonists, such as eritoran. Small-molecule modulators of TLR4, such as MD2-I and tricyclic antidepressants, offer more promising prospects than peptides, given their convenience in oral administration and lower cost. Herein we mainly discuss the mechanisms and clinical prospects of TLR4 agonists and antagonists.
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Affiliation(s)
- Jing Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100032, China
| | - Adam Csakai
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Jialin Jin
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, 100082, China
- Physikalisch-Astronomische Fakultät, Abbe School of Photonics, Jena, 07743, Germany
| | - Fengchun Zhang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100032, China.
| | - Hang Yin
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, 80309-0596, USA.
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, 100082, China.
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211
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Armanious A, Aeppli M, Jacak R, Refardt D, Sigstam T, Kohn T, Sander M. Viruses at Solid-Water Interfaces: A Systematic Assessment of Interactions Driving Adsorption. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:732-43. [PMID: 26636722 DOI: 10.1021/acs.est.5b04644] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Adsorption to solid-water interfaces is a major process governing the fate of waterborne viruses in natural and engineered systems. The relative contributions of different interaction forces to adsorption and their dependence on the physicochemical properties of the viruses remain, however, only poorly understood. Herein, we systematically studied the adsorption of four bacteriophages (MS2, fr, GA, and Qβ) to five model surfaces with varying surface chemistries and to three dissolved organic matter adlayers, as a function of solution pH and ionic strength, using quartz crystal microbalance with dissipation monitoring. The viruses were selected to have similar sizes and shapes but different surface charges, polarities, and topographies, as identified by modeling the distributions of amino acids in the virus capsids. Virus-sorbent interactions were governed by long-ranged electrostatics and favorable contributions from the hydrophobic effect, and shorter-ranged van der Waals interactions were of secondary importance. Steric effects depended on the topographic irregularities on both the virus and sorbent surfaces. Differences in the adsorption characteristics of the tested viruses were successfully linked to differences in their capsid surface properties. Besides identifying the major interaction forces, this work highlights the potential of computable virus surface charge and polarity descriptors to predict virus adsorption to solid-water interfaces.
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Affiliation(s)
- Antonius Armanious
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne, CH-1015, Switzerland
| | | | - Ronald Jacak
- Applied Physics Laboratory, Johns Hopkins University , Laurel, Maryland 20723, United States
| | | | - Thérèse Sigstam
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne, CH-1015, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne, CH-1015, Switzerland
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212
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Schenkelberg CD, Bystroff C. Protein backbone ensemble generation explores the local structural space of unseen natural homologs. Bioinformatics 2016; 32:1454-61. [PMID: 26787668 DOI: 10.1093/bioinformatics/btw001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 01/03/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Mutations in homologous proteins affect changes in the backbone conformation that involve a complex interplay of forces which are difficult to predict. Protein design algorithms need to anticipate these backbone changes in order to accurately calculate the energy of the structure given an amino acid sequence, without knowledge of the final, designed sequence. This is related to the problem of predicting small changes in the backbone between highly similar sequences. RESULTS We explored the ability of the Rosetta suite of protein design tools to move the backbone from its position in one structure (template) to its position in a close homologous structure (target) as a function of the diversity of a backbone ensemble constructed using the template structure, the percent sequence identity between the template and target, and the size of local zone being considered in the ensemble. We describe a pareto front in the likelihood of moving the backbone toward the target as a function of ensemble diversity and zone size. The equations and protocols presented here will be useful for protein design. AVAILABILITY AND IMPLEMENTATION PyRosetta scripts available at www.bioinfo.rpi.edu/bystrc/downloads.html#ensemble CONTACT bystrc@rpi.edu.
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Affiliation(s)
| | - Christopher Bystroff
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
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213
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Hallen MA, Donald BR. comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. J Comput Biol 2016; 23:311-21. [PMID: 26761641 DOI: 10.1089/cmb.2015.0188] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Practical protein design problems require designing sequences with a combination of affinity, stability, and specificity requirements. Multistate protein design algorithms model multiple structural or binding "states" of a protein to address these requirements. comets provides a new level of versatile, efficient, and provable multistate design. It provably returns the minimum with respect to sequence of any desired linear combination of the energies of multiple protein states, subject to constraints on other linear combinations. Thus, it can target nearly any combination of affinity (to one or multiple ligands), specificity, and stability (for multiple states if needed). Empirical calculations on 52 protein design problems showed comets is far more efficient than the previous state of the art for provable multistate design (exhaustive search over sequences). comets can handle a very wide range of protein flexibility and can enumerate a gap-free list of the best constraint-satisfying sequences in order of objective function value.
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Affiliation(s)
- Mark A Hallen
- 1 Department of Computer Science, Levine Science Research Center, Duke University , North Carolina
- 2 Department of Biochemistry, Duke University Medical Center , Durham, North Carolina
| | - Bruce R Donald
- 1 Department of Computer Science, Levine Science Research Center, Duke University , North Carolina
- 2 Department of Biochemistry, Duke University Medical Center , Durham, North Carolina
- 3 Department of Chemistry, Duke University , Durham, North Carolina
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214
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Sandhya S, Mudgal R, Kumar G, Sowdhamini R, Srinivasan N. Protein sequence design and its applications. Curr Opin Struct Biol 2016; 37:71-80. [PMID: 26773478 DOI: 10.1016/j.sbi.2015.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 01/14/2023]
Abstract
Design of proteins has far-reaching potentials in diverse areas that span repurposing of the protein scaffold for reactions and substrates that they were not naturally meant for, to catching a glimpse of the ephemeral proteins that nature might have sampled during evolution. These non-natural proteins, either in synthesized or virtual form have opened the scope for the design of entities that not only rival their natural counterparts but also offer a chance to visualize the protein space continuum that might help to relate proteins and understand their associations. Here, we review the recent advances in protein engineering and design, in multiple areas, with a view to drawing attention to their future potential.
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Affiliation(s)
- Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Richa Mudgal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India; IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560 012, India
| | - Gayatri Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences-TIFR, UAS-GKVK Campus, Bangalore 560065, India
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215
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Jou JD, Jain S, Georgiev IS, Donald BR. BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. J Comput Biol 2016; 23:413-24. [PMID: 26744898 DOI: 10.1089/cmb.2015.0194] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sparse energy functions that ignore long range interactions between residue pairs are frequently used by protein design algorithms to reduce computational cost. Current dynamic programming algorithms that fully exploit the optimal substructure produced by these energy functions only compute the GMEC. This disproportionately favors the sequence of a single, static conformation and overlooks better binding sequences with multiple low-energy conformations. Provable, ensemble-based algorithms such as A* avoid this problem, but A* cannot guarantee better performance than exhaustive enumeration. We propose a novel, provable, dynamic programming algorithm called Branch-Width Minimization* (BWM*) to enumerate a gap-free ensemble of conformations in order of increasing energy. Given a branch-decomposition of branch-width w for an n-residue protein design with at most q discrete side-chain conformations per residue, BWM* returns the sparse GMEC in O([Formula: see text]) time and enumerates each additional conformation in merely O([Formula: see text]) time. We define a new measure, Total Effective Search Space (TESS), which can be computed efficiently a priori before BWM* or A* is run. We ran BWM* on 67 protein design problems and found that TESS discriminated between BWM*-efficient and A*-efficient cases with 100% accuracy. As predicted by TESS and validated experimentally, BWM* outperforms A* in 73% of the cases and computes the full ensemble or a close approximation faster than A*, enumerating each additional conformation in milliseconds. Unlike A*, the performance of BWM* can be predicted in polynomial time before running the algorithm, which gives protein designers the power to choose the most efficient algorithm for their particular design problem.
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Affiliation(s)
- Jonathan D Jou
- 1 Department of Computer Science, Duke University , Durham, North Carolina
| | - Swati Jain
- 1 Department of Computer Science, Duke University , Durham, North Carolina.,2 Department of Biochemistry, Duke University Medical Center , Durham, North Carolina.,3 Department of Computational Biology and Bioinformatics Program, Duke University , Durham, North Carolina
| | - Ivelin S Georgiev
- 1 Department of Computer Science, Duke University , Durham, North Carolina
| | - Bruce R Donald
- 1 Department of Computer Science, Duke University , Durham, North Carolina.,2 Department of Biochemistry, Duke University Medical Center , Durham, North Carolina.,4 Department of Chemistry, Duke University , Durham, North Carolina
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216
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Sammond DW, Kastelowitz N, Himmel ME, Yin H, Crowley MF, Bomble YJ. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms. PLoS One 2016; 11:e0145848. [PMID: 26741367 PMCID: PMC4704809 DOI: 10.1371/journal.pone.0145848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.
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Affiliation(s)
- Deanne W Sammond
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, Colorado, 80309, United States of America
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, Colorado, 80309, United States of America
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
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217
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Sharmila DJS, Jino Blessy J. Molecular dynamics of sialic acid analogues complex with cholera toxin and DFT optimization of ethylene glycol-mediated zinc nanocluster conjugation. J Biomol Struct Dyn 2016; 35:182-206. [PMID: 26733187 DOI: 10.1080/07391102.2015.1136689] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cholera is an infectious disease caused by cholera toxin (CT) protein of bacterium Vibrio cholerae. A sequence of sialic acid (N-acetylneuraminic acid, NeuNAc or Neu5Ac) analogues modified in its C-5 position is modelled using molecular modelling techniques and docked against the CT followed by molecular dynamics simulations. Docking results suggest better binding affinity of NeuNAc analogue towards the binding site of CT. The NeuNAc analogues interact with the active site residues GLU:11, TYR:12, HIS:13, GLY:33, LYS:34, GLU:51, GLN:56, HIE:57, ILE:58, GLN:61, TRP:88, ASN:90 and LYS:91 through intermolecular hydrogen bonding. Analogues N-glycolyl-NeuNAc, N-Pentanoyl-NeuNAc and N-Propanoyl-NeuNAc show the least XPGscore (docking score) of -9.90, -9.16, and -8.91, respectively, and glide energy of -45.99, -42.14 and -41.66 kcal/mol, respectively. Stable nature of CT-N-glycolyl-NeuNAc, CT-N-Pentanoyl-NeuNAc and CT-N-Propanoyl-NeuNAc complexes was verified through molecular dynamics simulations, each for 40 ns using the software Desmond. All the nine NeuNAc analogues show better score for drug-like properties, so could be considered as suitable candidates for drug development for cholera infection. To improve the enhanced binding mode of NeuNAc analogues towards CT, the nine NeuNAc analogues are conjugated with Zn nanoclusters through ethylene glycol (EG) as carriers. The NeuNAc analogues conjugated with EG-Zn nanoclusters show better binding energy towards CT than the unconjugated nine NeuNAc analogues. The electronic structural optimization of EG-Zn nanoclusters was carried out for optimizing their performance as better delivery vehicles for NeuNAc analogues through density functional theory calculations. These sialic acid analogues may be considered as novel leads for the design of drug against cholera and the EG-Zn nanocluster may be a suitable carrier for sialic acid analogues.
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Affiliation(s)
- D Jeya Sundara Sharmila
- a Department of Nano Science and Technology , Tamil Nadu Agricultural University , Coimbatore 641003 , Tamil Nadu , India
| | - J Jino Blessy
- b Department of Bioinformatics , Karunya University , Karunya Nagar, Coimbatore 641 114 , Tamil Nadu , India
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218
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Tinberg CE, Khare SD. Improving Binding Affinity and Selectivity of Computationally Designed Ligand-Binding Proteins Using Experiments. Methods Mol Biol 2016; 1414:155-171. [PMID: 27094290 DOI: 10.1007/978-1-4939-3569-7_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The ability to de novo design proteins that can bind small molecules has wide implications for synthetic biology and medicine. Combining computational protein design with the high-throughput screening of mutagenic libraries of computationally designed proteins is emerging as a general approach for creating binding proteins with programmable binding modes, affinities, and selectivities. The computational step enables the creation of a binding site in a protein that otherwise does not (measurably) bind the intended ligand, and targeted mutagenic screening allows for validation and refinement of the computational model as well as provides orders-of-magnitude increases in the binding affinity. Deep sequencing of mutagenic libraries can provide insights into the mutagenic binding landscape and enable further affinity improvements. Moreover, in such a combined computational-experimental approach where the binding mode is preprogrammed and iteratively refined, selectivity can be achieved (and modulated) by the placement of specified amino acid side chain groups around the ligand in defined orientations. Here, we describe the experimental aspects of a combined computational-experimental approach for designing-using the software suite Rosetta-proteins that bind a small molecule of choice and engineering, using fluorescence-activated cell sorting and high-throughput yeast surface display, high affinity and ligand selectivity. We illustrated the utility of this approach by performing the design of a selective digoxigenin (DIG)-binding protein that, after affinity maturation, binds DIG with picomolar affinity and high selectivity over structurally related steroids.
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Affiliation(s)
- Christine E Tinberg
- Department of Biochemistry, University of Washington, Seattle, WA, 98109, USA.
- Amgen, South San Francisco, CA, 94080, USA.
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers State University of New Jersey, Piscataway, NJ, 08854, USA
- Center for Integrative Proteomics Research, Rutgers State University of New Jersey, Piscataway, NJ, 08854, USA
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219
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Abstract
The Rosetta macromolecular modeling software is a versatile, rapidly developing set of tools that are now being routinely utilized to address state-of-the-art research challenges in academia and industrial research settings. A Rosetta Conference (RosettaCon) describing updates to the Rosetta source code is held annually. Every two years, a Rosetta Conference (RosettaCon) special collection describing the results presented at the annual conference by participating RosettaCommons labs is published by the Public Library of Science (PLOS). This is the introduction to the third RosettaCon 2014 Special Collection published by PLOS.
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Affiliation(s)
- Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, United States of America
- * E-mail: (SDK); (TAW)
| | - Timothy A. Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, United States of America
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI, United States of America
- * E-mail: (SDK); (TAW)
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220
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Pottel J, Moitessier N. Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering. J Chem Inf Model 2015; 55:2657-71. [PMID: 26623941 DOI: 10.1021/acs.jcim.5b00525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein engineers have long been hard at work to harness biocatalysts as a natural source of regio-, stereo-, and chemoselectivity in order to carry out chemistry (reactions and/or substrates) not previously achieved with these enzymes. The extreme labor demands and exponential number of mutation combinations have induced computational advances in this domain. The first step in our virtual approach is to predict the correct conformations upon mutation of residues (i.e., rebuilding side chains). For this purpose, we opted for a combination of molecular mechanics and statistical data. In this work, we have developed automated computational tools to extract protein structural information and created conformational libraries for each amino acid dependent on a variable number of parameters (e.g., resolution, flexibility, secondary structure). We have also developed the necessary tool to apply the mutation and optimize the conformation accordingly. For side-chain conformation prediction, we obtained overall average root-mean-square deviations (RMSDs) of 0.91 and 1.01 Å for the 18 flexible natural amino acids within two distinct sets of over 3000 and 1500 side-chain residues, respectively. The commonly used dihedral angle differences were also evaluated and performed worse than the state of the art. These two metrics are also compared. Furthermore, we generated a family-specific library for kinases that produced an average 2% lower RMSD upon side-chain reconstruction and a residue-specific library that yielded a 17% improvement. Ultimately, since our protein engineering outlook involves using our docking software, Fitted/Impacts, we applied our mutation protocol to a benchmarked data set for self- and cross-docking. Our side-chain reconstruction does not hinder our docking software, demonstrating differences in pose prediction accuracy of approximately 2% (RMSD cutoff metric) for a set of over 200 protein/ligand structures. Similarly, when docking to a set of over 100 kinases, side-chain reconstruction (using both general and biased conformation libraries) had minimal detriment to the docking accuracy.
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Affiliation(s)
- Joshua Pottel
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8
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221
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Kinjo AR. Liquid-theory analogy of direct-coupling analysis of multiple-sequence alignment and its implications for protein structure prediction. Biophys Physicobiol 2015; 12:117-9. [PMID: 27493860 PMCID: PMC4736835 DOI: 10.2142/biophysico.12.0_117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/10/2015] [Indexed: 12/01/2022] Open
Abstract
The direct-coupling analysis is a powerful method for protein contact prediction, and enables us to extract “direct” correlations between distant sites that are latent in “indirect” correlations observed in a protein multiple-sequence alignment. I show that the direct correlation can be obtained by using a formulation analogous to the Ornstein-Zernike integral equation in liquid theory. This formulation intuitively illustrates how the indirect or apparent correlation arises from an infinite series of direct correlations, and provides interesting insights into protein structure prediction.
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Affiliation(s)
- Akira R Kinjo
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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222
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Tak Kam VW, Goddard WA. Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements. J Chem Theory Comput 2015; 4:2160-9. [PMID: 26620487 DOI: 10.1021/ct800196k] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a new strategy for protein side-chain placement that uses flat-bottom potentials for rotamer scoring. The extent of the flat bottom depends on the coarseness of the rotamer library and is optimized for libraries ranging from diversities of 0.2 Å to 5.0 Å. The parameters reported here were optimized for forcefields using Lennard-Jones 12-6 van der Waals potential with DREIDING parameters but are expected to be similar for AMBER, CHARMM, and other forcefields. This Side-Chain Rotamer Excitation Analysis Method is implemented in the SCREAM software package. Similar scoring function strategies should be useful for ligand docking, virtual ligand screening, and protein folding applications.
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Affiliation(s)
- Victor Wai Tak Kam
- Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125
| | - William A Goddard
- Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125
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223
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López-Sagaseta J, Malito E, Rappuoli R, Bottomley MJ. Self-assembling protein nanoparticles in the design of vaccines. Comput Struct Biotechnol J 2015; 14:58-68. [PMID: 26862374 PMCID: PMC4706605 DOI: 10.1016/j.csbj.2015.11.001] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/10/2015] [Indexed: 01/09/2023] Open
Abstract
For over 100 years, vaccines have been one of the most effective medical interventions for reducing infectious disease, and are estimated to save millions of lives globally each year. Nevertheless, many diseases are not yet preventable by vaccination. This large unmet medical need demands further research and the development of novel vaccines with high efficacy and safety. Compared to the 19th and early 20th century vaccines that were made of killed, inactivated, or live-attenuated pathogens, modern vaccines containing isolated, highly purified antigenic protein subunits are safer but tend to induce lower levels of protective immunity. One strategy to overcome the latter is to design antigen nanoparticles: assemblies of polypeptides that present multiple copies of subunit antigens in well-ordered arrays with defined orientations that can potentially mimic the repetitiveness, geometry, size, and shape of the natural host-pathogen surface interactions. Such nanoparticles offer a collective strength of multiple binding sites (avidity) and can provide improved antigen stability and immunogenicity. Several exciting advances have emerged lately, including preclinical evidence that this strategy may be applicable for the development of innovative new vaccines, for example, protecting against influenza, human immunodeficiency virus, and respiratory syncytial virus. Here, we provide a concise review of a critical selection of data that demonstrate the potential of this field. In addition, we highlight how the use of self-assembling protein nanoparticles can be effectively combined with the emerging discipline of structural vaccinology for maximum impact in the rational design of vaccine antigens.
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Affiliation(s)
| | - Enrico Malito
- GlaxoSmithKline Vaccines S.r.l., Via Fiorentina 1, 53100 Siena, Italy
| | - Rino Rappuoli
- GlaxoSmithKline Vaccines S.r.l., Via Fiorentina 1, 53100 Siena, Italy
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224
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Simoncini D, Allouche D, de Givry S, Delmas C, Barbe S, Schiex T. Guaranteed Discrete Energy Optimization on Large Protein Design Problems. J Chem Theory Comput 2015; 11:5980-9. [DOI: 10.1021/acs.jctc.5b00594] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - David Allouche
- INRA MIAT, UR 875, Castanet-Tolosan, 31326 Cedex, France
| | - Simon de Givry
- INRA MIAT, UR 875, Castanet-Tolosan, 31326 Cedex, France
| | - Céline Delmas
- INRA MIAT, UR 875, Castanet-Tolosan, 31326 Cedex, France
| | - Sophie Barbe
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
| | - Thomas Schiex
- INRA MIAT, UR 875, Castanet-Tolosan, 31326 Cedex, France
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225
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Klesmith JR, Bacik JP, Michalczyk R, Whitehead TA. Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli. ACS Synth Biol 2015; 4:1235-43. [PMID: 26369947 DOI: 10.1021/acssynbio.5b00131] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic metabolic pathways often suffer from low specific productivity, and new methods that quickly assess pathway functionality for many thousands of variants are urgently needed. Here we present an approach that enables the rapid and parallel determination of sequence effects on flux for complete gene-encoding sequences. We show that this method can be used to determine the effects of over 8000 single point mutants of a pyrolysis oil catabolic pathway implanted in Escherichia coli. Experimental sequence-function data sets predicted whether fitness-enhancing mutations to the enzyme levoglucosan kinase resulted from enhanced catalytic efficiency or enzyme stability. A structure of one design incorporating 38 mutations elucidated the structural basis of high fitness mutations. One design incorporating 15 beneficial mutations supported a 15-fold improvement in growth rate and greater than 24-fold improvement in enzyme activity relative to the starting pathway. This technique can be extended to improve a wide variety of designed pathways.
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Affiliation(s)
- Justin R. Klesmith
- Department
of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - John-Paul Bacik
- Bioscience
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ryszard Michalczyk
- Bioscience
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Timothy A. Whitehead
- Department
of Chemical Engineering and Materials Science, Michigan State University, East
Lansing, Michigan 48824, United States
- Department
of Biosystems and Agricultural Engineering, Michigan State University, East
Lansing, Michigan 48824, United States
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226
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De novo protein conformational sampling using a probabilistic graphical model. Sci Rep 2015; 5:16332. [PMID: 26541939 PMCID: PMC4635387 DOI: 10.1038/srep16332] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/13/2015] [Indexed: 11/08/2022] Open
Abstract
Efficient exploration of protein conformational space remains challenging especially for large proteins when assembling discretized structural fragments extracted from a protein structure data database. We propose a fragment-free probabilistic graphical model, FUSION, for conformational sampling in continuous space and assess its accuracy using ‘blind’ protein targets with a length up to 250 residues from the CASP11 structure prediction exercise. The method reduces sampling bottlenecks, exhibits strong convergence, and demonstrates better performance than the popular fragment assembly method, ROSETTA, on relatively larger proteins with a length of more than 150 residues in our benchmark set. FUSION is freely available through a web server at http://protein.rnet.missouri.edu/FUSION/.
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227
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Della Corte D, Wildberg A, Schröder GF. Protein structure refinement with adaptively restrained homologous replicas. Proteins 2015; 84 Suppl 1:302-13. [PMID: 26441154 DOI: 10.1002/prot.24939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/02/2015] [Accepted: 09/29/2015] [Indexed: 12/27/2022]
Abstract
A novel protein refinement protocol is presented which utilizes molecular dynamics (MD) simulations of an ensemble of adaptively restrained homologous replicas. This approach adds evolutionary information to the force field and reduces random conformational fluctuations by coupling of several replicas. It is shown that this protocol refines the majority of models from the CASP11 refinement category and that larger conformational changes of the starting structure are possible than with current state of the art methods. The performance of this protocol in the CASP11 experiment is discussed. We found that the quality of the refined model is correlated with the structural variance of the coupled replicas, which therefore provides a good estimator of model quality. Furthermore, some remarkable refinement results are discussed in detail. Proteins 2016; 84(Suppl 1):302-313. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Dennis Della Corte
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, 52425, Germany
| | - André Wildberg
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, 52425, Germany. .,Physics Department, University of Düsseldorf, Düsseldorf, 40225, Germany.
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228
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Bazzoli A, Kelow SP, Karanicolas J. Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions. PLoS One 2015; 10:e0140359. [PMID: 26484863 PMCID: PMC4617380 DOI: 10.1371/journal.pone.0140359] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 09/24/2015] [Indexed: 11/25/2022] Open
Abstract
Protein-protein interactions are among today’s most exciting and promising targets for therapeutic intervention. To date, identifying small-molecules that selectively disrupt these interactions has proven particularly challenging for virtual screening tools, since these have typically been optimized to perform well on more “traditional” drug discovery targets. Here, we test the performance of the Rosetta energy function for identifying compounds that inhibit protein interactions, when these active compounds have been hidden amongst pools of “decoys.” Through this virtual screening benchmark, we gauge the effect of two recent enhancements to the functional form of the Rosetta energy function: the new “Talaris” update and the “pwSHO” solvation model. Finally, we conclude by developing and validating a new weight set that maximizes Rosetta’s ability to pick out the active compounds in this test set. Looking collectively over the course of these enhancements, we find a marked improvement in Rosetta’s ability to identify small-molecule inhibitors of protein-protein interactions.
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Affiliation(s)
- Andrea Bazzoli
- Center for Computational Biology, University of Kansas, 2030 Becker Dr., Lawrence, Kansas, 66045–7534, United States of America
| | - Simon P. Kelow
- Center for Computational Biology, University of Kansas, 2030 Becker Dr., Lawrence, Kansas, 66045–7534, United States of America
| | - John Karanicolas
- Center for Computational Biology, University of Kansas, 2030 Becker Dr., Lawrence, Kansas, 66045–7534, United States of America
- Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, Kansas, 66045–7534, United States of America
- * E-mail:
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229
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Effects of Non-Natural Amino Acid Incorporation into the Enzyme Core Region on Enzyme Structure and Function. Int J Mol Sci 2015; 16:22735-53. [PMID: 26402667 PMCID: PMC4613333 DOI: 10.3390/ijms160922735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/02/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022] Open
Abstract
Techniques to incorporate non-natural amino acids (NNAAs) have enabled biosynthesis of proteins containing new building blocks with unique structures, chemistry, and reactivity that are not found in natural amino acids. It is crucial to understand how incorporation of NNAAs affects protein function because NNAA incorporation may perturb critical function of a target protein. This study investigates how the site-specific incorporation of NNAAs affects catalytic properties of an enzyme. A NNAA with a hydrophobic and bulky sidechain, 3-(2-naphthyl)-alanine (2Nal), was site-specifically incorporated at six different positions in the hydrophobic core of a model enzyme, murine dihydrofolate reductase (mDHFR). The mDHFR variants with a greater change in van der Waals volume upon 2Nal incorporation exhibited a greater reduction in the catalytic efficiency. Similarly, the steric incompatibility calculated using RosettaDesign, a protein stability calculation program, correlated with the changes in the catalytic efficiency.
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230
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Ó Conchúir S, Barlow KA, Pache RA, Ollikainen N, Kundert K, O'Meara MJ, Smith CA, Kortemme T. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PLoS One 2015; 10:e0130433. [PMID: 26335248 PMCID: PMC4559433 DOI: 10.1371/journal.pone.0130433] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022] Open
Abstract
The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks) to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.
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Affiliation(s)
- Shane Ó Conchúir
- California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Kyle A. Barlow
- Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, California, United States of America
| | - Roland A. Pache
- California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Noah Ollikainen
- Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, California, United States of America
| | - Kale Kundert
- Graduate Program in Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Matthew J. O'Meara
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Colin A. Smith
- California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, California, United States of America
| | - Tanja Kortemme
- California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Biophysics, University of California San Francisco, San Francisco, California, United States of America
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231
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Exploring the ‘aggregation-prone’ core of human Cystatin C: A structural study. J Struct Biol 2015; 191:272-80. [DOI: 10.1016/j.jsb.2015.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/21/2015] [Accepted: 07/30/2015] [Indexed: 12/16/2022]
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232
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Alahuhta M, Taylor LE, Brunecky R, Sammond DW, Michener W, Adams MWW, Himmel ME, Bomble YJ, Lunin V. The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1946-54. [PMID: 26327384 PMCID: PMC4556314 DOI: 10.1107/s1399004715013760] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/20/2015] [Indexed: 11/10/2022]
Abstract
The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase (PL3) enzyme has been thoroughly characterized using a series of point mutations, X-ray crystallography, pK(a) calculations and biochemical assays. The X-ray structures of seven PL3 active-site mutants, five of them in complex with intact trigalacturonic acid, were solved and characterized structurally, biochemically and computationally. The results confirmed that Lys108 is the catalytic base, but there is no clear candidate for the catalytic acid. However, the reaction mechanism can also be explained by an antiperiplanar trans-elimination reaction, in which Lys108 abstracts a proton from the C5 atom without the help of simultaneous proton donation by an acidic residue. An acidified water molecule completes the anti β-elimination reaction by protonating the O4 atom of the substrate. Both the C5 hydrogen and C4 hydroxyl groups of the substrate must be orientated in axial configurations, as for galacturonic acid, for this to be possible. The wild-type C. bescii PL3 displays a pH optimum that is lower than that of Bacillus subtilis PL1 according to activity measurements, indicating that C. bescii PL3 has acquired a lower pH optimum by utilizing lysine instead of arginine as the catalytic base, as well as by lowering the pK(a) of the catalytic base in a unique active-site environment.
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Affiliation(s)
- Markus Alahuhta
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Larry E. Taylor
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Roman Brunecky
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Deanne W. Sammond
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - William Michener
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
| | - Michael E. Himmel
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Yannick J. Bomble
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Vladimir Lunin
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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233
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Lapidoth GD, Baran D, Pszolla GM, Norn C, Alon A, Tyka MD, Fleishman SJ. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences. Proteins 2015; 83:1385-406. [PMID: 25670500 PMCID: PMC4881815 DOI: 10.1002/prot.24779] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/13/2015] [Accepted: 01/26/2015] [Indexed: 12/20/2022]
Abstract
Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity.
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Affiliation(s)
- Gideon D. Lapidoth
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dror Baran
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gabriele M. Pszolla
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christoffer Norn
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Alon
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael D. Tyka
- Google Inc., 1600 Amphitheatre Pkwy, Mountain View, CA 94043
| | - Sarel J. Fleishman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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234
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Tian Y, Huang X, Zhu Y. Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm. J Mol Model 2015; 21:191. [PMID: 26162695 DOI: 10.1007/s00894-015-2742-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/24/2015] [Indexed: 01/06/2023]
Abstract
Enzyme amino-acid sequences at ligand-binding interfaces are evolutionarily optimized for reactions, and the natural conformation of an enzyme-ligand complex must have a low free energy relative to alternative conformations in native-like or non-native sequences. Based on this assumption, a combined energy function was developed for enzyme design and then evaluated by recapitulating native enzyme sequences at ligand-binding interfaces for 10 enzyme-ligand complexes. In this energy function, the electrostatic interaction between polar or charged atoms at buried interfaces is described by an explicitly orientation-dependent hydrogen-bonding potential and a pairwise-decomposable generalized Born model based on the general side chain in the protein design framework. The energy function is augmented with a pairwise surface-area based hydrophobic contribution for nonpolar atom burial. Using this function, on average, 78% of the amino acids at ligand-binding sites were predicted correctly in the minimum-energy sequences, whereas 84% were predicted correctly in the most-similar sequences, which were selected from the top 20 sequences for each enzyme-ligand complex. Hydrogen bonds at the enzyme-ligand binding interfaces in the 10 complexes were usually recovered with the correct geometries. The binding energies calculated using the combined energy function helped to discriminate the active sequences from a pool of alternative sequences that were generated by repeatedly solving a series of mixed-integer linear programming problems for sequence selection with increasing integer cuts.
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Affiliation(s)
- Ye Tian
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
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235
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015; 2015:3371-3390. [PMID: 27630532 PMCID: PMC5019575 DOI: 10.1002/ejic.201500470] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/26/2022]
Abstract
A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron-oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Vincenzo Pavone
- Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco San Francisco, CA 94158, USA
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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236
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Sevy AM, Jacobs TM, Crowe JE, Meiler J. Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences. PLoS Comput Biol 2015; 11:e1004300. [PMID: 26147100 PMCID: PMC4493036 DOI: 10.1371/journal.pcbi.1004300] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 04/27/2015] [Indexed: 11/18/2022] Open
Abstract
Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD) paradigm. Multi-specificity design (MSD), on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON). The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain) an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design "promiscuous", polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.
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Affiliation(s)
- Alexander M. Sevy
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Tim M. Jacobs
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
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237
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Manipulating the substrate specificity of murine dihydrofolate reductase enzyme using an expanded set of amino acids. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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238
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Slutzki M, Reshef D, Barak Y, Haimovitz R, Rotem-Bamberger S, Lamed R, Bayer EA, Schueler-Furman O. Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface. J Biol Chem 2015; 290:13654-66. [PMID: 25833947 PMCID: PMC4447945 DOI: 10.1074/jbc.m115.651208] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 11/06/2022] Open
Abstract
Interactions between cohesin and dockerin modules play a crucial role in the assembly of multienzyme cellulosome complexes. Although intraspecies cohesin and dockerin modules bind in general with high affinity but indiscriminately, cross-species binding is rare. Here, we combined ELISA-based experiments with Rosetta-based computational design to evaluate the contribution of distinct residues at the Clostridium thermocellum cohesin-dockerin interface to binding affinity, specificity, and promiscuity. We found that single mutations can show distinct and significant effects on binding affinity and specificity. In particular, mutations at cohesin position Asn(37) show dramatic variability in their effect on dockerin binding affinity and specificity: the N37A mutant binds promiscuously both to cognate (C. thermocellum) as well as to non-cognate Clostridium cellulolyticum dockerin. N37L in turn switches binding specificity: compared with the wild-type C. thermocellum cohesin, this mutant shows significantly increased preference for C. cellulolyticum dockerin combined with strongly reduced binding to its cognate C. thermocellum dockerin. The observation that a single mutation can overcome the naturally observed specificity barrier provides insights into the evolutionary dynamics of this system that allows rapid modulation of binding specificity within a high affinity background.
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Affiliation(s)
- Michal Slutzki
- From the Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dan Reshef
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, 9112102 Jerusalem, Israel, and
| | - Yoav Barak
- From the Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Rachel Haimovitz
- From the Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, 9112102 Jerusalem, Israel, and
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Ramat Aviv, Israel
| | - Edward A Bayer
- From the Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, 9112102 Jerusalem, Israel, and
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239
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Sasaki Y, Margolin Z, Borgo B, Havranek JJ, Milbrandt J. Characterization of Leber Congenital Amaurosis-associated NMNAT1 Mutants. J Biol Chem 2015; 290:17228-38. [PMID: 26018082 DOI: 10.1074/jbc.m115.637850] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Indexed: 01/27/2023] Open
Abstract
Leber congenital amaurosis 9 (LCA9) is an autosomal recessive retinal degeneration condition caused by mutations in the NAD(+) biosynthetic enzyme NMNAT1. This condition leads to early blindness but no other consistent deficits have been reported in patients with NMNAT1 mutations despite its central role in metabolism and ubiquitous expression. To study how these mutations affect NMNAT1 function and ultimately lead to the retinal degeneration phenotype, we performed detailed analysis of LCA-associated NMNAT1 mutants, including the expression, nuclear localization, enzymatic activity, secondary structure, oligomerization, and promotion of axonal and cellular integrity in response to injury. In many assays, most mutants produced results similar to wild type NMNAT1. Indeed, NAD(+) synthetic activity is unlikely to be a primary mechanism underlying retinal degeneration as most LCA-associated NMNAT1 mutants had normal enzymatic activity. In contrast, the secondary structure of many NMNAT1 mutants was relatively less stable as they lost enzymatic activity after heat shock, whereas wild type NMNAT1 retains significant activity after this stress. These results suggest that LCA-associated NMNAT1 mutants are more vulnerable to stressful conditions that lead to protein unfolding, a potential contributor to the retinal degeneration observed in this syndrome.
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Affiliation(s)
- Yo Sasaki
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Zachary Margolin
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Benjamin Borgo
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - James J Havranek
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jeffrey Milbrandt
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
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240
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Willis JR, Sapparapu G, Murrell S, Julien JP, Singh V, King HG, Xia Y, Pickens JA, LaBranche CC, Slaughter JC, Montefiori DC, Wilson IA, Meiler J, Crowe JE. Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth. J Clin Invest 2015; 125:2523-31. [PMID: 25985274 DOI: 10.1172/jci80693] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/19/2015] [Indexed: 01/08/2023] Open
Abstract
Several HIV envelope-targeting (Env-targeting) antibodies with broad and potent neutralizing activity have been identified and shown to have unusual features. Of these, the PG9 antibody has a long heavy chain complementarity determining region 3 (HCDR3) and possesses unique structural elements that interact with protein and glycan features of the HIV Env glycoprotein. Here, we used the Rosetta software suite to design variants of the PG9 antibody HCDR3 loop with the goal of identifying variants with increased potency and breadth of neutralization for diverse HIV strains. One variant, designated PG9_N100(F)Y, possessed increased potency and was able to neutralize a diverse set of PG9-resistant HIV strains, including those lacking the Env N160 glycan, which is critical for PG9 binding. An atomic resolution structure of the PG9_N100(F)Y fragment antigen binding (Fab) confirmed that the mutated residue retains the paratope surface when compared with WT PG9. Differential scanning calorimetry experiments revealed that the mutation caused a modest increase in thermodynamic stability of the Fab, a feature predicted by the computational model. Our findings suggest that thermodynamic stabilization of the long HCDR3 in its active conformation is responsible for the increased potency of PG9_N100(F)Y, and strategies aimed at stabilizing this region in other HIV antibodies could become an important approach to in silico optimization of antibodies.
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241
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Nechay MR, Valdez CE, Alexandrova AN. Computational Treatment of Metalloproteins. J Phys Chem B 2015; 119:5945-56. [DOI: 10.1021/acs.jpcb.5b00028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michael R. Nechay
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Crystal E. Valdez
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
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242
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Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B. Computational de novo design of a four-helix bundle protein--DND_4HB. Protein Sci 2015; 24:434-45. [PMID: 25287625 PMCID: PMC4380976 DOI: 10.1002/pro.2577] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/30/2014] [Accepted: 09/30/2014] [Indexed: 11/09/2022]
Abstract
The de novo design of proteins is a rigorous test of our understanding of the key determinants of protein structure. The helix bundle is an interesting de novo design model system due to the diverse topologies that can be generated from a few simple α-helices. Previously, noncomputational studies demonstrated that connecting amphipathic helices together with short loops can sometimes generate helix bundle proteins, regardless of the bundle's exact sequence. However, using such methods, the precise positions of helices and side chains cannot be predetermined. Since protein function depends on exact positioning of residues, we examined if sequence design tools in the program Rosetta could be used to design a four-helix bundle with a predetermined structure. Helix position was specified using a folding procedure that constrained the design model to a defined topology, and iterative rounds of rotamer-based sequence design and backbone refinement were used to identify a low energy sequence for characterization. The designed protein, DND_4HB, unfolds cooperatively (Tm >90°C) and a NMR solution structure shows that it adopts the target helical bundle topology. Helices 2, 3, and 4 agree very closely with the design model (backbone RMSD = 1.11 Å) and >90% of the core side chain χ1 and χ2 angles are correctly predicted. Helix 1 lies in the target groove against the other helices, but is displaced 3 Å along the bundle axis. This result highlights the potential of computational design to create bundles with atomic-level precision, but also points at remaining challenges for achieving specific positioning between amphipathic helices.
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Affiliation(s)
- Grant S Murphy
- Department of Chemistry, University of North Carolina at Chapel HillChapel Hill, North Carolina, 27599-3290
| | | | - Bryan S Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel HillChapel Hill, North Carolina, 27599-7260
| | - Mischa C Machius
- Center for Structural Biology, University of North Carolina at Chapel HillChapel Hill, North Carolina, 27599
| | - Surya V Pulavarti
- Department of Chemistry, State University of New York at BuffaloBuffalo, New York, 14260
- Northeast Structural Genomics ConsortiumBuffalo, New York, 14260
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at BuffaloBuffalo, New York, 14260
- Northeast Structural Genomics ConsortiumBuffalo, New York, 14260
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel HillChapel Hill, North Carolina, 27599-7260
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel HillChapel Hill, North Carolina, 27599
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243
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Tsutakawa SE, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT, Tainer JA, Ivanov I. Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response. Structure 2015; 23:724-733. [PMID: 25773143 DOI: 10.1016/j.str.2015.02.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/28/2015] [Accepted: 02/09/2015] [Indexed: 11/18/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) is a pivotal replication protein, which also controls cellular responses to DNA damage. Posttranslational modification of PCNA by SUMO and ubiquitin modulate these responses. How the modifiers alter PCNA-dependent DNA repair and damage tolerance pathways is largely unknown. We used hybrid methods to identify atomic models of PCNAK107-Ub and PCNAK164-SUMO consistent with small-angle X-ray scattering data of these complexes in solution. We show that SUMO and ubiquitin have distinct modes of association to PCNA. Ubiquitin adopts discrete docked binding positions. By contrast, SUMO associates by simple tethering and adopts extended flexible conformations. These structural differences are the result of the opposite electrostatic potentials of SUMO and Ub. The unexpected contrast in conformational behavior of Ub-PCNA and SUMO-PCNA has implications for interactions with partner proteins, interacting surfaces accessibility, and access points for pathway regulation.
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Affiliation(s)
- Susan E Tsutakawa
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Chunli Yan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302 USA
| | - Xiaojun Xu
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302 USA
| | | | - Bret D Freudenthal
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242 USA
| | - Kun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716 USA
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716 USA
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242 USA
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA
- Skaggs Institute for Chemical Biology, La Jolla, CA, 92037 USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302 USA
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244
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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245
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Pearson AD, Mills JH, Song Y, Nasertorabi F, Han GW, Baker D, Stevens RC, Schultz PG. Transition states. Trapping a transition state in a computationally designed protein bottle. Science 2015; 347:863-867. [PMID: 25700516 PMCID: PMC4581533 DOI: 10.1126/science.aaa2424] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl. This latter moiety was introduced biosynthetically as the side chain of the noncanonical amino acid p-biphenylalanine. Through iterative rounds of computational design and structural analysis, we identified a protein in which the side chain of p-biphenylalanine is trapped in the energetically disfavored, coplanar conformation of the TS of the bond rotation reaction.
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Affiliation(s)
- Aaron D. Pearson
- Department of Chemistry, and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeremy H. Mills
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Yifan Song
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Fariborz Nasertorabi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Gye Won Han
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute (HHMI), University of Washington, Seattle, WA 98195, USA
| | - Raymond C. Stevens
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Peter G. Schultz
- Department of Chemistry, and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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246
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Gorham R, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive C, Floudas CA, Radeke MJ, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. J Med Chem 2015; 58:814-26. [PMID: 25494040 PMCID: PMC4306506 DOI: 10.1021/jm501345y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Indexed: 01/21/2023]
Abstract
Compstatin peptides are complement inhibitors that bind and inhibit cleavage of complement C3. Peptide binding is enhanced by hydrophobic interactions; however, poor solubility promotes aggregation in aqueous environments. We have designed new compstatin peptides derived from the W4A9 sequence (Ac-ICVWQDWGAHRCT-NH2, cyclized between C2 and C12), based on structural, computational, and experimental studies. Furthermore, we developed and utilized a computational framework for the design of peptides containing non-natural amino acids. These new compstatin peptides contain polar N-terminal extensions and non-natural amino acid substitutions at positions 4 and 9. Peptides with α-modified non-natural alanine analogs at position 9, as well as peptides containing only N-terminal polar extensions, exhibited similar activity compared to W4A9, as quantified via ELISA, hemolytic, and cell-based assays, and showed improved solubility, as measured by UV absorbance and reverse-phase HPLC experiments. Because of their potency and solubility, these peptides are promising candidates for therapeutic development in numerous complement-mediated diseases.
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Affiliation(s)
- Ronald
D. Gorham
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
| | - David L. Forest
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - George A. Khoury
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - James Smadbeck
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Consuelo N. Beecher
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Evangeline D. Healy
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Phanourios Tamamis
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus
| | - Georgios Archontis
- Department
of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus
| | - Cynthia
K. Larive
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Christodoulos A. Floudas
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Monte J. Radeke
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Lincoln V. Johnson
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Dimitrios Morikis
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
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247
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Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, Gregg CJ, Stoddard BL, Church GM. Biocontainment of genetically modified organisms by synthetic protein design. Nature 2015; 518:55-60. [PMID: 25607366 DOI: 10.1038/nature14121] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
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Affiliation(s)
- Daniel J Mandell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Marc J Lajoie
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Program in Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Michael T Mee
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Ryo Takeuchi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Gleb Kuznetsov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Julie E Norville
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher J Gregg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - George M Church
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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248
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Jou JD, Jain S, Georgiev I, Donald BR. BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. LECTURE NOTES IN COMPUTER SCIENCE 2015. [DOI: 10.1007/978-3-319-16706-0_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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249
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Jacobs TM, Yumerefendi H, Kuhlman B, Leaver-Fay A. SwiftLib: rapid degenerate-codon-library optimization through dynamic programming. Nucleic Acids Res 2014; 43:e34. [PMID: 25539925 PMCID: PMC4357694 DOI: 10.1093/nar/gku1323] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Degenerate codon (DC) libraries efficiently address the experimental library-size limitations of directed evolution by focusing diversity toward the positions and toward the amino acids (AAs) that are most likely to generate hits; however, manually constructing DC libraries is challenging, error prone and time consuming. This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit, improving on the existing integer-linear programming formulation. It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library. In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits. Surprisingly, the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1; it effectively side-steps the degeneracy of the genetic code. Our algorithm is freely available through our web server and solves most design problems in about a second.
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Affiliation(s)
- Timothy M Jacobs
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hayretin Yumerefendi
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian Kuhlman
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Andrew Leaver-Fay
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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250
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Negron C, Keating AE. A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit. J Am Chem Soc 2014; 136:16544-56. [PMID: 25337788 PMCID: PMC4277747 DOI: 10.1021/ja507847t] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Indexed: 12/11/2022]
Abstract
Molecular engineering of protein assemblies, including the fabrication of nanostructures and synthetic signaling pathways, relies on the availability of modular parts that can be combined to give different structures and functions. Currently, a limited number of well-characterized protein interaction components are available. Coiled-coil interaction modules have been demonstrated to be useful for biomolecular design, and many parallel homodimers and heterodimers are available in the coiled-coil toolkit. In this work, we sought to design a set of orthogonal antiparallel homodimeric coiled coils using a computational approach. There are very few antiparallel homodimers described in the literature, and none have been measured for cross-reactivity. We tested the ability of the distance-dependent statistical potential DFIRE to predict orientation preferences for coiled-coil dimers of known structure. The DFIRE model was then combined with the CLASSY multistate protein design framework to engineer sets of three orthogonal antiparallel homodimeric coiled coils. Experimental measurements confirmed the successful design of three peptides that preferentially formed antiparallel homodimers that, furthermore, did not interact with one additional previously reported antiparallel homodimer. Two designed peptides that formed higher-order structures suggest how future design protocols could be improved. The successful designs represent a significant expansion of the existing protein-interaction toolbox for molecular engineers.
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Affiliation(s)
- Christopher Negron
- Program
in Computational and Systems Biology and Departments of Biology and Biological
Engineering, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 021393, United States
| | - Amy E. Keating
- Program
in Computational and Systems Biology and Departments of Biology and Biological
Engineering, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 021393, United States
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