Ilan Samish | Weizmann Institute of Science (original) (raw)

Papers by Ilan Samish

Wiley World Scientific CRC Press

Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for... more Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth andmaturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a “CPD 101”. These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of highand low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions...

Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for... more Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth andmaturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a “CPD 101”. These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of highand low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions...

Crystal structures, the major source of protein structural information, are often regarded as sta... more Crystal structures, the major source of protein structural information, are often regarded as static 3D snapshots of dynamic macromolecules. Thus, study of protein dynamics is often confined to computationally heavy simulations. Instead, here we data-mine membrane-protein structures directly. We show how local regions of distinct flexibility are fine-tuned to control specific functions. Protein features considered during the analysis include intra-protein cavities, B-factors normalized in a unique manner, and intrinsic degrees of freedom. These are correlated with evolutionary conservation, packing motifs, mutagenesis simulations, local deformations, functional pathways, and experimental validation. First, we show how local flexibility acclimatizes photosynthetic energy conversion across a wide range of temperatures, from sub-tropical habitats to scalding hot springs. A group of hitherto unrecognized intra-protein cavities and adjacent packing motifs jointly impart localized flexibi...

Our analysis demonstrates that backbone-mediated interhelical hydrogen-bonds cluster laterally in... more Our analysis demonstrates that backbone-mediated interhelical hydrogen-bonds cluster laterally in the conserved core of transmembrane helical proteins. Each residue's propensity to bear these interactions is in correlation with the residue's packing-value scale; giving biophysical meaning to this phenomenological scale. Residues participating in such an intersubunit, structurally conserved H-bond in reaction centers of photosystem II were combinatorially mutated and characterized in silico and in vivo suggesting that Hbond reversible association regulates protein-gated electron transfer. Similar motifs may be involved in folding and conformational flexibility of other membrane proteins. Hence, these findings provide new parameters for structure and function prediction. Contact: ilan.samish@weizmann.ac.il INTRODUCTION Membrane protein conformational gating plays key roles in protein systems (Spencer and Rees 2002). Although functionally distinct in many catalytic cycles, the ...

Translational Vision Science & Technology

Scientific reports, Jan 3, 2018

Photosystem II (PSII) reaction centre D1 protein of oxygenic phototrophs is pivotal for sustainin... more Photosystem II (PSII) reaction centre D1 protein of oxygenic phototrophs is pivotal for sustaining photosynthesis. Also, it is targeted by herbicides and herbicide-resistant weeds harbour single amino acid substitutions in D1. Conservation of D1 primary structure is seminal in the photosynthetic performance in many diverse species. In this study, we analysed built-in and environmentally-induced (high temperature and high photon fluency - HT/HL) phenotypes of two D1 mutants of Chlamydomonas reinhardtii with Ala250Arg (A250R) and Ser264Lys (S264K) substitutions. Both mutations differentially affected efficiency of electron transport and oxygen production. In addition, targeted metabolomics revealed that the mutants undergo specific differences in primary and secondary metabolism, namely, amino acids, organic acids, pigments, NAD, xanthophylls and carotenes. Levels of lutein, β-carotene and zeaxanthin were in sync with their corresponding gene transcripts in response to HT/HL stress tr...

The journal of physical chemistry. B, Jan 27, 2017

Redox reactions play key roles in fundamental biological processes. The related spatial organizat... more Redox reactions play key roles in fundamental biological processes. The related spatial organization of donors and acceptors is assumed to undergo evolutionary optimization facilitating charge mobilization within the relevant biological context. Experimental information from submolecular functional sites is needed to understand the organization strategies and driving forces involved in the self-development of structure-function relationships. Here we exploit chemically resolved electrical measurements (CREM) to probe the atom-specific electrostatic potentials (ESPs) in artificial arrays of bacteriochlorophyll (BChl) derivatives that provide model systems for photoexcited (hot) electron donation and withdrawal. On the basis of computations we show that native BChl's in the photosynthetic reaction center (RC) self-assemble at their ground-state as aligned gates for functional charge transfer. The combined computational and experimental results further reveal how site-specific pola...

Methods in Molecular Biology, 2017

Http Dx Doi Org 10 1146 Annurev Physchem 032210 103509, Mar 31, 2011

Computational protein design (CPD) has established itself as a leading field in basic and applied... more Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo-(or other) stability to specific requested reactions such as protein–protein binding, enzymatic reactions, or nanotech-nology applications. The design scheme may encompass small regions of the proteins or the entire protein. In either case, the design may aim at the side-chains or at the full backbone conformation. Herein, the main framework for the process is outlined highlighting key elements in the CPD iterative cycle. These include the very definition of CPD, the diverse goals of CPD, components of the CPD protocol, methods for searching sequence and structure space, scoring functions, and augmenting the CPD with other optimization tools. Taken together, this chapter aims to introduce the framework of CPD.

Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for... more Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a " CPD 101 ". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high-and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs. Future challenges also include dissemination of CPD software to the general use of life-sciences researchers and the emphasis of success within an in vivo milieu. CPD increases our understanding of protein structure and function and the relationships between the two along with the application of such know-how for the benefit of mankind. Applied aspects range from biological drugs, via healthier and tastier food products to nanotechnology and environmentally friendly enzymes replacing toxic chemicals utilized in the industry.

Interquinone Q A − → Q B electron-transfer (ET) in isolated photosystem II reaction centers (PSII... more Interquinone Q A − → Q B electron-transfer (ET) in isolated photosystem II reaction centers (PSII-RC) is protein-gated. The temperature-dependent gating frequency " k " is described by the Eyring equation till levelling off at T ≥ 240 °K. Although central to photosynthesis, the gating mechanism has not been resolved and due to experimental limitations, could not be explored in vivo. Here we mimic the temperature dependency of " k " by enlarging V D1-208 , the volume of a single residue at the crossing point of the D1 and D2 PSII-RC subunits in Synechocystis 6803 whole cells. By controlling the interactions of the D1/D2 subunits, V D1-208 (or 1/T) determines the frequency of attaining an ET-active conformation. Decelerated ET, impaired photosynthesis, D1 repair rate and overall cell physiology upon increasing V D1-208 to above 130 Å 3 , rationalize the >99% conservation of small residues at D1-208 and its homologous motif in non-oxygenic bacteria. The experimental means and resolved mechanism are relevant for numerous transmembrane protein-gated reactions. PSII-RCs and RCs of green nonsulfur bacteria (Chloroflexi), purple bacteria (phototrophic Proteobacteria) and the newly discovered photosynthetic Gemmatimonadetes 1 , are Type-II RCs responsible for light-induced charge separation across the photosynthetic membrane 2. The functional core of PSII RCs comprises ten transmembrane (TM) helices of the D1 and D2 subunits, which display C2 pseudo-symmetry. The d and e helices of the two subu-nits form a four-helix bundle that holds the ET-facilitating cofactors (Fig. 1a). The luminal arms of these four TM helices (hereafter, denoted d1, d2, e1, e2) coordinate a non-heme iron and bind Q A and Q B on d2 and d1, respectively. These components define the electron acceptor side of the RC complex. The cytosolic arm of the helices harbors the electron-donor side of the complex, including a cluster of four chlorophylls and two pheophytins 3. The primary ET reaction comprises ultrafast, light-induced tunneling of an electron across the clustered pigments, followed by reduction of Q A 4–7

Wiley World Scientific CRC Press

Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for... more Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth andmaturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a “CPD 101”. These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of highand low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions...

Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for... more Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth andmaturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a “CPD 101”. These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of highand low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions...

Crystal structures, the major source of protein structural information, are often regarded as sta... more Crystal structures, the major source of protein structural information, are often regarded as static 3D snapshots of dynamic macromolecules. Thus, study of protein dynamics is often confined to computationally heavy simulations. Instead, here we data-mine membrane-protein structures directly. We show how local regions of distinct flexibility are fine-tuned to control specific functions. Protein features considered during the analysis include intra-protein cavities, B-factors normalized in a unique manner, and intrinsic degrees of freedom. These are correlated with evolutionary conservation, packing motifs, mutagenesis simulations, local deformations, functional pathways, and experimental validation. First, we show how local flexibility acclimatizes photosynthetic energy conversion across a wide range of temperatures, from sub-tropical habitats to scalding hot springs. A group of hitherto unrecognized intra-protein cavities and adjacent packing motifs jointly impart localized flexibi...

Our analysis demonstrates that backbone-mediated interhelical hydrogen-bonds cluster laterally in... more Our analysis demonstrates that backbone-mediated interhelical hydrogen-bonds cluster laterally in the conserved core of transmembrane helical proteins. Each residue's propensity to bear these interactions is in correlation with the residue's packing-value scale; giving biophysical meaning to this phenomenological scale. Residues participating in such an intersubunit, structurally conserved H-bond in reaction centers of photosystem II were combinatorially mutated and characterized in silico and in vivo suggesting that Hbond reversible association regulates protein-gated electron transfer. Similar motifs may be involved in folding and conformational flexibility of other membrane proteins. Hence, these findings provide new parameters for structure and function prediction. Contact: ilan.samish@weizmann.ac.il INTRODUCTION Membrane protein conformational gating plays key roles in protein systems (Spencer and Rees 2002). Although functionally distinct in many catalytic cycles, the ...

Translational Vision Science & Technology

Scientific reports, Jan 3, 2018

Photosystem II (PSII) reaction centre D1 protein of oxygenic phototrophs is pivotal for sustainin... more Photosystem II (PSII) reaction centre D1 protein of oxygenic phototrophs is pivotal for sustaining photosynthesis. Also, it is targeted by herbicides and herbicide-resistant weeds harbour single amino acid substitutions in D1. Conservation of D1 primary structure is seminal in the photosynthetic performance in many diverse species. In this study, we analysed built-in and environmentally-induced (high temperature and high photon fluency - HT/HL) phenotypes of two D1 mutants of Chlamydomonas reinhardtii with Ala250Arg (A250R) and Ser264Lys (S264K) substitutions. Both mutations differentially affected efficiency of electron transport and oxygen production. In addition, targeted metabolomics revealed that the mutants undergo specific differences in primary and secondary metabolism, namely, amino acids, organic acids, pigments, NAD, xanthophylls and carotenes. Levels of lutein, β-carotene and zeaxanthin were in sync with their corresponding gene transcripts in response to HT/HL stress tr...

The journal of physical chemistry. B, Jan 27, 2017

Redox reactions play key roles in fundamental biological processes. The related spatial organizat... more Redox reactions play key roles in fundamental biological processes. The related spatial organization of donors and acceptors is assumed to undergo evolutionary optimization facilitating charge mobilization within the relevant biological context. Experimental information from submolecular functional sites is needed to understand the organization strategies and driving forces involved in the self-development of structure-function relationships. Here we exploit chemically resolved electrical measurements (CREM) to probe the atom-specific electrostatic potentials (ESPs) in artificial arrays of bacteriochlorophyll (BChl) derivatives that provide model systems for photoexcited (hot) electron donation and withdrawal. On the basis of computations we show that native BChl's in the photosynthetic reaction center (RC) self-assemble at their ground-state as aligned gates for functional charge transfer. The combined computational and experimental results further reveal how site-specific pola...

Methods in Molecular Biology, 2017

Http Dx Doi Org 10 1146 Annurev Physchem 032210 103509, Mar 31, 2011

Computational protein design (CPD) has established itself as a leading field in basic and applied... more Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo-(or other) stability to specific requested reactions such as protein–protein binding, enzymatic reactions, or nanotech-nology applications. The design scheme may encompass small regions of the proteins or the entire protein. In either case, the design may aim at the side-chains or at the full backbone conformation. Herein, the main framework for the process is outlined highlighting key elements in the CPD iterative cycle. These include the very definition of CPD, the diverse goals of CPD, components of the CPD protocol, methods for searching sequence and structure space, scoring functions, and augmenting the CPD with other optimization tools. Taken together, this chapter aims to introduce the framework of CPD.

Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for... more Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a " CPD 101 ". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high-and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs. Future challenges also include dissemination of CPD software to the general use of life-sciences researchers and the emphasis of success within an in vivo milieu. CPD increases our understanding of protein structure and function and the relationships between the two along with the application of such know-how for the benefit of mankind. Applied aspects range from biological drugs, via healthier and tastier food products to nanotechnology and environmentally friendly enzymes replacing toxic chemicals utilized in the industry.

Interquinone Q A − → Q B electron-transfer (ET) in isolated photosystem II reaction centers (PSII... more Interquinone Q A − → Q B electron-transfer (ET) in isolated photosystem II reaction centers (PSII-RC) is protein-gated. The temperature-dependent gating frequency " k " is described by the Eyring equation till levelling off at T ≥ 240 °K. Although central to photosynthesis, the gating mechanism has not been resolved and due to experimental limitations, could not be explored in vivo. Here we mimic the temperature dependency of " k " by enlarging V D1-208 , the volume of a single residue at the crossing point of the D1 and D2 PSII-RC subunits in Synechocystis 6803 whole cells. By controlling the interactions of the D1/D2 subunits, V D1-208 (or 1/T) determines the frequency of attaining an ET-active conformation. Decelerated ET, impaired photosynthesis, D1 repair rate and overall cell physiology upon increasing V D1-208 to above 130 Å 3 , rationalize the >99% conservation of small residues at D1-208 and its homologous motif in non-oxygenic bacteria. The experimental means and resolved mechanism are relevant for numerous transmembrane protein-gated reactions. PSII-RCs and RCs of green nonsulfur bacteria (Chloroflexi), purple bacteria (phototrophic Proteobacteria) and the newly discovered photosynthetic Gemmatimonadetes 1 , are Type-II RCs responsible for light-induced charge separation across the photosynthetic membrane 2. The functional core of PSII RCs comprises ten transmembrane (TM) helices of the D1 and D2 subunits, which display C2 pseudo-symmetry. The d and e helices of the two subu-nits form a four-helix bundle that holds the ET-facilitating cofactors (Fig. 1a). The luminal arms of these four TM helices (hereafter, denoted d1, d2, e1, e2) coordinate a non-heme iron and bind Q A and Q B on d2 and d1, respectively. These components define the electron acceptor side of the RC complex. The cytosolic arm of the helices harbors the electron-donor side of the complex, including a cluster of four chlorophylls and two pheophytins 3. The primary ET reaction comprises ultrafast, light-induced tunneling of an electron across the clustered pigments, followed by reduction of Q A 4–7