Shuguang Zhang

• Ph.D.
• Principal Investigator at Massachusetts Institute of Technology

Objective Human integral membrane enzymes are essential for catalyzing a wide range of biochemical reactions and regulating key cellular processes. However, studying these enzymes remains challenging due to their hydrophobic nature, which necessitates the use of detergents. This study explores whether applying the QTY code can reduce the hydrophobi...

Human mitochondrial Complex I is one of the largest multi-subunit membrane protein megacomplexes, which plays a critical role in oxidative phosphorylation and ATP production. It is also involved in many neurodegenerative diseases. However, studying its structure and the mechanisms underlying proton translocation remains challenging due to the hydro...

The molecular mechanism of olfaction, namely, how we smell with limited olfactory receptors to recognize exceedingly diverse and large numbers of scents remains unknown despite the recent advances in chemistry, chemical, structural, and molecular biology. Olfactory receptors are notoriously difficult to study because they are fully embedded in the...

Context Beta-barrel enzymes are an important area of study in the field of structural biology. These proteins serve crucial roles, acting as porins, transporters, enzymes, virulence factors, and receptors. Recent research has unveiled a novel role for beta-barrel enzymes in the bacterial integral membrane as sentinels. They remain inactive when the...

We present here a generalizable approach to de-biasing and de-trending before clustering complex datasets, using the specific example of prostate cancer diagnosis from gas chromatography-mass spectrometry ion chromatograms. We endeavor to mimic the olfactory cancer diagnostic prowess of trained dogs to establish, in perceptual space (as opposed to...

Transmembrane potassium ion channels are crucial for ion transport, metabolism, and signaling, and serve as promising targets for anti-cancer therapies. However, their hydrophobic transmembrane nature requires detergents, posing a major bottleneck for experimental handling. In this paper, we present a structural bioinformatics study of six experime...

Objective Glutamate transporters play a key role in central nervous system physiology by maintaining excitatory neurotransmitter homeostasis. Biological assemblies of the transporters, consisting of cyclic homotrimers, emerge as a crucial aspect of glutamate transporter modulation. Hence targeting heteromerization promises an effective approach for...

Objective Glutamate transporters play a crucial role in neurotransmitter homeostasis, but studying their structure and function is challenging due to their membrane-bound nature. This study aims to investigate whether water-soluble QTY-variants of glutamate transporters EAA1, EAA2 and EAA3 retain the conformational characteristics and dynamics of n...

Membrane proteins are critical to biological processes and central to life sciences and modern medicine. However, membrane proteins are notoriously challenging to study, mainly owing to difficulties dictated by their highly hydrophobic nature. Previously, we reported QTY code, which is a simple method for designing water-soluble membrane proteins....

Glutamate transporters play key roles in nervous physiology by modulating excitatory neurotransmitter levels, when malfunctioning, involving in a wide range of neurological and physiological disorders. However, integral transmembrane proteins including the glutamate transporters remain notoriously difficult to study, due to their localization withi...

Monoamine transporters including transporters for serotonin, dopamine, and norepinephrine play key roles in monoaminergic synaptic signaling, involving in the molecular etiology of a wide range of neurological and physiological disorders. Despite being crucial drug targets, the study of transmembrane proteins remains challenging due to their locali...

Human ATP-binding cassette (ABC) transporters are one of the largest families of membrane proteins and perform diverse functions. Many of them are associated with multidrug resistance that often results in cancer treatment with poor outcomes. Here, we present the structural bioinformatics study of six human ABC membrane transporters with experiment...

G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. Howev...

Chemokine receptors play crucial roles in fundamental biological processes. Their malfunction may result in many diseases, including cancer, autoimmune diseases, and HIV. The oligomerization of chemokine receptors holds significant functional implications that directly affect their signaling patterns and pharmacological responses. However, the olig...

Therapeutic monoclonal antibodies are the most rapidly growing class of molecular medicine, and they are beneficial to the treatment of a broad spectrum of human diseases. However, the aggregation of antibodies during the process of manufacture, distribution, and storage poses significant challenges, potentially compromising efficacy and inducing a...

Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations between protein functions and tumor-related mechanisms are still unclear. We present here the CrMP-Sol database (https://bio-gateway.aigene.org.cn/...

Beta-barrel outer membrane proteins (OMP) are integral components of Gram-negative bacteria, eukaryotic mitochondria, and chloroplasts. They play essential roles in various cellular processes including nutrient transport, membrane stability, host-pathogen interactions, antibiotic resistance and more. The advent of AlphaFold2 for accurate protein st...

Helices are ubiquitous in art and nature. Independent of their pitch and sense of rotation (handedness), helices in sculpture, painting, architecture, scientific illustrations, conference announcements, logos, and advertising are eye-catching and aesthetically pleasing. Helices can turn either clockwise (right-handed helix) or anti-clockwise (left-...

Affinity-based biosensing can enable point-of-care diagnostics and continuous health monitoring, which commonly follows bottom-up approaches and is inherently constrained by bioprobes' intrinsic properties, batch-to-batch consistency, and stability in biofluids. We present a biomimetic top-down platform to circumvent such difficulties by combining...

Human serum albumin (HSA) is a highly water-soluble protein with 67% alpha-helix content and three distinct domains (I, II, and III). HSA offers a great promise in drug delivery with enhanced permeability and retention effect. But it is hindered by protein denaturation during drug entrapment or conjugation that result in distinct cellular transport...

Solute carrier transporters are integral membrane proteins, and are important for diverse cellular nutrient transports, metabolism, energy demand, and other vital biological activities. They have recently been implicated in pancreatic cancer and other cancer metastasis, angiogenesis, programmed cell death and proliferation, cell metabolism and chem...

Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer prot...

Solute carrier transporters are integral membrane proteins, and are important for diverse cellular nutrient transports, metabolism, energy demand, and other vital biological activities. They have recently been implicated in pancreatic cancer and other cancer metastasis, angiogenesis, programmed cell death and proliferation, cell metabolism and chem...

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Linus Pauling in 1950 published a three-dimensional model for a universal protein secondary structure motif which he initially called the alpha-spiral. Jack Dunitz, then a postdoc in Pauling's lab suggested to Pauling that the term helix is more accurate than spiral when describing the right-handed peptide and protein coiled structures. Pauling agr...

Membrane transporters including glucose transporters (GLUTs) are involved in cellular energy supplies, cell metabolism and other vital biological activities. They have also been implicated in cancer proliferation and metastasis, thus they represent an important target in combatting cancer. However, membrane transporters are very difficult to study...

Fifty years ago, the first atomic-resolution structure of a nucleic acid double helix, the mini-duplex (ApU)2, revealed details of basepair geometry, stacking, sugar conformation, and backbone torsion angles, thereby superseding earlier models based on x-ray fiber diffraction, including the original DNA double helix proposed by Watson and Crick. Ju...

‘Alpha helix’ was not Linus Pauling’s first choice of a name for the protein structural motif. Egli and Zhang recount what the original name was, why it was changed and what is between the alpha helix and the DNA double helix.

Water-soluble expression and purification are of considerable importance for protein identification and characterization. However, there has been a lack of an effective method for water-soluble expression of membrane proteins, which has severely hampered their studies.

Prior to introduction of the first DNA–protein structure, Ned Seeman et al. correctly conceived how proteins recognize specific sequences in double-helix nucleic acids.

Well-defined scaffold hydrogels made of self-assembling peptides have found their way into clinical products. By examining the properties and applications of two self-assembling peptides—EAK16 and RADA16—we highlight the potential for translating designer biological scaffolds into commercial products.

Accurate predictions of 3-dimensional protein structures by AlphaFold2 is a game-changer for biology, especially for structural biology. Here we present the studies of several native chemokine receptors including CCR5, CCR9, CXCR2 and CXCR4 determined by X-ray crystallography, and their water-soluble QTY counter parts predicted by AlphaFold2. In th...

G protein-coupled receptors (GPCRs) are vital for diverse biological functions, including vision, smell, and aging. They are involved in a wide range of diseases, and are among the most important targets of medicinal drugs. Tools that facilitate GPCR studies or GPCR-based technologies or therapies are thus critical to develop. Here we report using...

Short peptides are ubiquitous in nature. They are found as hormones, pheromones, antibacterial and antifungal agents in innate immunity systems, toxins, and pesticides. But no one seriously considered that peptides could be useful as scaffold hydrogel materials. There has been a significant change since 1990 after the discovery of an ionic self-com...

Well‐defined nanofiber scaffold hydrogels made of self‐assembling peptides have found their way into various 3D tissue culture and clinical products. I reflect initial puzzlement of the unexpected discovery, gradual understanding of how these peptides undergo self‐assembly, to eventually translating designer biological scaffolds into commercial pro...

It was posited that functionalities of GPCRs require full-length sequences that are negated by residue deletions. Here we report that significantly truncated nfCCR5QTY and nfCXCR4QTY still bind native ligands. Receptor-ligand interactions were discovered from yeast 2-hybrid screening and confirmed by mating selection. Two nfCCR5QTY (SZ218a, SZ190b)...

Cytokine release syndrome (CRS), or "cytokine storm," is the leading side effect during CAR-T therapy that is potentially life-threatening. It also plays a critical role in viral infections such as COVID-19. Therefore, efficient removal of excessive cytokines is essential for treatment. We previously reported a novel protein modification tool calle...

Significance There are 20 chemokine receptors that bind their respective chemokines. It is not currently understood how these structurally similar receptors distinguish their ligands; namely, how EC loops and transmembrane domains of these receptors are involved in ligand-binding activities. With the detergent-free GPCRs, we show that it is now pos...

Membrane proteins, especially the α-helical ones such as G-protein coupled receptors (GPCRs), are considered extremely important owing to their significant biological roles. However, their expression and purification pose difficulties because of their poor solubility in water, which seriously impedes research progress in this field. Recently, QTY m...

Significance The QTY (glutamine, threonine, and tyrosine) code-designed detergent-free chemokine receptors may be useful in many applications. The QTY variants may be useful not only as reagents in deorphanization studies but also for designing biologics to treat cancer and autoimmune or infectious diseases. The QTY code allows membrane proteins to...

Membrane proteins are notoriously difficult to study, but the ability to do so could aid in the development of therapeutic drugs and novel technologies. Peptide surfactants can help facilitate membrane protein studies. They can aid in the expression and solubilization of membrane proteins, and enhance their activity or stability. They can even keep...

Peptides are ubiquitous in nature and useful in many fields, from agriculture as pesticides, in medicine as antibacterial and antifungal drugs founded in the innate immune systems, to medicinal chemistry as hormones. However, the concept of peptides as materials was not recognized until 1990 when a self-assembling peptide as a repeating segment in...

In exemplary implementations of this invention, an electronic olfactor determines whether a scent being tested matches the scent of a positive control. The electronic olfactor can perform this scent matching even in a changing olfactory environment, and even if the positive control scent is a combination of hundreds or thousands of different odoran...

Uncontrolled bleeding from traumatic wounds is a major factor in deaths resulting from military conflict, accidents, disasters and crime. Self-assembling peptide nanofibers have shown superior hemostatic activity and herein we elucidate their mechanism by visualizing the formation of nanofiber-based clots that aggregate blood components with a simi...

The abundant pigment-protein membrane complex photosystem-I (PS-I) is at the heart of the Earth’s energy cycle. It is the central molecule in the “Z-scheme” of photosynthesis, converting sunlight into the chemical energy of life. Commandeering this intricately organized photosynthetic nanocircuitry and re-wiring it to produce electricity carries th...

One of molecular biology's intellectual leaders, Alex Rich made fundamental discoveries concerning nucleic acids and ribosomes, which served not only as a foundation for modern biology but also spurred the field of biotechnology.

Insects transmit numerous devastating diseases, including malaria, dengue fever, and sleeping sickness. Olfactory cues guide insects to their hosts, and are thus responsible for disease transmission. Understanding the molecular basis of insect olfaction could facilitate the development of interventions. The first step is to heterologously overexpre...

Amphiphilic self-assembling peptides are functional materials which, depending on the amino acid sequence, the peptide length and the physicochemical conditions, form a variety of nanostructures including nanovesicles, nanotubes and nanovalves. We designed lipid-like peptides with an aspartic acid or lysine hydrophilic head and a hydrophobic tail c...

The first bottleneck in olfactory receptor (OR) structural and functional studies is to produce sufficient quantities of soluble, functional, and stable receptors. Other production systems have been used and summarized in other chapters of this book. We here show that commercial cell-free in vitro translation systems can be used to produce milligra...

The first bottleneck in olfactory receptor (OR) studies is producing sufficient quantities of soluble, -functional, and stable receptors. Commercial cell-free in vitro translation systems can be used to produce milligrams of soluble and functional receptors within several hours directly from plasmid DNA. The receptors can be purified using immunoaf...

Recently, several designed D- and L-chiral self-assembling peptides have been shown to undergo conformational transformation under temperature and pH influences, and they provide further evidence that the secondary structures are flexible to their environmental conditions. Inspired from the first self-assembly peptide, we not only subsequently expa...

Amino Acids, Peptides and Proteins comprises a comprehensive review of significant developments at this biology/chemistry interface. Each volume of this Specialist Periodical Report opens with an overview of amino acids and their applications. Volume 37 marks the return of the series after a five-year hiatus, with Professors Etelka Farkas (Debrecen...

Designer peptides with self-assembling properties form nanofibers which are further organized to form a hydrogel consisting of up to 99.5% water. We present here the encapsulation of neural stem cells into peptide nanofiber hydrogel scaffolds. This results in three-dimensional (3-D) neural tissue cultures in which neural stem cells differentiate in...

Biomedical researchers have become increasingly aware of the limitations of the conventional two-dimensional (2-D) tissue cell cultures where most tissue cell studies have been carried out. They are now searching and testing three-dimensional (3-D) cell culture systems, something between a Petri dish and an animal, such as a mouse. The important im...

Chirality is absolutely central in chemistry and biology. The recent findings of chiral self-assembling peptides' remarkable chemical complementarity and structural compatibility make it one of the most inspired designer materials and structures in nanobiotechnology. The emerging field of designer chemistry and biology further explores biological a...

In the last few years, a variety of self-assembling short peptides that consist exclusively of simple amino acids have been designed and modified. These peptides exhibit self-assembling dynamic behaviors. At the molecular structural level, they form α-helical, β-sheet and β-hairpins structures in water. These structures further undergo spontaneous...

Recombinant expression and purification of metallo-enzymes, including hydrogenases, at high-yields is challenging due to complex, and enzyme specific, post-translational maturation processes. Low fidelities of maturation result in preparations containing a significant fraction of inactive, apo-protein that are not suitable for biophysical or crysta...

The detergents used to solubilize GPCRs can make crystal growth the rate-limiting step in determining their structure. The Kobilka laboratory showed that insertion of T4-lysozyme (T4L) in the 3rd intracellular loop is a promising strategy towards increasing the solvent-exposed receptor area, and hence the number of possible lattice-forming contacts...

The release kinetics for human immunoglobulin (IgG) through the permeable structure of nanofiber scaffold hydrogels consisting of the ac-(RADA)(4)-CONH(2) and ac-(KLDL)(3)-CONH(2) self-assembling peptides were studied during a period of 3 months. Self assembling peptides are a class of stimuli-responsive materials which undergo sol-gel transition i...

The rapid promotion of angiogenesis is critical for tissue engineering and regenerative medicine. The angiogenic activity of tissue-engineered scaffolds has already been the major criterion for choosing and designing ideal biological materials. We here report systematic in vivo studies on the angiogenic activity of two functionalized self-assemblin...

Cell and tissue engineering therapies for regenerative medicine as well as cell-based assays require an understanding of the interactions between cells with the surrounding microenvironment at the nanoscale. Engineering a cell-interactive scaffold therefore entails control over the nanostructure of the biomaterial. Peptides that are able to self-as...

The abundant pigment-protein membrane complex photosystem-I (PS-I) is at the heart of the Earth's energy cycle. It is the central molecule in the "Z-scheme" of photosynthesis, converting sunlight into the chemical energy of life. Commandeering this intricately organized photosynthetic nanocircuitry and re-wiring it to produce electricity carries th...

Supplementary Information

The abundant pigment-protein membrane complex photosystem-I (PS-I) is at the heart of the Earth's energy cycle. It is the central molecule in the "Z-scheme'' of photosynthesis, converting sunlight into the chemical energy of life. Commandeering this intricately organized photosynthetic nanocircuitry and re-wiring it to produce electricity carries t...

Short, self-assembling peptides form a variety of stable nanostructures used for the rational design of functional devices. Peptides serve as organic templates for conjugating biorecognition elements, and assembling ordered nanoparticle arrays and hybrid supramolecular structures. We are witnessing the emergence of a new phase of bionanotechnology,...

The vomeronasal system is one of several fine-tuned scent-detecting signaling systems in mammals. However, despite significant efforts, how these receptors detect scent remains an enigma. One reason is the lack of sufficient purified receptors to perform detailed biochemical, biophysical and structural analyses. Here we report the ability to expres...

Surfactant peptide properties and experimental concentrations. (DOC)

A crucial bottleneck in membrane protein studies, particularly G-protein coupled receptors, is the notorious difficulty of finding an optimal detergent that can solubilize them and maintain their stability and function. Here we report rapid production of 12 unique mammalian olfactory receptors using short designer lipid-like peptides as detergents....

Multi-spanning integral membrane proteins, including G-protein coupled receptors (GPCR), ion channels, and ion transporters, comprise a major class of drug targets. However, despite their vital importance, most molecular structures of membrane proteins remain elusive. This is largely due to lack of effective materials and methods to stabilize their...

Membrane proteins, particularly G-protein coupled receptors (GPCRs), are notoriously difficult to express. Using commercial E. coli cell-free systems with the detergent Brij-35, we could rapidly produce milligram quantities of 13 unique GPCRs. Immunoaffinity purification yielded receptors at >90% purity. Secondary structure analysis using circular...

Here we report the study of two bioengineered variants of human trace amine-associated receptor 5 (hTAAR5) that were expressed in stable tetracycline-inducible HEK293S cell lines. A systematic detergent screen showed that fos-choline-14 was the optimal detergent to solubilize and subsequently purify the receptors. Milligram quantities of both hTAAR...

Supplementary information

A list of the detergents screened for optimal solubilization of human FPR3 expressed in HEK293 cells. (DOC)

G-protein coupled receptors (GPCRs) participate in a wide range of vital regulations of our physiological actions. They are also of pharmaceutical importance and have become many therapeutic targets for a number of disorders and diseases. Purified GPCR-based approaches including structural study and novel biophysical and biochemical function analys...

Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the main limitations for its comme...

Two major bottlenecks in elucidating the structure and function of membrane proteins are the difficulty of producing large quantities of functional receptors, and stabilizing them for a sufficient period of time. Selecting the right surfactant is thus crucial. Here we report using peptide surfactants in commercial Escherichia coli cell-free systems...