scholarly journals Constructing synthetic-protein assemblies from de novo designed 310 helices

2021 ◽  
Author(s):  
Prasun Kumar ◽  
Neil G. Paterson ◽  
Jonathan Clayden ◽  
Derek N. Woolfson
Keyword(s):  
Rational Design ◽  
De Novo ◽  
Protein Structures ◽  
Water Soluble ◽  
Design Solution ◽  
Protein Assemblies ◽  
Synthetic Protein ◽  
Hydrophobic Cores ◽  
Α Helix ◽  
Helical Folding

Compared with the iconic α helix, 310 helices occur much less frequently in protein structures. The different 310-helical parameters lead to energetically less favourable internal energies, and a reduced tendency to pack into defined higher-order structures. Consequently, in natural proteins, 310 helices rarely extend past 6 residues, and do not form regular supersecondary, tertiary, or quaternary interactions. Here, we show that despite their absence in nature, synthetic protein-like assemblies can be built from 310 helices. We report the rational design, solution-phase characterisation, and an X-ray crystal structure for water-soluble bundles of 310 helices with consolidated hydrophobic cores. The design uses 6-residue repeats informed by analysing natural 310 helices, and incorporates aminoisobutyric acid residues. Design iterations reveal a tipping point between α-helical and 310-helical folding, and identify features required for stabilising assemblies in this unexplored region of protein-structure space.

scholarly journals De Novo Protein Design of Photochemical Reaction Centers

2021 ◽  
Author(s):  
Nathan Ennist ◽  
Zhenyu Zhao ◽  
Steven Stayrook ◽  
Bohdana Discher ◽  
P Leslie 'Les' Dutton ◽  
...  
Keyword(s):  
Reaction Center ◽  
Charge Separation ◽  
Rational Design ◽  
De Novo ◽  
Metal Cluster ◽  
Protein Structures ◽  
Essential Elements ◽  
Reaction Centers ◽  
Transient Absorption Spectroscopy

Abstract Natural photosynthetic protein complexes capture sunlight to power the energetic catalysis that supports life on Earth. Yet these natural protein structures carry an evolutionary legacy of complexity and fragility that encumbers protein reengineering efforts and obfuscates the underlying design rules for light-driven charge separation. De novo development of a simplified photosynthetic reaction center protein can clarify practical engineering principles needed to build new enzymes for efficient solar-to-fuel energy conversion. Here we report the rational design, X-ray crystal structure, and electron transfer activity of a multi-cofactor protein that incorporates essential elements of photosynthetic reaction centers. This highly stable, modular artificial protein framework can be reconstituted in vitro with interchangeable redox centers for nanometer-scale photochemical charge separation. Transient absorption spectroscopy demonstrates Photosystem II-like tyrosine and metal cluster oxidation, and we measure charge separation lifetimes exceeding 100 ms, ideal for light-activated catalysis. This de novo-designed reaction center builds upon engineering guidelines established for charge separation in earlier synthetic photochemical triads and modified natural proteins, and it shows how synthetic biology may lead to a new generation of genetically encoded, light-powered catalysts for solar fuel production.

scholarly journals Rational Design of Programmable Monodisperse Semi-Synthetic Protein Nanomaterials Containing Engineered Disulfide Functionality

2021 ◽  
Author(s):  
Pavankumar Janardhan Bhandari ◽  
Britto S Sandanaraj
Keyword(s):  
Nucleic Acid ◽  
Disulfide Bond ◽  
Rational Design ◽  
Inorganic Nanoparticles ◽  
Stimuli Responsive ◽  
Protein Assemblies ◽  
Intelligent Materials ◽  
Synthetic Protein ◽  
Responsive Behavior ◽  
Reversible Nature

AbstractThe reversible nature of disulfide functionality has been exploited to design intelligent materials such as nanocapsules, micelles, vesicles, inorganic nanoparticles, peptide and nucleic acid nanodevices. However, to our knowledge, there are no reports on design of semi-synthetic protein assemblies containing an engineered disulfide bond. Towards that end, herein, we disclose a new chemical methodology for the construction redox-sensitive protein assemblies using monodisperse facially amphiphilic protein-dendron bioconjugates. The disulfide functionality is strategically placed between the dendron and protein domains. The custom designed bioconjugates self-assembled into nanoscopic objects of a defined size dictated by the nature of dendron domain. The stimuli-responsive behavior of the protein assemblies is demonstrated using a suitable redox trigger.

scholarly journals De novo protein design, a retrospective

2020 ◽  
Vol 53 ◽  
Author(s):  
Ivan V. Korendovych ◽  
William F. DeGrado
Keyword(s):  
Membrane Protein ◽  
Protein Design ◽  
First Principles ◽  
Rational Design ◽  
De Novo ◽  
Dynamic Properties ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Physical Models ◽  
And Function

Abstract Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.

scholarly journals Protofold II: Enhanced Model and Implementation for Kinetostatic Protein Folding1

2015 ◽  
Vol 6 (3) ◽  
Author(s):  
Pouya Tavousi ◽  
Morad Behandish ◽  
Horea T. Ilieş ◽  
Kazem Kazerounian
Keyword(s):  
Structure Prediction ◽  
Graphics Processing Units ◽  
De Novo ◽  
Sequence Data ◽  
Protein Structures ◽  
Three Dimensional ◽  
Small Time ◽  
Water Soluble ◽  
Folding Process ◽  
Aqueous Solvent

A reliable prediction of three-dimensional (3D) protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the Protofold package can overcome some of the key difficulties faced by other de novo structure prediction methods, such as the very small time steps required by the molecular dynamics (MD) approaches or the very large number of samples needed by the Monte Carlo (MC) sampling techniques. In this paper, we improve the free energy formulation used in Protofold by including the typically underrated entropic effects, imparted due to differences in hydrophobicity of the chemical groups, which dominate the folding of most water-soluble proteins. In addition to the model enhancement, we revisit the numerical implementation by redesigning the algorithms and introducing efficient data structures that reduce the expected complexity from quadratic to linear. Moreover, we develop and optimize parallel implementations of the algorithms on both central and graphics processing units (CPU/GPU) achieving speed-ups up to two orders of magnitude on the GPU. Our simulations are consistent with the general behavior observed in the folding process in aqueous solvent, confirming the effectiveness of model improvements. We report on the folding process at multiple levels, namely, the formation of secondary structural elements and tertiary interactions between secondary elements or across larger domains. We also observe significant enhancements in running times that make the folding simulation tractable for large molecules.

scholarly journals Metal templated design of protein interfaces

2009 ◽  
Vol 107 (5) ◽  
pp. 1827-1832 ◽  
Author(s):  
Eric N. Salgado ◽  
Xavier I. Ambroggio ◽  
Jeffrey D. Brodin ◽  
Richard A. Lewis ◽  
Brian Kuhlman ◽  
...  
Keyword(s):  
Rational Design ◽  
Time Course ◽  
De Novo ◽  
Large Fraction ◽  
Metal Coordination ◽  
Protein Assemblies ◽  
Evolutionary Pathway ◽  
Unique Protein ◽  
Protein Interfaces ◽  
Noncovalent Bonding

Metal coordination is a key structural and functional component of a large fraction of proteins. Given this dual role we considered the possibility that metal coordination may have played a templating role in the early evolution of protein folds and complexes. We describe here a rational design approach, Metal Templated Interface Redesign (MeTIR), that mimics the time course of a hypothetical evolutionary pathway for the formation of stable protein assemblies through an initial metal coordination event. Using a folded monomeric protein, cytochrome cb562, as a building block we show that its non-self-associating surface can be made self-associating through a minimal number of mutations that enable Zn coordination. The protein interfaces in the resulting Zn-directed, D2-symmetrical tetramer are subsequently redesigned, yielding unique protein architectures that self-assemble in the presence or absence of metals. Aside from its evolutionary implications, MeTIR provides a route to engineer de novo protein interfaces and metal coordination environments that can be tuned through the extensive noncovalent bonding interactions in these interfaces.

scholarly journals Membrane-spanning α-helical barrels as tractable protein-design targets

2017 ◽  
Vol 372 (1726) ◽  
pp. 20160213 ◽  
Author(s):  
Ai Niitsu ◽  
Jack W. Heal ◽  
Kerstin Fauland ◽  
Andrew R. Thomson ◽  
Derek N. Woolfson
Keyword(s):  
Protein Structure ◽  
Protein Design ◽  
De Novo ◽  
Protein Structures ◽  
Coiled Coil ◽  
Deep Understanding ◽  
Data Bank ◽  
Water Soluble ◽  
Limiting Factor ◽  
Membrane Spanning

The rational ( de novo ) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of ‘scaffolds’ for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix–helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels—that is, symmetric bundles of five or more helices with central accessible channels—there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.

scholarly journals Rational Design of Molecularly Imprinted Polymers Using Quaternary Ammonium Cations for Glyphosate Detection

Sensors ◽  
2021 ◽  
Vol 21 (1) ◽  
pp. 296
Author(s):  
Mashaalah Zarejousheghani ◽  
Alaa Jaafar ◽  
Hendrik Wollmerstaedt ◽  
Parvaneh Rahimi ◽  
Helko Borsdorf ◽  
...  
Keyword(s):  
Molecularly Imprinted Polymers ◽  
Quaternary Ammonium ◽  
Photoelectron Spectroscopy ◽  
Rational Design ◽  
Water Soluble ◽  
Trimethylammonium Chloride ◽  
Molecularly Imprinted ◽  
Functional Monomers ◽  
Imprinted Polymers ◽  
Quaternary Ammonium Cations

Molecularly imprinted polymers have emerged as cost-effective and rugged artificial selective sorbents for combination with different sensors. In this study, quaternary ammonium cations, as functional monomers, were systematically evaluated to design imprinted polymers for glyphosate as an important model compound for electrically charged and highly water-soluble chemical compounds. To this aim, a small pool of monomers were used including (3-acrylamidopropyl)trimethylammonium chloride, [2-(acryloyloxy)ethyl]trimethylammonium chloride, and diallyldimethylammonium chloride. The simultaneous interactions between three positively charged monomers and glyphosate were preliminary evaluated using statistical design of the experiment method. Afterwards, different polymers were synthesized at the gold surface of the quartz crystal microbalance sensor using optimized and not optimized glyphosate-monomers ratios. All synthesized polymers were characterized using atomic force microscopy, contact angle, Fourier-transform infrared, and X-ray photoelectron spectroscopy. Evaluated functional monomers showed promise as highly efficient functional monomers, when they are used together and at the optimized ratio, as predicted by the statistical method. Obtained results from the modified sensors were used to develop a simple model describing the binding characteristics at the surface of the different synthesized polymers. This model helps to develop new synthesis strategies for rational design of the highly selective imprinted polymers and to use as a sensing platform for water soluble and polar targets.

scholarly journals Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fengbin Wang ◽  
Ordy Gnewou ◽  
Charles Modlin ◽  
Leticia C. Beltran ◽  
Chunfu Xu ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Synthetic Peptide ◽  
Quaternary Structure ◽  
De Novo ◽  
Rational Approach ◽  
Lateral Interactions ◽  
Protein Assemblies ◽  
Self Assembling ◽  
Arginine Residues ◽  
Insight Into

AbstractThe exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.

scholarly journals De novo design of a reversible phosphorylation-dependent switch for membrane targeting

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Leon Harrington ◽  
Jordan M. Fletcher ◽  
Tamara Heermann ◽  
Derek N. Woolfson ◽  
Petra Schwille
Keyword(s):  
Protein Interactions ◽  
Lipid Membrane ◽  
De Novo ◽  
Protein Localization ◽  
Protein Structures ◽  
Spatiotemporal Pattern ◽  
Membrane Targeting ◽  
Protein Protein Interactions ◽  
Reversible Phosphorylation ◽  
Potential Applications

AbstractModules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a ‘cargo’ molecule reversibly to a permanent membrane ‘anchor’; and (ii) creating a ‘membrane-avidity switch’ that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells.

scholarly journals Optimization in S-SAD phasing - difference between solved and unsolved structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C613-C613
Author(s):  
Jan Stránský ◽  
Tomáš Kovaľ ◽  
Lars Østergaard ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
...  
Keyword(s):  
Data Processing ◽  
De Novo ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Sad Phasing ◽  
Optimal Values ◽  
Grant Agency ◽  
Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

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